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2: Basic Cell Chemistry - Chemical Compounds and their Interactions - Biology

2: Basic Cell Chemistry - Chemical Compounds and their Interactions - Biology


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  • 2.1: Water
    There is no life without water. In this chapter, water will be used to review some very basic ideas in chemistry, particularly as applies to cell and molecular biology.
  • 2.2: Acids and Bases
    The release of H+ and OH— are not limited to water molecules, and many compounds do so in aqueous solutions. These compounds can be classified as acids (raising the free H+ concentration) or bases (increasing the free hydroxyl concentration]. The extent to which acids and bases donate or remove protons is measured on the pH scale, which is a logarithmic scale of relative H+ concentration.
  • 2.3: Carbon
    The major constituent molecules in all living organisms are based on carbon. Carbon has versatility stemming from its four outer shell electrons, allowing the possibility of four covalent bonds with a variety of partners, including very stable carbon-carbon covalent bonds. Because of this, long carbon chains can form the backbone of more complex molecules and makes possible the great diversity of macromolecules found in the cell.
  • 2.4: Sugars
    Sugars, and glucose in particular, are important molecules for cells because they are the primary energy source. Sugars have the general chemical formula CH₂O and can be joined together almost infinitely for storage. However, because they are hydrophilic, they allow water molecules to intercalate between them, and cannot pack as efficiently as fats, which are hydrophobic and thus exclude water. On the other hand, the sugars can be mobilized for use more quickly.
  • 2.5: Nucleotides
    Nucleotides, the building blocks of RNA and DNA, are themselves composed of a pentose sugar attached to a nitrogenous base on one side and a phosphate group on another. The sugar is either the 5-carbon sugar ribose or its close cousin, deoxyribose (the “deoxy” refers to a “missing” hydroxyl group on the 2-carbon, which has an H instead). The attached nitrogenous base can be a purine, which is a 6-member ring fused to a 5-member ring, or a pyrimidine, which is a single 6-membered ring.
  • 2.6: Amino Acids
    Most of the major molecules of the cell - whether structural, like cellular equivalents of a building’s girders and beams, or mechanical, like enzymes that take apart or put together other molecules, are proteins. Proteins interact with a wide variety of other molecules, though any given interaction is usually quite specific. The specificity is determined in part by electrical attraction between the molecules.
  • 2.7: Fatty Acids
    Unlike monosaccharides, nucleotides, and amino acids, fatty acids are not monomers that are linked together to form much larger molecules. Although fatty acids can be linked together, for example, into triacylglycerols or phospholipids, they are not linked directly to one another, and generally no more than three in a given molecule. The fatty acids themselves are long chains of carbon atoms topped off with a carboxyl group. The length of the chain vary, but most are between 14 and 20 carbons.

Thumbnail: Oleic acid is a fatty acid that occurs naturally in various animal and vegetable fats and oils. I can have several conformer including cis and trans forms (Publci Domain; Benjah-bmm27 via Wikipedia)


3.1: Types of Chemical Compounds and their Formulas

The atoms in all substances that contain multiple atoms are held together by electrostatic interactions&mdashinteractions between electrically charged particles such as protons and electrons. Electrostatic attraction between oppositely charged species (positive and negative) results in a force that causes them to move toward each other, like the attraction between opposite poles of two magnets. In contrast, electrostatic repulsion between two species with the same charge (either both positive or both negative) results in a force that causes them to repel each other, as do the same poles of two magnets. Atoms form chemical compounds when the attractive electrostatic interactions between them are stronger than the repulsive interactions. Collectively, the attractive interactions between atoms are called chemical bonds.

Chemical bonds are generally divided into two fundamentally different types: ionic and covalent. In reality, however, the bonds in most substances are neither purely ionic nor purely covalent, but lie on a spectrum between these extremes. Although purely ionic and purely covalent bonds represent extreme cases that are seldom encountered in any but very simple substances, a brief discussion of these two extremes helps explain why substances with different kinds of chemical bonds have very different properties. Ionic compounds consist of positively and negatively charged ions held together by strong electrostatic forces, whereas covalent compounds generally consist of molecules, which are groups of atoms in which one or more pairs of electrons are shared between bonded atoms. In a covalent bond, atoms are held together by the electrostatic attraction between the positively charged nuclei of the bonded atoms and the negatively charged electrons they share. This discussion of structures and formulas begins by describing covalent compounds. The energetic factors involved in bond formation are described in more quantitative detail in later.

Ionic compounds consist of ions of opposite charges held together by strong electrostatic forces, whereas pairs of electrons are shared between bonded atoms in covalent compounds.


Chemistry and Chemical Biology (CHEM)

Intended for freshmen in the College of Science. Introduces students to liberal arts familiarizes them with their major develops the academic skills necessary to succeed (analytical ability and critical thinking) provides grounding in the culture and values of the University community and helps to develop interpersonal skills—in short, familiarizes students with all skills needed to become a successful university student.

CHEM 1101. General Chemistry for Health Sciences. (4 Hours)

Provides a one-semester introduction to general chemistry for the health sciences. Covers the fundamentals of elements and atoms ionic and molecular structure chemical reactions and their stoichiometry, energetics, rates, and equilibriums and the properties of matter as gases, liquids, solids, and solutions. Other topics include acids and bases, and nuclear chemistry. Applications to the health sciences are included throughout.

Attribute(s): NUpath Natural/Designed World

CHEM 1102. Lab for CHEM 1101. (1 Hour)

Accompanies CHEM 1101. Covers a range of topics from the course, such as qualitative and quantitative analysis and the characteristics of chemical and physical processes. Includes measurements of heat transfer, rate and equilibrium constants, and the effects of temperature and catalysts. Emphasis is on aqueous acid-base reactions and the properties and uses of buffer systems.

CHEM 1103. Recitation for CHEM 1101. (0 Hours)

Accompanies CHEM 1101. Covers various topics from the course.

CHEM 1104. Organic Chemistry for Health Sciences. (4 Hours)

Provides a one-semester introduction to organic chemistry for the health sciences. Covers the fundamentals of the structure, nomenclature, properties, and reactions of the compounds of carbon. Also introduces biological chemistry including amino acids, proteins, carbohydrates, lipids, nucleic acids, hormones, neurotransmitters, and drugs. Applications to the health sciences are included throughout.

Prerequisite(s): CHEM 1101 with a minimum grade of D

CHEM 1105. Lab for CHEM 1104. (1 Hour)

Accompanies CHEM 1104. Covers a range of topics from the course, such as the properties and elementary reactions of hydrocarbons, alcohols, ethers, carbonyl compounds, carbohydrates, and amines.

CHEM 1106. Recitation for CHEM 1104. (0 Hours)

Accompanies CHEM 1104. Covers various topics from the course.

CHEM 1107. Introduction to Forensic Science. (4 Hours)

Introduces students to the field of forensic science from both a scientific and a legal perspective. Examines the challenges and methodologies of crime scene investigation, forensic biology, and forensic chemistry. Provides real-world case studies and examines some misrepresentations of forensics by television dramas. Emphasizes scientific evidence associated with topics such as DNA analysis, drug abuse, and explosion investigations, as well as other relevant topics.

Attribute(s): NUpath Natural/Designed World

CHEM 1109. The Chemistry of Food and Cooking. (4 Hours)

Introduces a number of basic scientific principles in the methodology of cooking, food preparation, and the enjoyment of food. Focuses on the chemistry and molecular bases of food, reactivity under various conditions, molecular gastronomy, geographic and cultural influences on food, and food as preventative medicine. Class demonstrations of various cooking techniques illustrate different chemical principles between food and cooking. Designed for students who do not plan to major in the natural sciences.

Attribute(s): NUpath Natural/Designed World

CHEM 1151. General Chemistry for Engineers. (4 Hours)

Corresponds to one semester of study in important areas of modern chemistry, such as details of the gaseous, liquid, and solid states of matter intra- and intermolecular forces and phase diagrams. Presents the energetics and spontaneity of chemical reactions in the context of chemical thermodynamics, while their extent and speed is discussed through topics in chemical equilibria and kinetics. Aspects of electrochemical energy storage and work are considered in relation to batteries, fuel, and electrolytic cells.

Corequisite(s): CHEM 1153

Attribute(s): NUpath Natural/Designed World

CHEM 1153. Recitation for CHEM 1151. (0 Hours)

Accompanies CHEM 1151. Offers a weekly sixty-five-minute drill/discussion session conducted by chemistry faculty or graduate teaching assistants. Discusses the homework assignments of CHEM 1151 in detail with emphasis on student participation.

Corequisite(s): CHEM 1151

CHEM 1161. General Chemistry for Science Majors. (4 Hours)

Introduces the principles of chemistry, focusing on the particulate nature of matter and its interactions and reactions that form the basis for the underlying molecular dynamics of living systems. Presents basic concepts of chemical bonding and intermolecular interactions for molecules and molecules’ behavior in aqueous solutions with examples from biologically relevant molecules. Introduces kinetics and chemical thermodynamics with examples from biological systems. Offers students an opportunity to obtain a framework for understanding the chemical basis for different methods for separating and purifying biological compounds.

Attribute(s): NUpath Natural/Designed World

CHEM 1162. Lab for CHEM 1161. (1 Hour)

Accompanies CHEM 1161. Introduces basic laboratory techniques. Covers a range of topics including qualitative and quantitative analysis and the characteristics of chemical and physical processes.

CHEM 1163. Recitation for CHEM 1161. (0 Hours)

Accompanies CHEM 1161. Covers various topics from the course. Offers students an opportunity to work interactively with instructors and other students to learn and apply the knowledge acquired in lecture.

CHEM 1211. General Chemistry 1. (4 Hours)

Introduces the principles of chemistry, focusing on the states and structure of matter and chemical stoichiometry. Presents basic concepts and definitions, moles, gas laws, atomic structure, periodic properties and chemical bonding, all within a contextual framework.

Attribute(s): NUpath Natural/Designed World

CHEM 1212. Lab for CHEM 1211. (1 Hour)

Accompanies CHEM 1211. Covers a range of topics from the course including qualitative and quantitative analysis and the characteristics of chemical and physical processes.

CHEM 1213. Recitation for CHEM 1211. (0 Hours)

Accompanies CHEM 1211. Covers various topics from the course.

CHEM 1214. General Chemistry 2. (4 Hours)

Continues CHEM 1211. Introduces the principles of chemical equilibrium, the rates and mechanisms of chemical reactions, and energy considerations in chemical transformations. Covers solutions, chemical kinetics, chemical equilibria, chemical thermodynamics, electrochemistry, and chemistry of the representative elements. Such contextual themes as energy resources, smog formation, and acid rain illustrate the principles discussed.

Prerequisite(s): CHEM 1211 with a minimum grade of D

Attribute(s): NUpath Natural/Designed World

CHEM 1215. Lab for CHEM 1214. (1 Hour)

Accompanies CHEM 1214. Covers a range of topics from the course, such as measurements of heat transfer, rate and equilibrium constants, and the effects of temperature and catalysts. Particular attention is paid to aqueous acid-base reactions and to the properties and uses of buffer systems. Quantitative analysis of chemical and physical systems is emphasized throughout.

CHEM 1216. Recitation for CHEM 1214. (0 Hours)

Accompanies CHEM 1214. Covers various topics from the course.

CHEM 1990. Elective. (1-4 Hours)

Offers elective credit for courses taken at other academic institutions. May be repeated without limit.

CHEM 2161. Concepts in Chemistry. (4 Hours)

Explores basic concepts of thermodynamics electrochemistry and nuclear, supramolecular, and solid-state chemistry in the context of modern materials. Emphasizes connecting the particulate nature of matter to the properties of substances and patterns of chemical reactivity.

Attribute(s): NUpath Writing Intensive

CHEM 2162. Lab for CHEM 2161. (1 Hour)

Accompanies CHEM 2161. Offers hands-on exploration of the basic concepts of electrochemistry and of nuclear, supramolecular, and solid-state chemistry.

CHEM 2163. Recitation for CHEM 2161. (0 Hours)

Accompanies CHEM 2161. Covers various topics from the course. Offers students an opportunity to work interactively with instructors and other students to learn and apply the knowledge acquired in lecture.

CHEM 2311. Organic Chemistry 1. (4 Hours)

Introduces nomenclature, preparation, properties, stereochemistry, and reactions of common organic compounds. Presents correlations between the structure of organic compounds and their physical and chemical properties, and mechanistic interpretation of organic reactions. Includes chemistry of hydrocarbons and their functional derivatives.

Prerequisite(s): CHEM 1151 with a minimum grade of D or CHEM 1214 with a minimum grade of D or CHEM 1220 with a minimum grade of D or CHEM 1161 with a minimum grade of D

Corequisite(s): CHEM 2312

CHEM 2312. Lab for CHEM 2311. (1 Hour)

Accompanies CHEM 2311. Introduces basic laboratory techniques, such as distillation, crystallization, extraction, chromatography, characterization by physical methods, and measurement of optical rotation. These techniques serve as the foundation for the synthesis, purification, and characterization of products from microscale syntheses integrated with CHEM 2311.

Corequisite(s): CHEM 2311

CHEM 2313. Organic Chemistry 2. (4 Hours)

Continues CHEM 2311. Focuses on additional functional group chemistry including alcohols, ethers, carbonyl compounds, and amines, and also examines chemistry relevant to molecules of nature. Introduces spectroscopic methods for structural identification.

Prerequisite(s): CHEM 2311 with a minimum grade of D or CHEM 2315 with a minimum grade of D

Corequisite(s): CHEM 2314

CHEM 2314. Lab for CHEM 2313. (1 Hour)

Accompanies CHEM 2313. Basic laboratory techniques from CHEM 2312 are applied to chemical reactions of alcohols, ethers, carbonyl compounds, carbohydrates, and amines. Introduces basic laboratory techniques including infrared (IR) spectroscopy and nuclear magnetic resonance (NMR) spectronomy as analytical methods for characterization of organic molecules.

Corequisite(s): CHEM 2313

CHEM 2315. Organic Chemistry 1 for Chemistry Majors. (4 Hours)

Reviews the basics of bonding and thermodynamics of organic compounds as well as conformational and stereochemical considerations. Presents the structure, nomenclature, and reactivity of hydrocarbons and their functional derivatives. Highlights key reaction mechanisms, providing an introduction to the methodology of organic synthesis.

Prerequisite(s): CHEM 1214 with a minimum grade of C- or CHEM 1220 with a minimum grade of C-

CHEM 2316. Lab for CHEM 2315. (2 Hours)

Accompanies CHEM 2315. Introduces basic laboratory techniques, such as distillation, crystallization, extraction, chromatography, characterization by physical methods, and measurement of optical rotation. These techniques serve as the foundation for the synthesis, purification, and characterization of products from microscale syntheses integrated with CHEM 2315.

CHEM 2317. Organic Chemistry 2 for Chemistry Majors. (4 Hours)

Continues CHEM 2315. Extends the study of functional groups commonly found in organic compounds, further emphasizing conceptual mastery of the relationship between structure and reactivity. Introduces structural identification of organic compounds using contemporary spectroscopic methods such as IR, MS, and NMR. Other topics include structure and reactivity of conjugated and aromatic systems, the chemistry of ethers and epoxides, and the chemistry of carbonyl-containing compounds including aldehydes, ketones, carboxylic acids, and carboxylic acid derivatives. Offers students an opportunity to develop skills in planning multistep syntheses using the retrosynthesis approach and proposing mechanisms for chemical transformations.

Prerequisite(s): CHEM 2311 with a minimum grade of C- or CHEM 2315 with a minimum grade of C-

Attribute(s): NUpath Creative Express/Innov

CHEM 2318. Lab for CHEM 2317. (2 Hours)

Accompanies CHEM 2317. Introduces basic laboratory techniques including infrared (IR) spectroscopy and nuclear magnetic resonance (NMR) spectronomy as analytical methods for characterization of organic molecules. These methods serve as the basis for characterization of products from microscale syntheses.

CHEM 2319. Recitation for CHEM 2311. (0 Hours)

Offers students opportunities to work interactively with instructors and other students to learn and apply the understandings acquired in lab and lecture.

CHEM 2320. Recitation for CHEM 2313. (0 Hours)

Offers students opportunities to work interactively with instructors and other students to learn and apply the understandings acquired in lab and lecture.

CHEM 2321. Analytical Chemistry. (4 Hours)

Introduces the principles and practices in the field of analytical chemistry. Focuses on development of a quantitative understanding of homogeneous and heterogeneous equilibria phenomena as applied to acid-base and complexometric titrations, rudimentary separations, optical spectroscopy, electrochemistry, and statistics.

Prerequisite(s): (CHEM 1151 with a minimum grade of C- or CHEM 1214 with a minimum grade of C- or CHEM 1220 with a minimum grade of C- or CHEM 1161 with a minimum grade of C-) (CHEM 2311 with a minimum grade of C- or CHEM 2315 with a minimum grade of C-)

Attribute(s): NUpath Analyzing/Using Data, NUpath Writing Intensive

CHEM 2322. Lab for CHEM 2321. (1 Hour)

Accompanies CHEM 2321. Lab experiments provide hands-on experience in the analytical methods introduced in CHEM 2321, specifically, silver chloride gravimetry, complexometric titrations, acid-base titrations, UV-vis spectroscopy, cyclic voltammetry, Karl Fischer coulometry, and modern chromatrographic methods.

CHEM 2323. Recitation for CHEM 2321. (0 Hours)

Accompanies CHEM 2321 and CHEM 2322. Covers various topics from the course. Offers students an opportunity to work interactively with instructors and other students to learn and apply the knowledge acquired in lecture and lab.

CHEM 2324. Recitation for CHEM 2315. (0 Hours)

Accompanies CHEM 2315 and CHEM 2316. Offers students an opportunity to work interactively with instructors and other students to learn and apply the knowledge acquired in lab and lecture.

CHEM 2325. Recitation for CHEM 2317. (0 Hours)

Accompanies CHEM 2317 and CHEM 2318. Offers students an opportunity to work interactively with instructors and other students to learn and apply the knowledge acquired in lab and lecture.

CHEM 2990. Elective. (1-4 Hours)

Offers elective credit for courses taken at other academic institutions. May be repeated without limit.

CHEM 2991. Research in Chemistry and Chemical Biology. (1-4 Hours)

Offers an opportunity to conduct introductory-level research or creative endeavors under faculty supervision.

CHEM 3331. Bioanalytical Chemistry. (4 Hours)

Offers students an opportunity to obtain a broad familiarity with bioanalytical chemistry at the undergraduate level. After reviewing basic principles of analytical chemistry, the course covers biomolecular analysis by modern methods, including chromatography, electrophoresis, mass spectrometry, and immunohistochemistry. Studies genomics, proteomics, biosensors, bioassays, and protein/DNA sequencing. Exposes students to technical literature and modern applications in biochemistry, molecular biology, and chemistry.

Prerequisite(s): (CHEM 1151 with a minimum grade of C- or CHEM 1161 with a minimum grade of C- or CHEM 1214 with a minimum grade of C- or CHEM 1220 with a minimum grade of C-) (CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or BIOL 3611 with a minimum grade of C-) (ENGL 1102 with a minimum grade of C or ENGL 1111 with a minimum grade of C or ENGW 1102 with a minimum grade of C or ENGW 1111 with a minimum grade of C)

Corequisite(s): CHEM 3332

Attribute(s): NUpath Analyzing/Using Data, NUpath Writing Intensive

CHEM 3332. Lab for CHEM 3331. (1 Hour)

Accompanies CHEM 3331. Offers students an opportunity to apply modern analytical instrumentation to a selection of relevant applications as they relate to research and development labs in the biotechnology and pharmaceutical industry.

Corequisite(s): CHEM 3331

CHEM 3401. Chemical Thermodynamics and Kinetics. (4 Hours)

Traces the development of chemical thermodynamics through the three major laws of thermodymamics. These are applied to thermochemistry, chemical reaction and phase equilibria, and the physical behavior of multicomponent systems. Emphasizes quantitative interpretation of physical measurements.

Prerequisite(s): (MATH 1252 with a minimum grade of C- or MATH 1342 with a minimum grade of C-) (CHEM 1214 with a minimum grade of C- or CHEM 1220 with a minimum grade of C- or CHEM 1151 with a minimum grade of C- or CHEM 1161 with a minimum grade of C-) (PHYS 1155 (may be taken concurrently) with a minimum grade of C- or PHYS 1165 (may be taken concurrently) with a minimum grade of C-)

Corequisite(s): CHEM 3402

CHEM 3402. Lab for CHEM 3401. (1 Hour)

Accompanies CHEM 3401. Demonstrates the measurement of selected physical chemical phenomena presented in CHEM 3401, introducing experimental protocol and methods of data analysis. Experiments include investigations of gas nonideality and critical phenomena, electrochemical measurement of equilibrium, construction of phase diagrams, and bomb and differential scanning calorimetry.

Corequisite(s): CHEM 3401

CHEM 3403. Quantum Chemistry and Spectroscopy. (4 Hours)

Studies the theory of quantum chemistry with applications to spectroscopy. Presents some simple quantum mechanical (QM) models, including the particle in a box, rigid rotor, and harmonic oscillator, followed by treatments of electrons in atoms and molecules. Microwave, infrared, Raman, NMR, ESR, atomic absorption, atomic emission, and UV-Vis spectroscopy are discussed in detail.

Prerequisite(s): (CHEM 3401 with a minimum grade of C- or CHEM 3421 with a minimum grade of C- or CHEM 3431 with a minimum grade of C- or CHME 3322 with a minimum grade of C-) MATH 1342 with a minimum grade of C- (PHYS 1155 with a minimum grade of C- or PHYS 1165 with a minimum grade of C-)

Corequisite(s): CHEM 3404

CHEM 3404. Lab for CHEM 3403. (1 Hour)

Accompanies CHEM 3403. Explores the principles covered in CHEM 3403 by laboratory experimentation. Experiments include measurement of reaction kinetics, such as excited state dynamics, measurement of gas transport properties, atomic and molecular absorption and emission spectroscopy, infrared spectroscopy of molecular vibrations, and selected applications of fluorimetry.

Corequisite(s): CHEM 3403

CHEM 3410. Environmental Geochemistry. (4 Hours)

Offers students who wish to work in the geosciences or environmental science and engineering fields, including on the land, in freshwater, or the oceans, an opportunity to understand the geochemical principles that shape the natural and managed environment. Seeks to provide a context for understanding the natural elemental cycles and environmental problems through studies in atmospheric, terrestrial, freshwater, and marine geochemistry. Topics include fundamental geochemical principles environmental mineralogy organic and isotope geochemistry the global carbon, nitrogen, and phosphorous cycles atmospheric pollution environmental photochemistry and human-natural climate change feedbacks. ENVR 3410 and CHEM 3410 are cross-listed.

Attribute(s): NUpath Analyzing/Using Data, NUpath Natural/Designed World

CHEM 3431. Physical Chemistry. (4 Hours)

Offers an in-depth survey of physical chemistry. Emphasizes applications in modern research, including examples from biochemistry. Topics include the laws of thermodynamics and their molecular interpretation equilibrium in chemical and biochemical systems molecular transport kinetics, including complex enzyme mechanisms and an introduction to spectroscopy and the underlying concepts of quantum chemistry.

Prerequisite(s): ((CHEM 1214 with a minimum grade of C- or CHEM 1220 with a minimum grade of C-) or (CHEM 1151 with a minimum grade of C- or CHEM 1161 with a minimum grade of C-)) (MATH 1252 with a minimum grade of C- or MATH 1342 with a minimum grade of C-) (PHYS 1147 with a minimum grade of C- or PHYS 1155 with a minimum grade of C- or PHYS 1165 with a minimum grade of C- or PHYS 1175 with a minimum grade of C-)

Corequisite(s): CHEM 3432

CHEM 3432. Lab for CHEM 3431. (1 Hour)

Accompanies CHEM 3431. Covers practical skills in physical chemistry with an emphasis on current practice in chemistry, biochemistry, and pharmaceutical science. Introduces both ab initio and biological molecular modeling, differential scanning calorimetry, polymer characterization, protein unfolding and protein/ligand binding, electronic absorption spectroscopy, and synthesis of nanoparticles or quantum dots.

Corequisite(s): CHEM 3431

CHEM 3501. Inorganic Chemistry. (4 Hours)

Presents the following topics: basic concepts of molecular topologies, coordination compounds, coordination chemistry, isomerism, electron-transfer reactions, substitution reactions, molecular rearrangements and reactions at ligands, and biochemical applications.

Prerequisite(s): (CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-)

Attribute(s): NUpath Writing Intensive

CHEM 3502. Lab for CHEM 3501. (1 Hour)

Offers a laboratory course in inorganic chemistry with experiments and projects that track with the topics discussed in CHEM 3501. Designed to provide laboratory experience with the synthesis of coordination compounds and with the instrumental methods used to characterize them.

CHEM 3503. Recitation for CHEM 3501. (0 Hours)

Offers students additional opportunities to work interactively with instructors and other students to learn and apply the concepts presented in CHEM 3501.

CHEM 3505. Introduction to Bioinorganic Chemistry. (4 Hours)

Explores basic concepts of molecular topologies, coordination compounds, coordination chemistry, isomerism, electron-transfer reactions, substitution reactions, molecular rearrangements, and reactions at ligands in the context of metal-based drugs, imaging agents, and metalloenzymes.

Prerequisite(s): (CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-)

Attribute(s): NUpath Writing Intensive

CHEM 3506. Lab for CHEM 3505. (1 Hour)

Offers a laboratory course in inorganic chemistry with experiments and projects that track with the topics discussed in CHEM 3505. Designed for students who have mastered basic laboratory techniques in general and organic chemistry. Introduces new synthetic techniques and applies modern analytical characterization tools not previously used in other laboratory courses (such as CHEM 3522 and CHEM 3532).

CHEM 3507. Recitation for CHEM 3505. (0 Hours)

Offers students additional opportunities to work interactively with instructors and other students to learn and apply the concepts presented in CHEM 3505.

CHEM 3521. Instrumental Methods of Analysis. (1 Hour)

Introduces the instrumental methods of analysis used in all fields of chemistry, with an emphasis on understanding not only the fundamental principles of each method but also the basics of the design and operation of the relevant instrumentation.

Prerequisite(s): CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-

Corequisite(s): CHEM 3522

CHEM 3522. Instrumental Methods of Analysis Lab. (4 Hours)

Accompanies CHEM 3521. Lab experiments provide hands-on experience in the instrumental methods of analysis discussed in CHEM 3521, such as high-performance liquid chromatography, gas chromatography, mass spectrometry, capillary electrophoresis, atomic absorption, cyclic voltammetry, and UV-vis spectroscopy.

Prerequisite(s): CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-

Corequisite(s): CHEM 3521

CHEM 3531. Chemical Synthesis Characterization. (1 Hour)

Introduces advanced techniques in chemical synthesis and characterization applicable to organic, inorganic, and organometallic compounds. Techniques used include working under inert atmosphere, working with liquefied gases, and handling moisture-sensitive reagents, NMR, IR, and UV-vis spectroscopy.

Prerequisite(s): CHEM 2317 with a minimum grade of C-

Corequisite(s): CHEM 3532

CHEM 3532. Chemical Synthesis Characterization Lab. (4 Hours)

Acompanies CHEM 3531. Covers topics from the course through various experiments.

Prerequisite(s): (CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C-)

Corequisite(s): CHEM 3531

CHEM 3990. Elective. (1-4 Hours)

Offers elective credit for courses taken at other academic institutions. May be repeated without limit.

CHEM 4456. Organic Chemistry 3: Organic Chemistry of Drug Design and Development. (4 Hours)

Offers students majoring in chemistry an opportunity to apply the principles gained in two semesters of organic chemistry and chemical biology to a relevant disciplinary context. The discovery, design, and development of biologically active compounds for medical purposes uses knowledge and techniques gained in both organic synthesis and chemical biology. It directs those skills to incorporate specific chemical features into organic compounds to meet biological criteria. As such, it seeks to develop problem-solving skills that are valuable across a range of chemical disciplines and not confined to synthetic organic chemistry alone.

Prerequisite(s): CHEM 2317 with a minimum grade of C-

Corequisite(s): CHEM 4457

CHEM 4457. Lab for CHEM 4456. (2 Hours)

Accompanies CHEM 4456. Includes literature research activities, field trips, case studies, and presentations. Offers students an opportunity to prepare for a wider range of career options.

Corequisite(s): CHEM 4456

CHEM 4460. Enzymes: Chemistry and Chemical Biology. (4 Hours)

Focuses on enzymes: their chemistry, mechanisms, and applications. Examines the underlying chemical and mechanistic principles. Introduces the techniques and approaches in enzymology. Bridges the gap between classroom learning and real-world practice in the related fields, e.g., medicinal chemistry, chemical biology, engineering, and pharmaceutical research.

Prerequisite(s): CHEM 2313 with a minimum grade of C-

CHEM 4620. Introduction to Protein Chemistry. (4 Hours)

Introduces protein chemistry in the context of molecular medicine. Discusses analytical methods used to elucidate the origin, structure, function, and purification of proteins. Surveys the synthesis and chemical properties of structurally and functionally diverse proteins, including globular, membrane, and fibrous proteins. Discusses the role of intra- and intermolecular interactions in determining protein conformation, protein folding, and in their enzymatic activity. Intended for undergraduate students without prior experience in protein chemistry.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-

CHEM 4621. Introduction to Chemical Biology. (4 Hours)

Probes the structure and function of biological macromolecules and the chemical reactions carried out in living systems, including biological energetics. Discusses techniques to measure macromolecular interactions and the principles and forces governing such interactions. Offers students an opportunity to gain experience in reading and evaluating primary literature. Intended for undergraduate students with no prior knowledge of the field.

Prerequisite(s): (CHEM 2317 with a minimum grade of C- or CHEM 2313 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-) (CHEM 3401 (may be taken concurrently) with a minimum grade of C- or CHEM 3421 (may be taken concurrently) with a minimum grade of C- or CHEM 3431 (may be taken concurrently) with a minimum grade of C-)

Corequisite(s): CHEM 4622

CHEM 4622. Lab for CHEM 4621. (1 Hour)

Accompanies CHEM 4621. Complements and reinforces the concepts from CHEM 4621 with an emphasis on fundamental techniques. Offers students an opportunity to complete independent projects in modern chemical biology research.

Prerequisite(s): ENGW 1111 with a minimum grade of C or ENGW 1102 with a minimum grade of C or ENGL 1111 with a minimum grade of C or ENGL 1102 with a minimum grade of C

Corequisite(s): CHEM 4621

CHEM 4628. Introduction to Spectroscopy of Organic Compounds. (4 Hours)

Examines the application of modern spectroscopic techniques to the structural elucidation of small organic molecules. Emphasizes the use of H and C NMR spectroscopy supplemented with information from infrared spectroscopy and mass spectrometry. Explores both the practical and nonmathematical theoretical aspects of 1D and 2D NMR experiments. Topics include the chemical shift, coupling constants, the nuclear Overhauser effect and relaxation, and 2D homonuclear and heteronuclear correlation. Designed for chemists who do not have an extensive math or physics background no prior knowledge of NMR spectroscopy is assumed.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-

Corequisite(s): CHEM 4629

CHEM 4629. Identification of Organic Compounds. (2 Hours)

Introduces the use of the nuclear magnetic resonance (NMR) spectrometer and basic NMR experiments. Determines the identity of unknown organic compounds by the use of mass spectrometry, infrared spectroscopy, and 1D and 2D nuclear magnetic resonance spectroscopy.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-

Corequisite(s): CHEM 4628

CHEM 4750. Senior Research. (4 Hours)

Conducts original experimental work under the direction of members of the department on a project. Introduces experimental design based on literature and a variety of techniques depending upon the individual project.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-

Attribute(s): NUpath Capstone Experience, NUpath Writing Intensive

CHEM 4901. Undergraduate Research. (4 Hours)

Conducts original research under the direction of members of the department. May be repeated without limit.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C- or CHEM 2321 with a minimum grade of C-

Attribute(s): NUpath Integration Experience

CHEM 4970. Junior/Senior Honors Project 1. (4 Hours)

Focuses on in-depth project in which a student conducts research or produces a product related to the student’s major field. Combined with Junior/Senior Project 2 or college-defined equivalent for 8 credit honors project. May be repeated without limit.

Attribute(s): NUpath Capstone Experience

CHEM 4971. Junior/Senior Honors Project 2. (4 Hours)

Focuses on second semester of in-depth project in which a student conducts research or produces a product related to the student’s major field. May be repeated without limit.

Prerequisite(s): CHEM 4970 with a minimum grade of C

Attribute(s): NUpath Capstone Experience, NUpath Writing Intensive

CHEM 4990. Elective. (1-4 Hours)

Offers elective credit for courses taken at other academic institutions. May be repeated without limit.

CHEM 4991. Research. (4 Hours)

Offers an opportunity to conduct research under faculty supervision. May be repeated without limit.

Attribute(s): NUpath Integration Experience

CHEM 4992. Directed Study. (1-4 Hours)

Offers independent work under the direction of members of the department on a chosen topic. Course content depends on instructor. May be repeated without limit.

CHEM 4993. Independent Study. (1-4 Hours)

Offers independent work under the direction of members of the department on a chosen topic. Course content depends on instructor. May be repeated without limit.

CHEM 4994. Internship. (4 Hours)

Offers students an opportunity for internship work. May be repeated without limit.

Attribute(s): NUpath Integration Experience

CHEM 5179. Complex Fluids and Everyday Materials. (4 Hours)

Introduces intra- and intermolecular forces and moves on to material deformation in response to external stress, including polymeric elasticity. Covers topics in colloidal science and biological physics: the microscopic origins of suspension stability and biological self-assembly. Additional topics include “molecular gastronomy,” personal care and cleaning products, active materials, and experimental techniques. Studies of complex fluids and soft materials are highly interdisciplinary. Many everyday materials are combinations of the three phases of matter—solid, liquid, and gas—with unique material properties. “Complex fluids” and “soft matter” refer to suspensions, emulsions, foams, and gels, which include personal care items, household cleaners, and even food. Nearly all biological material can be described as a soft material.

CHEM 5460. Enzymes: Chemistry and Chemical Biology. (3 Hours)

Focuses on enzymes: their chemistry, mechanisms, and applications. Examines the underlying chemical and mechanistic principles. Introduces the techniques and approaches in enzymology. Bridges the gap between classroom learning and real-world practice in the related fields, e.g., medicinal chemistry, chemical biology, engineering, and pharmaceutical research.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C- or graduate program admission

CHEM 5501. Chemical Safety in the Research Laboratory. (1 Hour)

Covers the material needed to complete successfully all the online safety training that is required for our graduate students, best practices for the safe execution of common chemical laboratory procedures, advanced procedures, as well as incidents from the recent literature. Includes discussions of case studies on topics relevant for the safe and effective use of chemicals and other materials in a research laboratory environment. Undergraduates may enroll with permission of the instructor.

CHEM 5550. Introduction to Glycobiology and Glycoprotein Analysis. (3 Hours)

Covers the background and methods used for glycoprotein characterization. Offers students an opportunity to obtain the background needed to assess the analytical steps necessary for development of glycoprotein drugs. Analyzes regulatory issues behind glycoprotein drug development. Covers recent developments in analytical and regulatory sciences.

CHEM 5599. Introduction to Research Skills and Ethics in Chemistry. (0 Hours)

Seeks to prepare students for success in CHEM 5600 and in CHEM 7730. May be repeated once. Must be taken in consecutive semesters before registration into CHEM 5600 and CHEM 7730.

CHEM 5600. Research Skills and Ethics in Chemistry. (3 Hours)

Discusses ethics in science. Topics include documentation of work in your laboratory notebook, safety in a chemistry research laboratory, principles of experimental design, online computer searching to access chemical literature, reading and writing technical journal articles, preparation and delivery of an effective oral presentation, and preparation of a competitive research proposal.

Prerequisite(s): CHEM 5599 with a minimum grade of S

CHEM 5610. Polymer Chemistry. (3 Hours)

Discusses the synthesis and analysis of polymer materials. Covers mechanisms and kinetics of condensation/chain-growth polymerization reactions and strategies leading to well-defined polymer architectures and compositions, including living polymerizations (free radical, cationic, anionic), catalytic approaches, and postpolymerization functionalization. Discusses correlation of chemical composition and structure to physical properties and applications.

Prerequisite(s): ((CHEM 2317 with a minimum grade of C- or CHEM 2313 with a minimum grade of C-) (CHEM 3401 (may be taken concurrently) with a minimum grade of C- or CHEM 3421 (may be taken concurrently) with a minimum grade of C- or CHEM 3431 (may be taken concurrently) with a minimum grade of C-)) or graduate program admission

CHEM 5611. Analytical Separations. (3 Hours)

Describes the theory and practice of separating the components of complex mixtures in the gas and liquid phase. Also includes methods to enhance separation efficiency and detection sensitivity. Covers thin-layer, gas, and high-performance liquid chromatography (HPLC) and recently developed techniques based on HPLC including capillary and membrane-based separation, and capillary electrophoresis.

CHEM 5612. Principles of Mass Spectrometry. (3 Hours)

Describes the theory and practice of ion separation in electrostatic and magnetic fields and their subsequent detection. Topics include basic principles of ion trajectories in electrostatic and magnetic fields, design and operation of inlet systems and electron impact ionization, and mass spectra of organic compounds.

CHEM 5613. Optical Methods of Analysis. (3 Hours)

Describes the application of optical spectroscopy to qualitative and quantitative analysis. Includes the principles and application of emission, absorption, scattering and fluorescence spectroscopies, spectrometer design, elementary optics, and modern detection technologies.

CHEM 5614. Electroanalytical Chemistry. (3 Hours)

Describes the theory of electrode processes and modern electroanalytical experiments. Topics include the nature of the electrode-solution interface (double layer models), mass transfer (diffusion, migration, and convection), types of electrodes, reference electrodes, junction potentials, kinetics of electrode reactions, controlled potential methods (cyclic voltammetry, chronoamperometry), chronocoulometry and square wave voltammetry, and controlled current methods (chronopotentiometry).

CHEM 5616. Protein Mass Spectrometry. (3 Hours)

Offers students an opportunity to obtain a fundamental understanding of modern mass spectrometers, the ability to operate these instruments, and the ability to prepare biological samples. Undoubtedly the most popular analytical method in science, mass spectrometry is utilized in fields ranging from subatomic physics to biology. Focuses on the analysis of proteins, with applications including biomarker discovery, tissue characterization, detection of blood doping, drug discovery, and the characterization of protein-based therapeutics. By the end of the course, the student is expected to be able to solve a particular chemistry- or biology-related problem by choosing the appropriate sample preparation methods and mass spectrometer.

CHEM 5617. Protein Mass Spectrometry Laboratory. (3 Hours)

Offers students an opportunity to develop an appreciation of the appropriate choice of mass spectrometer for a particular application.

CHEM 5618. Advanced Mass Spectrometry. (3 Hours)

Applies earlier study of mass spectrometry (the principles of modern mass spectrometry hardware and spectral interpretation) to experimental design and data analysis of drugs, proteins, and proteomes. Examines how to choose the appropriate mass spectrometry method for a given biological problem find and acquire an exemplar data set and interpret the data as well as expert practitioners do. As one of the most popular analytical methods in science, mass spectrometry is utilized in fields ranging from subatomic physics to biology. Applications have an overarching theme of human health and include biomarker discovery and validation, tissue analysis (including alternatives to histopathology), and drug development.

Prerequisite(s): CHEM 5612 with a minimum grade of C

CHEM 5620. Protein Chemistry. (3 Hours)

Describes proteins (what they are, where they come from, and how they work) in the context of analytical analysis and molecular medicine. Discusses the chemical properties of proteins, protein synthesis, and the genetic origins of globular proteins in solution, membrane proteins, and fibrous proteins. Covers the physical intra- and intermolecular interactions that proteins undergo along with descriptions of protein conformation and methods of structural determination. Explores protein folding as well as protein degradation and enzymatic activity. Highlights protein purification and biophysical characterization in relation to protein analysis, drug design, and optimization.

CHEM 5621. Principles of Chemical Biology for Chemists. (3 Hours)

Explores the use of natural and unnatural small-molecule chemical tools to probe macromolecules, including affinity labeling and click chemistry. Covers nucleic acid sequencing technologies and solid-phase synthesis of nucleic acids and peptides. Discusses in-vitro selection techniques, aptamers, and quantitative issues in library construction. Uses molecular visualization software tools to investigate structures of macromolecules. Intended for graduate and advanced undergraduate students.

Prerequisite(s): ((CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-) (CHEM 3401 (may be taken concurrently) with a minimum grade of C- or CHEM 3421 (may be taken concurrently) with a minimum grade of C- or CHEM 3431 (may be taken concurrently) with a minimum grade of C-)) or graduate program admission

CHEM 5622. Lab for CHEM 5621. (1 Hour)

Accompanies CHEM 5621. Complements and reinforces the concepts from CHEM 5621 with emphasis on fundamental techniques. Offers an opportunity to complete independent projects in modern chemical biology research.

Prerequisite(s): ((CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-) (CHEM 3401 (may be taken concurrently) with a minimum grade of C- or CHEM 3421 (may be taken concurrently) with a minimum grade of C- or CHEM 3431 (may be taken concurrently) with a minimum grade of C-) (ENGL 1111 with a minimum grade of C or ENGL 1102 with a minimum grade of C or ENGW 1111 with a minimum grade of C or ENGW 1102 with a minimum grade of C)) or graduate program admission

Attribute(s): NUpath Writing Intensive

CHEM 5625. Chemistry and Design of Protein Pharmaceuticals. (3 Hours)

Covers the chemical transformations and protein engineering approaches to protein pharmaceuticals. Describes protein posttranslational modifications, such as oxidation, glycosylation, formation of isoaspartic acid, and disulfide. Then discusses bioconjugate chemistry, including those involved in antibody-drug conjugate and PEGylation. Finally, explores various protein engineering approaches, such as quality by design (QbD), to optimize the stability, immunogenicity, activity, and production of protein pharmaceuticals. Discusses the underlying chemical principles and enzymatic mechanisms as well.

Prerequisite(s): (CHEM 2317 with a minimum grade of C- or CHEM 2313 with a minimum grade of C- or graduate program admission) (CHEM 5620 (may be taken concurrently) with a minimum grade of C- or CHEM 5621 (may be taken concurrently) with a minimum grade of C-

CHEM 5626. Organic Synthesis 1. (3 Hours)

Surveys types of organic reactions including stereochemistry, influence of structure and medium, mechanistic aspects, and synthetic applications.

CHEM 5627. Mechanistic and Physical Organic Chemistry. (3 Hours)

Surveys tools used for elucidating mechanisms including thermodynamics, kinetics, solvent and isotope effects, and structure/reactivity relationships. Topics include molecular orbital theory, aromaticity, and orbital symmetry. Studies reactive intermediates including carbenes, carbonium ions, radicals, biradicals and carbanions, acidity, and photochemistry.

CHEM 5628. Principles of Spectroscopy of Organic Compounds. (3 Hours)

Studies how to determine organic structure based on proton and carbon nuclear magnetic resonance spectra, with additional information from mass and infrared spectra and elemental analysis. Presents descriptive theory of nuclear magnetic resonance experiments and applications of advanced techniques to structure determination. Includes relaxation, nuclear Overhauser effect, polarization transfer, and correlation in various one- and two- dimensional experiments. Requires graduate students to have one year of organic chemistry or equivalent.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C- or graduate program admission

CHEM 5629. Advanced Physical Organic Chemistry. (3 Hours)

Studies the importance of molecular orbital theory in stereoelectronic effects, thermal, and photochemical pericyclic reactions. Offers students an opportunity to obtain the reasoning skills to analyze an organic transformation and apply guiding structural and electronic principles to build intuition on the chemo-, stereo-, and regioselectivity of reactions. Some of these concepts include quantum mechanics, molecular orbital theory, structure and bonding, conformational analysis, hybridization, aromaticity, and hyperconjugation. Students engage in peer-review, literature presentations and collaborative problem solving.

CHEM 5630. Nucleic Acid Chemistry. (3 Hours)

Offers a broadband introduction to the field of nucleic acid chemistry. Nucleic acids are vital for biology, but their roles have been greatly expanded beyond storage of genetic information. The breadth of utility of nucleic acids stems from a precise understanding of their structures, modern means to synthesize and modify them, and the ability for nucleic acids to engage with varieties of enzymes/proteins and other synthetic/biological systems. Foundational topics include nucleic acid structure, physicochemical properties, syntheses of nucleosides/nucleotides/oligonucleotides, chemical modification of nucleic acids, methods to manipulate and analyze nucleic acids (e.g., PCR, sequencing, and electrophoresis). Advanced topics include nucleic acid therapeutics (e.g., siRNA, antisense technology, CRISPR, and aptamers) DNA damage and repair and DNA for materials science (e.g., DNA nanotechnology).

CHEM 5636. Statistical Thermodynamics. (3 Hours)

Briefly reviews classical thermodynamics before undertaking detailed coverage of statistical thermodynamics, including probability theory, the Boltzmann distribution, partition functions, ensembles, and statistically derived thermodynamic functions. Reconsiders the basic concepts of statistical thermodynamics from the modern viewpoint of information theory. Presents practical applications of the theory to problems of contemporary interest, including polymers and biopolymers, nanoscale systems, molecular modeling, and bioinformatics.

Prerequisite(s): CHEM 3401 with a minimum grade of C- or CHEM 3421 with a minimum grade of C- or CHEM 3431 with a minimum grade of C- or graduate program admission

CHEM 5638. Molecular Modeling. (3 Hours)

Introduces molecular modeling methods that are basic tools in the study of macromolecules. Is structured partly as a practical laboratory using a popular molecular modeling suite, and also aims to elucidate the underlying physical principles upon which molecular mechanics is based. These principles are presented in supplemental lectures or in laboratory workshops.

CHEM 5640. Biopolymeric Materials. (3 Hours)

Examines the structure, properties, and processing of biomaterials, the forms of matter that are produced by or interact with biological systems. One of the pillars of biomedical engineering is to use naturally derived and synthetic biomaterials to treat, augment, or replace human tissues.

CHEM 5641. Computational Chemistry. (3 Hours)

Introduces basic concepts, methods, techniques, and recent advances in computational chemistry and their relevance to experimental characterizations such as spectroscopy. Topics include electronic structure theory (wave function theory and density functional theory), principles of molecular dynamics simulations, multiscale modeling, machine learning, and quantum computing relevant to computational chemistry. Builds a theoretical foundation for students to properly choose computational methods to solve common research problems in chemistry, biochemistry, and materials science. Also introduces the field of research in computational chemistry. Suitable for advanced undergraduate students and graduate students who plan to conduct research in the field of computational chemistry or plan to utilize computational techniques to complement experimental research in the molecular sciences.

CHEM 5648. Chemical Principles and Application of Drug Metabolism and Pharmacokinetics. (3 Hours)

Offers students an opportunity to obtain a comprehensive grounding in the chemistry of drug metabolism and pharmacokinetics (DMPK) and its application to drug design and optimization. Multiple rounds of chemical synthesis and testing are usually required to discover new drugs with the appropriate balance of properties such as potency and selectivity, efficacy in preclinical models of disease, safety, and pharmacokinetics. Introduces students to modern tools and concepts utilized to screen for favorable DMPK properties, as well as methods to predict human PK from in vitro and preclinical data. Examines the linkage between drug levels in the body, pharmacodynamic response (PK/PD), and drug-drug interactions in the context of the iterative process of chemical drug synthesis.

CHEM 5651. Materials Chemistry of Renewable Energy. (3 Hours)

Studies renewable energy in terms of photovoltaics, photoelectrochemistry, fuel cells, batteries, and capacitors. Focuses on the aspects of each component and their relationships to one another.

Prerequisite(s): ((CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) CHEM 3403 with a minimum grade of C-) or graduate program admission

CHEM 5655. Molecular Symmetry and Group Theory. (3 Hours)

Covers symmetry operations point groups and classification of molecules into point groups as well as matrix representation of symmetry operations, orthogonality theorem, and its use in determining irreducible representation spanned by a basis. Studies decomposition of reducible representation and direct products, characters and character tables, and reviews quantum mechanics. Also covers infrared and Raman spectroscopy, normal modes of vibrations, determining symmetry of vibrations, the role of symmetry in selection rules, LCAO MO theory, Hückel method, electronic spectroscopy, and vibronic spectroscopy and symmetry.

CHEM 5660. Analytical Biochemistry. (3 Hours)

Covers the analysis of biological molecules, which include nucleic acids, proteins, carbohydrates, lipids, and metabolites. Discusses isolation, characterization, and quantification of these molecules.

CHEM 5672. Organic Synthesis 2. (3 Hours)

Continues CHEM 5626. Surveys types of organic reactions including stereochemistry, influence of structure and medium, mechanistic aspects, and synthetic applications.

Prerequisite(s): CHEM 5626 with a minimum grade of C-

CHEM 5676. Bioorganic Chemistry. (3 Hours)

Covers host guest complexation by crown ethers, cryptands, podands, spherands, and so forth molecular recognition including self-replication peptide and protein structure coenzymes and metals in bioorganic chemistry nucleic acid structure interaction of DNA with proteins and small molecules including DNA-targeted drug design catalytic RNA and catalytic antibodies.

Prerequisite(s): (CHEM 5626 with a minimum grade of C- CHEM 5627 with a minimum grade of C-) or graduate program admission

CHEM 5688. Principles of Nuclear Magnetic Resonance. (3 Hours)

Presents the physical principles underlying magnetic resonance spectroscopy, including Fourier transform theory, classical and quantum-mechanical treatments of spin angular momentum, the Bloch equations, and spin relaxation. Covers fundamental concepts in time domain magnetic resonance methods, including pulse sequences, selective pulses, phase cycling, coherence pathways, field gradients, and nonuniform sampling. Surveys the NMR methods most commonly applied to chemical structural analysis, including pure shift NMR 2D correlation (COSY, DQF-COSY, TOCSY, HSQC, HMBC) methods and cross-relaxation (NOESY, ROESY) methods.

CHEM 5700. Topics in Organic Chemistry. (3 Hours)

Offers various topics within the breadth of organic chemistry. Intended to meet the needs and interests of students. Topics could range from the physical and material aspects of organic chemistry to the biochemical and biomedical aspects of organic chemistry. Undergraduate students who have completed a second semester of organic chemistry with a grade of at least C– may be admitted with permission of instructor. May be repeated once.

CHEM 5904. Seminar. (1 Hour)

Focuses on oral reports by master of science and PlusOne participants on current research topics in chemistry and chemical biology. May be repeated up to two times.

CHEM 5976. Directed Study. (1-4 Hours)

Offers independent work under the direction of members of the department on a chosen topic. Course content depends on instructor. May be repeated without limit.

CHEM 5984. Research. (1-6 Hours)

Offers an opportunity to conduct research under faculty supervision. May be repeated up to three times for up to 6 total credits.

CHEM 6500. Cheminformatics. (3 Hours)

Introduces the subject of cheminformatics. Focuses on informatic, or computer, methods to solve chemical problems. Focuses on the approaches to mine data, looking at structural similarities, and evaluating compound designs and libraries for diversity and other characteristics. In addition, briefly discusses molecular modelling of proteins.

CHEM 6962. Elective. (1-4 Hours)

Offers elective credit for courses taken at other academic institutions. May be repeated without limit.

CHEM 7247. Advances in Nanomaterials. (3 Hours)

Designed to provide an entry-level perspective of solid-state chemistry both from a fundamental and applied perspective. Discusses the basic aspects of materials science encompassing broad areas of structure, physical properties, and classification in the context of both bulk and surface (thin films, interfaces) properties.

CHEM 7305. Special Topics in Inorganic and Materials Chemistry. (3 Hours)

Presents selected topics of current importance in inorganic and materials chemistry. May be repeated without limit.

CHEM 7317. Analytical Biotechnology. (3 Hours)

Focuses on the analytical methods used for the characterization of recombinant DNA-derived proteins for human therapeutic use. Combines the description of advanced analytical methods, in particular HPLC and mass spectrometry, with protein chemistry. An important aspect is the development of a method that can identify protein modifications that are present in a product as a result of biosynthetic modifications, contaminants, or degradative reactions. Provides an integrative overview of the role of analytical methods at the different stages of development and production of protein therapeutics including upstream (cell line development, cell culture), downstream (recovery and purifications), formulation development, stability studies, and clinical assay.

CHEM 7710. Laboratory Rotations in Chemistry and Chemical Biology. (0 Hours)

Offers an opportunity for students to gain exposure to research laboratories in the department to help them choose a thesis advisor and project.

CHEM 7730. Advanced Laboratory Methods. (4 Hours)

Seeks to provide intensive practical laboratory training in a chosen thematic area. Students select from organic and medicinal chemistry, physical and materials chemistry, or analytical and biological chemistry. The course involves a common practical training module followed by specialized modules in the chosen concentration area. The practical training features a combination of formal laboratory instruction coupled with rotation through selected research laboratories. Full-time PhD students only.

Prerequisite(s): CHEM 5599 with a minimum grade of C-

CHEM 7750. Advanced Problem Solving. (3 Hours)

Designed to provide skills necessary to lead advanced problem-solving case studies. Faculty mentors in one of three thematic areas chosen from organic and medicinal chemistry, physical and materials chemistry, or analytical and biological chemistry assign casework to students for presentation and analysis in group sessions. Students are required to provide rational solutions to complex problems derived from the contemporary literature and engage in dialogue with faculty mentors to justify their analysis. The faculty mentors assign grades to reflect intellectual maturity and ability of the students to display creative, independent thinking. Full-time PhD students who have successfully completed qualifying examinations only.

CHEM 7962. Elective. (1-4 Hours)

Offers elective credit for courses taken at other academic institutions. May be repeated without limit.

CHEM 7990. Thesis. (1-4 Hours)

Offers thesis supervision by members of the department. May be repeated without limit.

CHEM 7996. Thesis Continuation. (0 Hours)

Offers continuing thesis supervision by members of the department.

CHEM 8504. Graduate Seminar. (1 Hour)

Focuses on oral reports by the participants on current research topics in chemistry and chemical biology. May be repeated without limit.

CHEM 8960. Exam Preparation—Doctoral. (0 Hours)

Offers the student the opportunity to prepare for and take the PhD qualifying exams (cumulative exams).

CHEM 8984. Research. (1-6 Hours)

Offers the chance to conduct original research, written thesis thereon, or to the establishment of doctoral candidacy. May be repeated without limit.

CHEM 8986. Research. (0 Hours)

Offers the student the opportunity to conduct full-time research for the master’s degree. May be repeated without limit.

CHEM 9000. PhD Candidacy Achieved. (0 Hours)

Indicates successful completion of the doctoral comprehensive exam.

CHEM 9984. Research. (1-4 Hours)

Offers an opportunity to conduct research under faculty supervision. May be repeated without limit.

CHEM 9986. Research. (0 Hours)

Offers the student the opportunity to conduct full-time research for the PhD. May be repeated without limit.

CHEM 9990. Dissertation Term 1. (0 Hours)

Offers the student the opportunity to conduct theoretical and experimental research for the PhD degree. Open to chemical biology students.

Prerequisite(s): CHEM 9000 with a minimum grade of S

CHEM 9991. Dissertation Term 2. (0 Hours)

Offers dissertation supervision by members of the department.

Prerequisite(s): CHEM 9990 with a minimum grade of S

CHEM 9996. Dissertation Continuation. (0 Hours)

Offers dissertation supervision by members of the department. Open to chemical biology students.

Prerequisite(s): CHEM 9991 with a minimum grade of S or Dissertation Check with a score of REQ


Bachelor of Science (BS)

CHEM 1000. Chemistry/Chemical Biology at Northeastern. (1 Hour)

Intended for freshmen in the College of Science. Introduces students to liberal arts familiarizes them with their major develops the academic skills necessary to succeed (analytical ability and critical thinking) provides grounding in the culture and values of the University community and helps to develop interpersonal skills—in short, familiarizes students with all skills needed to become a successful university student.

CHEM 1101. General Chemistry for Health Sciences. (4 Hours)

Provides a one-semester introduction to general chemistry for the health sciences. Covers the fundamentals of elements and atoms ionic and molecular structure chemical reactions and their stoichiometry, energetics, rates, and equilibriums and the properties of matter as gases, liquids, solids, and solutions. Other topics include acids and bases, and nuclear chemistry. Applications to the health sciences are included throughout.

Attribute(s): NUpath Natural/Designed World

CHEM 1102. Lab for CHEM 1101. (1 Hour)

Accompanies CHEM 1101. Covers a range of topics from the course, such as qualitative and quantitative analysis and the characteristics of chemical and physical processes. Includes measurements of heat transfer, rate and equilibrium constants, and the effects of temperature and catalysts. Emphasis is on aqueous acid-base reactions and the properties and uses of buffer systems.

CHEM 1103. Recitation for CHEM 1101. (0 Hours)

Accompanies CHEM 1101. Covers various topics from the course.

CHEM 1104. Organic Chemistry for Health Sciences. (4 Hours)

Provides a one-semester introduction to organic chemistry for the health sciences. Covers the fundamentals of the structure, nomenclature, properties, and reactions of the compounds of carbon. Also introduces biological chemistry including amino acids, proteins, carbohydrates, lipids, nucleic acids, hormones, neurotransmitters, and drugs. Applications to the health sciences are included throughout.

Prerequisite(s): CHEM 1101 with a minimum grade of D

CHEM 1105. Lab for CHEM 1104. (1 Hour)

Accompanies CHEM 1104. Covers a range of topics from the course, such as the properties and elementary reactions of hydrocarbons, alcohols, ethers, carbonyl compounds, carbohydrates, and amines.

CHEM 1106. Recitation for CHEM 1104. (0 Hours)

Accompanies CHEM 1104. Covers various topics from the course.

CHEM 1107. Introduction to Forensic Science. (4 Hours)

Introduces students to the field of forensic science from both a scientific and a legal perspective. Examines the challenges and methodologies of crime scene investigation, forensic biology, and forensic chemistry. Provides real-world case studies and examines some misrepresentations of forensics by television dramas. Emphasizes scientific evidence associated with topics such as DNA analysis, drug abuse, and explosion investigations, as well as other relevant topics.

Attribute(s): NUpath Natural/Designed World

CHEM 1109. The Chemistry of Food and Cooking. (4 Hours)

Introduces a number of basic scientific principles in the methodology of cooking, food preparation, and the enjoyment of food. Focuses on the chemistry and molecular bases of food, reactivity under various conditions, molecular gastronomy, geographic and cultural influences on food, and food as preventative medicine. Class demonstrations of various cooking techniques illustrate different chemical principles between food and cooking. Designed for students who do not plan to major in the natural sciences.

Attribute(s): NUpath Natural/Designed World

CHEM 1151. General Chemistry for Engineers. (4 Hours)

Corresponds to one semester of study in important areas of modern chemistry, such as details of the gaseous, liquid, and solid states of matter intra- and intermolecular forces and phase diagrams. Presents the energetics and spontaneity of chemical reactions in the context of chemical thermodynamics, while their extent and speed is discussed through topics in chemical equilibria and kinetics. Aspects of electrochemical energy storage and work are considered in relation to batteries, fuel, and electrolytic cells.

Corequisite(s): CHEM 1153

Attribute(s): NUpath Natural/Designed World

CHEM 1153. Recitation for CHEM 1151. (0 Hours)

Accompanies CHEM 1151. Offers a weekly sixty-five-minute drill/discussion session conducted by chemistry faculty or graduate teaching assistants. Discusses the homework assignments of CHEM 1151 in detail with emphasis on student participation.

Corequisite(s): CHEM 1151

CHEM 1161. General Chemistry for Science Majors. (4 Hours)

Introduces the principles of chemistry, focusing on the particulate nature of matter and its interactions and reactions that form the basis for the underlying molecular dynamics of living systems. Presents basic concepts of chemical bonding and intermolecular interactions for molecules and molecules’ behavior in aqueous solutions with examples from biologically relevant molecules. Introduces kinetics and chemical thermodynamics with examples from biological systems. Offers students an opportunity to obtain a framework for understanding the chemical basis for different methods for separating and purifying biological compounds.

Attribute(s): NUpath Natural/Designed World

CHEM 1162. Lab for CHEM 1161. (1 Hour)

Accompanies CHEM 1161. Introduces basic laboratory techniques. Covers a range of topics including qualitative and quantitative analysis and the characteristics of chemical and physical processes.

CHEM 1163. Recitation for CHEM 1161. (0 Hours)

Accompanies CHEM 1161. Covers various topics from the course. Offers students an opportunity to work interactively with instructors and other students to learn and apply the knowledge acquired in lecture.

CHEM 1211. General Chemistry 1. (4 Hours)

Introduces the principles of chemistry, focusing on the states and structure of matter and chemical stoichiometry. Presents basic concepts and definitions, moles, gas laws, atomic structure, periodic properties and chemical bonding, all within a contextual framework.

Attribute(s): NUpath Natural/Designed World

CHEM 1212. Lab for CHEM 1211. (1 Hour)

Accompanies CHEM 1211. Covers a range of topics from the course including qualitative and quantitative analysis and the characteristics of chemical and physical processes.

CHEM 1213. Recitation for CHEM 1211. (0 Hours)

Accompanies CHEM 1211. Covers various topics from the course.

CHEM 1214. General Chemistry 2. (4 Hours)

Continues CHEM 1211. Introduces the principles of chemical equilibrium, the rates and mechanisms of chemical reactions, and energy considerations in chemical transformations. Covers solutions, chemical kinetics, chemical equilibria, chemical thermodynamics, electrochemistry, and chemistry of the representative elements. Such contextual themes as energy resources, smog formation, and acid rain illustrate the principles discussed.

Prerequisite(s): CHEM 1211 with a minimum grade of D

Attribute(s): NUpath Natural/Designed World

CHEM 1215. Lab for CHEM 1214. (1 Hour)

Accompanies CHEM 1214. Covers a range of topics from the course, such as measurements of heat transfer, rate and equilibrium constants, and the effects of temperature and catalysts. Particular attention is paid to aqueous acid-base reactions and to the properties and uses of buffer systems. Quantitative analysis of chemical and physical systems is emphasized throughout.

CHEM 1216. Recitation for CHEM 1214. (0 Hours)

Accompanies CHEM 1214. Covers various topics from the course.

CHEM 1990. Elective. (1-4 Hours)

Offers elective credit for courses taken at other academic institutions. May be repeated without limit.

CHEM 2161. Concepts in Chemistry. (4 Hours)

Explores basic concepts of thermodynamics electrochemistry and nuclear, supramolecular, and solid-state chemistry in the context of modern materials. Emphasizes connecting the particulate nature of matter to the properties of substances and patterns of chemical reactivity.

Attribute(s): NUpath Writing Intensive

CHEM 2162. Lab for CHEM 2161. (1 Hour)

Accompanies CHEM 2161. Offers hands-on exploration of the basic concepts of electrochemistry and of nuclear, supramolecular, and solid-state chemistry.

CHEM 2163. Recitation for CHEM 2161. (0 Hours)

Accompanies CHEM 2161. Covers various topics from the course. Offers students an opportunity to work interactively with instructors and other students to learn and apply the knowledge acquired in lecture.

CHEM 2311. Organic Chemistry 1. (4 Hours)

Introduces nomenclature, preparation, properties, stereochemistry, and reactions of common organic compounds. Presents correlations between the structure of organic compounds and their physical and chemical properties, and mechanistic interpretation of organic reactions. Includes chemistry of hydrocarbons and their functional derivatives.

Prerequisite(s): CHEM 1151 with a minimum grade of D or CHEM 1214 with a minimum grade of D or CHEM 1220 with a minimum grade of D or CHEM 1161 with a minimum grade of D

Corequisite(s): CHEM 2312

CHEM 2312. Lab for CHEM 2311. (1 Hour)

Accompanies CHEM 2311. Introduces basic laboratory techniques, such as distillation, crystallization, extraction, chromatography, characterization by physical methods, and measurement of optical rotation. These techniques serve as the foundation for the synthesis, purification, and characterization of products from microscale syntheses integrated with CHEM 2311.

Corequisite(s): CHEM 2311

CHEM 2313. Organic Chemistry 2. (4 Hours)

Continues CHEM 2311. Focuses on additional functional group chemistry including alcohols, ethers, carbonyl compounds, and amines, and also examines chemistry relevant to molecules of nature. Introduces spectroscopic methods for structural identification.

Prerequisite(s): CHEM 2311 with a minimum grade of D or CHEM 2315 with a minimum grade of D

Corequisite(s): CHEM 2314

CHEM 2314. Lab for CHEM 2313. (1 Hour)

Accompanies CHEM 2313. Basic laboratory techniques from CHEM 2312 are applied to chemical reactions of alcohols, ethers, carbonyl compounds, carbohydrates, and amines. Introduces basic laboratory techniques including infrared (IR) spectroscopy and nuclear magnetic resonance (NMR) spectronomy as analytical methods for characterization of organic molecules.

Corequisite(s): CHEM 2313

CHEM 2315. Organic Chemistry 1 for Chemistry Majors. (4 Hours)

Reviews the basics of bonding and thermodynamics of organic compounds as well as conformational and stereochemical considerations. Presents the structure, nomenclature, and reactivity of hydrocarbons and their functional derivatives. Highlights key reaction mechanisms, providing an introduction to the methodology of organic synthesis.

Prerequisite(s): CHEM 1214 with a minimum grade of C- or CHEM 1220 with a minimum grade of C-

CHEM 2316. Lab for CHEM 2315. (2 Hours)

Accompanies CHEM 2315. Introduces basic laboratory techniques, such as distillation, crystallization, extraction, chromatography, characterization by physical methods, and measurement of optical rotation. These techniques serve as the foundation for the synthesis, purification, and characterization of products from microscale syntheses integrated with CHEM 2315.

CHEM 2317. Organic Chemistry 2 for Chemistry Majors. (4 Hours)

Continues CHEM 2315. Extends the study of functional groups commonly found in organic compounds, further emphasizing conceptual mastery of the relationship between structure and reactivity. Introduces structural identification of organic compounds using contemporary spectroscopic methods such as IR, MS, and NMR. Other topics include structure and reactivity of conjugated and aromatic systems, the chemistry of ethers and epoxides, and the chemistry of carbonyl-containing compounds including aldehydes, ketones, carboxylic acids, and carboxylic acid derivatives. Offers students an opportunity to develop skills in planning multistep syntheses using the retrosynthesis approach and proposing mechanisms for chemical transformations.

Prerequisite(s): CHEM 2311 with a minimum grade of C- or CHEM 2315 with a minimum grade of C-

Attribute(s): NUpath Creative Express/Innov

CHEM 2318. Lab for CHEM 2317. (2 Hours)

Accompanies CHEM 2317. Introduces basic laboratory techniques including infrared (IR) spectroscopy and nuclear magnetic resonance (NMR) spectronomy as analytical methods for characterization of organic molecules. These methods serve as the basis for characterization of products from microscale syntheses.

CHEM 2319. Recitation for CHEM 2311. (0 Hours)

Offers students opportunities to work interactively with instructors and other students to learn and apply the understandings acquired in lab and lecture.

CHEM 2320. Recitation for CHEM 2313. (0 Hours)

Offers students opportunities to work interactively with instructors and other students to learn and apply the understandings acquired in lab and lecture.

CHEM 2321. Analytical Chemistry. (4 Hours)

Introduces the principles and practices in the field of analytical chemistry. Focuses on development of a quantitative understanding of homogeneous and heterogeneous equilibria phenomena as applied to acid-base and complexometric titrations, rudimentary separations, optical spectroscopy, electrochemistry, and statistics.

Prerequisite(s): (CHEM 1151 with a minimum grade of C- or CHEM 1214 with a minimum grade of C- or CHEM 1220 with a minimum grade of C- or CHEM 1161 with a minimum grade of C-) (CHEM 2311 with a minimum grade of C- or CHEM 2315 with a minimum grade of C-)

Attribute(s): NUpath Analyzing/Using Data, NUpath Writing Intensive

CHEM 2322. Lab for CHEM 2321. (1 Hour)

Accompanies CHEM 2321. Lab experiments provide hands-on experience in the analytical methods introduced in CHEM 2321, specifically, silver chloride gravimetry, complexometric titrations, acid-base titrations, UV-vis spectroscopy, cyclic voltammetry, Karl Fischer coulometry, and modern chromatrographic methods.

CHEM 2323. Recitation for CHEM 2321. (0 Hours)

Accompanies CHEM 2321 and CHEM 2322. Covers various topics from the course. Offers students an opportunity to work interactively with instructors and other students to learn and apply the knowledge acquired in lecture and lab.

CHEM 2324. Recitation for CHEM 2315. (0 Hours)

Accompanies CHEM 2315 and CHEM 2316. Offers students an opportunity to work interactively with instructors and other students to learn and apply the knowledge acquired in lab and lecture.

CHEM 2325. Recitation for CHEM 2317. (0 Hours)

Accompanies CHEM 2317 and CHEM 2318. Offers students an opportunity to work interactively with instructors and other students to learn and apply the knowledge acquired in lab and lecture.

CHEM 2990. Elective. (1-4 Hours)

Offers elective credit for courses taken at other academic institutions. May be repeated without limit.

CHEM 2991. Research in Chemistry and Chemical Biology. (1-4 Hours)

Offers an opportunity to conduct introductory-level research or creative endeavors under faculty supervision.

CHEM 3331. Bioanalytical Chemistry. (4 Hours)

Offers students an opportunity to obtain a broad familiarity with bioanalytical chemistry at the undergraduate level. After reviewing basic principles of analytical chemistry, the course covers biomolecular analysis by modern methods, including chromatography, electrophoresis, mass spectrometry, and immunohistochemistry. Studies genomics, proteomics, biosensors, bioassays, and protein/DNA sequencing. Exposes students to technical literature and modern applications in biochemistry, molecular biology, and chemistry.

Prerequisite(s): (CHEM 1151 with a minimum grade of C- or CHEM 1161 with a minimum grade of C- or CHEM 1214 with a minimum grade of C- or CHEM 1220 with a minimum grade of C-) (CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or BIOL 3611 with a minimum grade of C-) (ENGL 1102 with a minimum grade of C or ENGL 1111 with a minimum grade of C or ENGW 1102 with a minimum grade of C or ENGW 1111 with a minimum grade of C)

Corequisite(s): CHEM 3332

Attribute(s): NUpath Analyzing/Using Data, NUpath Writing Intensive

CHEM 3332. Lab for CHEM 3331. (1 Hour)

Accompanies CHEM 3331. Offers students an opportunity to apply modern analytical instrumentation to a selection of relevant applications as they relate to research and development labs in the biotechnology and pharmaceutical industry.

Corequisite(s): CHEM 3331

CHEM 3401. Chemical Thermodynamics and Kinetics. (4 Hours)

Traces the development of chemical thermodynamics through the three major laws of thermodymamics. These are applied to thermochemistry, chemical reaction and phase equilibria, and the physical behavior of multicomponent systems. Emphasizes quantitative interpretation of physical measurements.

Prerequisite(s): (MATH 1252 with a minimum grade of C- or MATH 1342 with a minimum grade of C-) (CHEM 1214 with a minimum grade of C- or CHEM 1220 with a minimum grade of C- or CHEM 1151 with a minimum grade of C- or CHEM 1161 with a minimum grade of C-) (PHYS 1155 (may be taken concurrently) with a minimum grade of C- or PHYS 1165 (may be taken concurrently) with a minimum grade of C-)

Corequisite(s): CHEM 3402

CHEM 3402. Lab for CHEM 3401. (1 Hour)

Accompanies CHEM 3401. Demonstrates the measurement of selected physical chemical phenomena presented in CHEM 3401, introducing experimental protocol and methods of data analysis. Experiments include investigations of gas nonideality and critical phenomena, electrochemical measurement of equilibrium, construction of phase diagrams, and bomb and differential scanning calorimetry.

Corequisite(s): CHEM 3401

CHEM 3403. Quantum Chemistry and Spectroscopy. (4 Hours)

Studies the theory of quantum chemistry with applications to spectroscopy. Presents some simple quantum mechanical (QM) models, including the particle in a box, rigid rotor, and harmonic oscillator, followed by treatments of electrons in atoms and molecules. Microwave, infrared, Raman, NMR, ESR, atomic absorption, atomic emission, and UV-Vis spectroscopy are discussed in detail.

Prerequisite(s): (CHEM 3401 with a minimum grade of C- or CHEM 3421 with a minimum grade of C- or CHEM 3431 with a minimum grade of C- or CHME 3322 with a minimum grade of C-) MATH 1342 with a minimum grade of C- (PHYS 1155 with a minimum grade of C- or PHYS 1165 with a minimum grade of C-)

Corequisite(s): CHEM 3404

CHEM 3404. Lab for CHEM 3403. (1 Hour)

Accompanies CHEM 3403. Explores the principles covered in CHEM 3403 by laboratory experimentation. Experiments include measurement of reaction kinetics, such as excited state dynamics, measurement of gas transport properties, atomic and molecular absorption and emission spectroscopy, infrared spectroscopy of molecular vibrations, and selected applications of fluorimetry.

Corequisite(s): CHEM 3403

CHEM 3410. Environmental Geochemistry. (4 Hours)

Offers students who wish to work in the geosciences or environmental science and engineering fields, including on the land, in freshwater, or the oceans, an opportunity to understand the geochemical principles that shape the natural and managed environment. Seeks to provide a context for understanding the natural elemental cycles and environmental problems through studies in atmospheric, terrestrial, freshwater, and marine geochemistry. Topics include fundamental geochemical principles environmental mineralogy organic and isotope geochemistry the global carbon, nitrogen, and phosphorous cycles atmospheric pollution environmental photochemistry and human-natural climate change feedbacks. ENVR 3410 and CHEM 3410 are cross-listed.

Attribute(s): NUpath Analyzing/Using Data, NUpath Natural/Designed World

CHEM 3431. Physical Chemistry. (4 Hours)

Offers an in-depth survey of physical chemistry. Emphasizes applications in modern research, including examples from biochemistry. Topics include the laws of thermodynamics and their molecular interpretation equilibrium in chemical and biochemical systems molecular transport kinetics, including complex enzyme mechanisms and an introduction to spectroscopy and the underlying concepts of quantum chemistry.

Prerequisite(s): ((CHEM 1214 with a minimum grade of C- or CHEM 1220 with a minimum grade of C-) or (CHEM 1151 with a minimum grade of C- or CHEM 1161 with a minimum grade of C-)) (MATH 1252 with a minimum grade of C- or MATH 1342 with a minimum grade of C-) (PHYS 1147 with a minimum grade of C- or PHYS 1155 with a minimum grade of C- or PHYS 1165 with a minimum grade of C- or PHYS 1175 with a minimum grade of C-)

Corequisite(s): CHEM 3432

CHEM 3432. Lab for CHEM 3431. (1 Hour)

Accompanies CHEM 3431. Covers practical skills in physical chemistry with an emphasis on current practice in chemistry, biochemistry, and pharmaceutical science. Introduces both ab initio and biological molecular modeling, differential scanning calorimetry, polymer characterization, protein unfolding and protein/ligand binding, electronic absorption spectroscopy, and synthesis of nanoparticles or quantum dots.

Corequisite(s): CHEM 3431

CHEM 3501. Inorganic Chemistry. (4 Hours)

Presents the following topics: basic concepts of molecular topologies, coordination compounds, coordination chemistry, isomerism, electron-transfer reactions, substitution reactions, molecular rearrangements and reactions at ligands, and biochemical applications.

Prerequisite(s): (CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-)

Attribute(s): NUpath Writing Intensive

CHEM 3502. Lab for CHEM 3501. (1 Hour)

Offers a laboratory course in inorganic chemistry with experiments and projects that track with the topics discussed in CHEM 3501. Designed to provide laboratory experience with the synthesis of coordination compounds and with the instrumental methods used to characterize them.

CHEM 3503. Recitation for CHEM 3501. (0 Hours)

Offers students additional opportunities to work interactively with instructors and other students to learn and apply the concepts presented in CHEM 3501.

CHEM 3505. Introduction to Bioinorganic Chemistry. (4 Hours)

Explores basic concepts of molecular topologies, coordination compounds, coordination chemistry, isomerism, electron-transfer reactions, substitution reactions, molecular rearrangements, and reactions at ligands in the context of metal-based drugs, imaging agents, and metalloenzymes.

Prerequisite(s): (CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-)

Attribute(s): NUpath Writing Intensive

CHEM 3506. Lab for CHEM 3505. (1 Hour)

Offers a laboratory course in inorganic chemistry with experiments and projects that track with the topics discussed in CHEM 3505. Designed for students who have mastered basic laboratory techniques in general and organic chemistry. Introduces new synthetic techniques and applies modern analytical characterization tools not previously used in other laboratory courses (such as CHEM 3522 and CHEM 3532).

CHEM 3507. Recitation for CHEM 3505. (0 Hours)

Offers students additional opportunities to work interactively with instructors and other students to learn and apply the concepts presented in CHEM 3505.

CHEM 3521. Instrumental Methods of Analysis. (1 Hour)

Introduces the instrumental methods of analysis used in all fields of chemistry, with an emphasis on understanding not only the fundamental principles of each method but also the basics of the design and operation of the relevant instrumentation.

Prerequisite(s): CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-

Corequisite(s): CHEM 3522

CHEM 3522. Instrumental Methods of Analysis Lab. (4 Hours)

Accompanies CHEM 3521. Lab experiments provide hands-on experience in the instrumental methods of analysis discussed in CHEM 3521, such as high-performance liquid chromatography, gas chromatography, mass spectrometry, capillary electrophoresis, atomic absorption, cyclic voltammetry, and UV-vis spectroscopy.

Prerequisite(s): CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-

Corequisite(s): CHEM 3521

CHEM 3531. Chemical Synthesis Characterization. (1 Hour)

Introduces advanced techniques in chemical synthesis and characterization applicable to organic, inorganic, and organometallic compounds. Techniques used include working under inert atmosphere, working with liquefied gases, and handling moisture-sensitive reagents, NMR, IR, and UV-vis spectroscopy.

Prerequisite(s): CHEM 2317 with a minimum grade of C-

Corequisite(s): CHEM 3532

CHEM 3532. Chemical Synthesis Characterization Lab. (4 Hours)

Acompanies CHEM 3531. Covers topics from the course through various experiments.

Prerequisite(s): (CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C-)

Corequisite(s): CHEM 3531

CHEM 3990. Elective. (1-4 Hours)

Offers elective credit for courses taken at other academic institutions. May be repeated without limit.

CHEM 4456. Organic Chemistry 3: Organic Chemistry of Drug Design and Development. (4 Hours)

Offers students majoring in chemistry an opportunity to apply the principles gained in two semesters of organic chemistry and chemical biology to a relevant disciplinary context. The discovery, design, and development of biologically active compounds for medical purposes uses knowledge and techniques gained in both organic synthesis and chemical biology. It directs those skills to incorporate specific chemical features into organic compounds to meet biological criteria. As such, it seeks to develop problem-solving skills that are valuable across a range of chemical disciplines and not confined to synthetic organic chemistry alone.

Prerequisite(s): CHEM 2317 with a minimum grade of C-

Corequisite(s): CHEM 4457

CHEM 4457. Lab for CHEM 4456. (2 Hours)

Accompanies CHEM 4456. Includes literature research activities, field trips, case studies, and presentations. Offers students an opportunity to prepare for a wider range of career options.

Corequisite(s): CHEM 4456

CHEM 4460. Enzymes: Chemistry and Chemical Biology. (4 Hours)

Focuses on enzymes: their chemistry, mechanisms, and applications. Examines the underlying chemical and mechanistic principles. Introduces the techniques and approaches in enzymology. Bridges the gap between classroom learning and real-world practice in the related fields, e.g., medicinal chemistry, chemical biology, engineering, and pharmaceutical research.

Prerequisite(s): CHEM 2313 with a minimum grade of C-

CHEM 4620. Introduction to Protein Chemistry. (4 Hours)

Introduces protein chemistry in the context of molecular medicine. Discusses analytical methods used to elucidate the origin, structure, function, and purification of proteins. Surveys the synthesis and chemical properties of structurally and functionally diverse proteins, including globular, membrane, and fibrous proteins. Discusses the role of intra- and intermolecular interactions in determining protein conformation, protein folding, and in their enzymatic activity. Intended for undergraduate students without prior experience in protein chemistry.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-

CHEM 4621. Introduction to Chemical Biology. (4 Hours)

Probes the structure and function of biological macromolecules and the chemical reactions carried out in living systems, including biological energetics. Discusses techniques to measure macromolecular interactions and the principles and forces governing such interactions. Offers students an opportunity to gain experience in reading and evaluating primary literature. Intended for undergraduate students with no prior knowledge of the field.

Prerequisite(s): (CHEM 2317 with a minimum grade of C- or CHEM 2313 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-) (CHEM 3401 (may be taken concurrently) with a minimum grade of C- or CHEM 3421 (may be taken concurrently) with a minimum grade of C- or CHEM 3431 (may be taken concurrently) with a minimum grade of C-)

Corequisite(s): CHEM 4622

CHEM 4622. Lab for CHEM 4621. (1 Hour)

Accompanies CHEM 4621. Complements and reinforces the concepts from CHEM 4621 with an emphasis on fundamental techniques. Offers students an opportunity to complete independent projects in modern chemical biology research.

Prerequisite(s): ENGW 1111 with a minimum grade of C or ENGW 1102 with a minimum grade of C or ENGL 1111 with a minimum grade of C or ENGL 1102 with a minimum grade of C

Corequisite(s): CHEM 4621

CHEM 4628. Introduction to Spectroscopy of Organic Compounds. (4 Hours)

Examines the application of modern spectroscopic techniques to the structural elucidation of small organic molecules. Emphasizes the use of H and C NMR spectroscopy supplemented with information from infrared spectroscopy and mass spectrometry. Explores both the practical and nonmathematical theoretical aspects of 1D and 2D NMR experiments. Topics include the chemical shift, coupling constants, the nuclear Overhauser effect and relaxation, and 2D homonuclear and heteronuclear correlation. Designed for chemists who do not have an extensive math or physics background no prior knowledge of NMR spectroscopy is assumed.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-

Corequisite(s): CHEM 4629

CHEM 4629. Identification of Organic Compounds. (2 Hours)

Introduces the use of the nuclear magnetic resonance (NMR) spectrometer and basic NMR experiments. Determines the identity of unknown organic compounds by the use of mass spectrometry, infrared spectroscopy, and 1D and 2D nuclear magnetic resonance spectroscopy.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-

Corequisite(s): CHEM 4628

CHEM 4750. Senior Research. (4 Hours)

Conducts original experimental work under the direction of members of the department on a project. Introduces experimental design based on literature and a variety of techniques depending upon the individual project.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-

Attribute(s): NUpath Capstone Experience, NUpath Writing Intensive

CHEM 4901. Undergraduate Research. (4 Hours)

Conducts original research under the direction of members of the department. May be repeated without limit.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C- or CHEM 2321 with a minimum grade of C-

Attribute(s): NUpath Integration Experience

CHEM 4970. Junior/Senior Honors Project 1. (4 Hours)

Focuses on in-depth project in which a student conducts research or produces a product related to the student’s major field. Combined with Junior/Senior Project 2 or college-defined equivalent for 8 credit honors project. May be repeated without limit.

Attribute(s): NUpath Capstone Experience

CHEM 4971. Junior/Senior Honors Project 2. (4 Hours)

Focuses on second semester of in-depth project in which a student conducts research or produces a product related to the student’s major field. May be repeated without limit.

Prerequisite(s): CHEM 4970 with a minimum grade of C

Attribute(s): NUpath Capstone Experience, NUpath Writing Intensive

CHEM 4990. Elective. (1-4 Hours)

Offers elective credit for courses taken at other academic institutions. May be repeated without limit.

CHEM 4991. Research. (4 Hours)

Offers an opportunity to conduct research under faculty supervision. May be repeated without limit.

Attribute(s): NUpath Integration Experience

CHEM 4992. Directed Study. (1-4 Hours)

Offers independent work under the direction of members of the department on a chosen topic. Course content depends on instructor. May be repeated without limit.

CHEM 4993. Independent Study. (1-4 Hours)

Offers independent work under the direction of members of the department on a chosen topic. Course content depends on instructor. May be repeated without limit.

CHEM 4994. Internship. (4 Hours)

Offers students an opportunity for internship work. May be repeated without limit.

Attribute(s): NUpath Integration Experience

CHEM 5179. Complex Fluids and Everyday Materials. (4 Hours)

Introduces intra- and intermolecular forces and moves on to material deformation in response to external stress, including polymeric elasticity. Covers topics in colloidal science and biological physics: the microscopic origins of suspension stability and biological self-assembly. Additional topics include “molecular gastronomy,” personal care and cleaning products, active materials, and experimental techniques. Studies of complex fluids and soft materials are highly interdisciplinary. Many everyday materials are combinations of the three phases of matter—solid, liquid, and gas—with unique material properties. “Complex fluids” and “soft matter” refer to suspensions, emulsions, foams, and gels, which include personal care items, household cleaners, and even food. Nearly all biological material can be described as a soft material.

CHEM 5460. Enzymes: Chemistry and Chemical Biology. (3 Hours)

Focuses on enzymes: their chemistry, mechanisms, and applications. Examines the underlying chemical and mechanistic principles. Introduces the techniques and approaches in enzymology. Bridges the gap between classroom learning and real-world practice in the related fields, e.g., medicinal chemistry, chemical biology, engineering, and pharmaceutical research.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C- or graduate program admission

CHEM 5501. Chemical Safety in the Research Laboratory. (1 Hour)

Covers the material needed to complete successfully all the online safety training that is required for our graduate students, best practices for the safe execution of common chemical laboratory procedures, advanced procedures, as well as incidents from the recent literature. Includes discussions of case studies on topics relevant for the safe and effective use of chemicals and other materials in a research laboratory environment. Undergraduates may enroll with permission of the instructor.

CHEM 5550. Introduction to Glycobiology and Glycoprotein Analysis. (3 Hours)

Covers the background and methods used for glycoprotein characterization. Offers students an opportunity to obtain the background needed to assess the analytical steps necessary for development of glycoprotein drugs. Analyzes regulatory issues behind glycoprotein drug development. Covers recent developments in analytical and regulatory sciences.

CHEM 5599. Introduction to Research Skills and Ethics in Chemistry. (0 Hours)

Seeks to prepare students for success in CHEM 5600 and in CHEM 7730. May be repeated once. Must be taken in consecutive semesters before registration into CHEM 5600 and CHEM 7730.

CHEM 5600. Research Skills and Ethics in Chemistry. (3 Hours)

Discusses ethics in science. Topics include documentation of work in your laboratory notebook, safety in a chemistry research laboratory, principles of experimental design, online computer searching to access chemical literature, reading and writing technical journal articles, preparation and delivery of an effective oral presentation, and preparation of a competitive research proposal.

Prerequisite(s): CHEM 5599 with a minimum grade of S

CHEM 5610. Polymer Chemistry. (3 Hours)

Discusses the synthesis and analysis of polymer materials. Covers mechanisms and kinetics of condensation/chain-growth polymerization reactions and strategies leading to well-defined polymer architectures and compositions, including living polymerizations (free radical, cationic, anionic), catalytic approaches, and postpolymerization functionalization. Discusses correlation of chemical composition and structure to physical properties and applications.

Prerequisite(s): ((CHEM 2317 with a minimum grade of C- or CHEM 2313 with a minimum grade of C-) (CHEM 3401 (may be taken concurrently) with a minimum grade of C- or CHEM 3421 (may be taken concurrently) with a minimum grade of C- or CHEM 3431 (may be taken concurrently) with a minimum grade of C-)) or graduate program admission

CHEM 5611. Analytical Separations. (3 Hours)

Describes the theory and practice of separating the components of complex mixtures in the gas and liquid phase. Also includes methods to enhance separation efficiency and detection sensitivity. Covers thin-layer, gas, and high-performance liquid chromatography (HPLC) and recently developed techniques based on HPLC including capillary and membrane-based separation, and capillary electrophoresis.

CHEM 5612. Principles of Mass Spectrometry. (3 Hours)

Describes the theory and practice of ion separation in electrostatic and magnetic fields and their subsequent detection. Topics include basic principles of ion trajectories in electrostatic and magnetic fields, design and operation of inlet systems and electron impact ionization, and mass spectra of organic compounds.

CHEM 5613. Optical Methods of Analysis. (3 Hours)

Describes the application of optical spectroscopy to qualitative and quantitative analysis. Includes the principles and application of emission, absorption, scattering and fluorescence spectroscopies, spectrometer design, elementary optics, and modern detection technologies.

CHEM 5614. Electroanalytical Chemistry. (3 Hours)

Describes the theory of electrode processes and modern electroanalytical experiments. Topics include the nature of the electrode-solution interface (double layer models), mass transfer (diffusion, migration, and convection), types of electrodes, reference electrodes, junction potentials, kinetics of electrode reactions, controlled potential methods (cyclic voltammetry, chronoamperometry), chronocoulometry and square wave voltammetry, and controlled current methods (chronopotentiometry).

CHEM 5616. Protein Mass Spectrometry. (3 Hours)

Offers students an opportunity to obtain a fundamental understanding of modern mass spectrometers, the ability to operate these instruments, and the ability to prepare biological samples. Undoubtedly the most popular analytical method in science, mass spectrometry is utilized in fields ranging from subatomic physics to biology. Focuses on the analysis of proteins, with applications including biomarker discovery, tissue characterization, detection of blood doping, drug discovery, and the characterization of protein-based therapeutics. By the end of the course, the student is expected to be able to solve a particular chemistry- or biology-related problem by choosing the appropriate sample preparation methods and mass spectrometer.

CHEM 5617. Protein Mass Spectrometry Laboratory. (3 Hours)

Offers students an opportunity to develop an appreciation of the appropriate choice of mass spectrometer for a particular application.

CHEM 5618. Advanced Mass Spectrometry. (3 Hours)

Applies earlier study of mass spectrometry (the principles of modern mass spectrometry hardware and spectral interpretation) to experimental design and data analysis of drugs, proteins, and proteomes. Examines how to choose the appropriate mass spectrometry method for a given biological problem find and acquire an exemplar data set and interpret the data as well as expert practitioners do. As one of the most popular analytical methods in science, mass spectrometry is utilized in fields ranging from subatomic physics to biology. Applications have an overarching theme of human health and include biomarker discovery and validation, tissue analysis (including alternatives to histopathology), and drug development.

Prerequisite(s): CHEM 5612 with a minimum grade of C

CHEM 5620. Protein Chemistry. (3 Hours)

Describes proteins (what they are, where they come from, and how they work) in the context of analytical analysis and molecular medicine. Discusses the chemical properties of proteins, protein synthesis, and the genetic origins of globular proteins in solution, membrane proteins, and fibrous proteins. Covers the physical intra- and intermolecular interactions that proteins undergo along with descriptions of protein conformation and methods of structural determination. Explores protein folding as well as protein degradation and enzymatic activity. Highlights protein purification and biophysical characterization in relation to protein analysis, drug design, and optimization.

CHEM 5621. Principles of Chemical Biology for Chemists. (3 Hours)

Explores the use of natural and unnatural small-molecule chemical tools to probe macromolecules, including affinity labeling and click chemistry. Covers nucleic acid sequencing technologies and solid-phase synthesis of nucleic acids and peptides. Discusses in-vitro selection techniques, aptamers, and quantitative issues in library construction. Uses molecular visualization software tools to investigate structures of macromolecules. Intended for graduate and advanced undergraduate students.

Prerequisite(s): ((CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-) (CHEM 3401 (may be taken concurrently) with a minimum grade of C- or CHEM 3421 (may be taken concurrently) with a minimum grade of C- or CHEM 3431 (may be taken concurrently) with a minimum grade of C-)) or graduate program admission

CHEM 5622. Lab for CHEM 5621. (1 Hour)

Accompanies CHEM 5621. Complements and reinforces the concepts from CHEM 5621 with emphasis on fundamental techniques. Offers an opportunity to complete independent projects in modern chemical biology research.

Prerequisite(s): ((CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) (CHEM 2321 with a minimum grade of C- or CHEM 2331 with a minimum grade of C- or CHEM 3331 with a minimum grade of C-) (CHEM 3401 (may be taken concurrently) with a minimum grade of C- or CHEM 3421 (may be taken concurrently) with a minimum grade of C- or CHEM 3431 (may be taken concurrently) with a minimum grade of C-) (ENGL 1111 with a minimum grade of C or ENGL 1102 with a minimum grade of C or ENGW 1111 with a minimum grade of C or ENGW 1102 with a minimum grade of C)) or graduate program admission

Attribute(s): NUpath Writing Intensive

CHEM 5625. Chemistry and Design of Protein Pharmaceuticals. (3 Hours)

Covers the chemical transformations and protein engineering approaches to protein pharmaceuticals. Describes protein posttranslational modifications, such as oxidation, glycosylation, formation of isoaspartic acid, and disulfide. Then discusses bioconjugate chemistry, including those involved in antibody-drug conjugate and PEGylation. Finally, explores various protein engineering approaches, such as quality by design (QbD), to optimize the stability, immunogenicity, activity, and production of protein pharmaceuticals. Discusses the underlying chemical principles and enzymatic mechanisms as well.

Prerequisite(s): (CHEM 2317 with a minimum grade of C- or CHEM 2313 with a minimum grade of C- or graduate program admission) (CHEM 5620 (may be taken concurrently) with a minimum grade of C- or CHEM 5621 (may be taken concurrently) with a minimum grade of C-

CHEM 5626. Organic Synthesis 1. (3 Hours)

Surveys types of organic reactions including stereochemistry, influence of structure and medium, mechanistic aspects, and synthetic applications.

CHEM 5627. Mechanistic and Physical Organic Chemistry. (3 Hours)

Surveys tools used for elucidating mechanisms including thermodynamics, kinetics, solvent and isotope effects, and structure/reactivity relationships. Topics include molecular orbital theory, aromaticity, and orbital symmetry. Studies reactive intermediates including carbenes, carbonium ions, radicals, biradicals and carbanions, acidity, and photochemistry.

CHEM 5628. Principles of Spectroscopy of Organic Compounds. (3 Hours)

Studies how to determine organic structure based on proton and carbon nuclear magnetic resonance spectra, with additional information from mass and infrared spectra and elemental analysis. Presents descriptive theory of nuclear magnetic resonance experiments and applications of advanced techniques to structure determination. Includes relaxation, nuclear Overhauser effect, polarization transfer, and correlation in various one- and two- dimensional experiments. Requires graduate students to have one year of organic chemistry or equivalent.

Prerequisite(s): CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C- or graduate program admission

CHEM 5629. Advanced Physical Organic Chemistry. (3 Hours)

Studies the importance of molecular orbital theory in stereoelectronic effects, thermal, and photochemical pericyclic reactions. Offers students an opportunity to obtain the reasoning skills to analyze an organic transformation and apply guiding structural and electronic principles to build intuition on the chemo-, stereo-, and regioselectivity of reactions. Some of these concepts include quantum mechanics, molecular orbital theory, structure and bonding, conformational analysis, hybridization, aromaticity, and hyperconjugation. Students engage in peer-review, literature presentations and collaborative problem solving.

CHEM 5630. Nucleic Acid Chemistry. (3 Hours)

Offers a broadband introduction to the field of nucleic acid chemistry. Nucleic acids are vital for biology, but their roles have been greatly expanded beyond storage of genetic information. The breadth of utility of nucleic acids stems from a precise understanding of their structures, modern means to synthesize and modify them, and the ability for nucleic acids to engage with varieties of enzymes/proteins and other synthetic/biological systems. Foundational topics include nucleic acid structure, physicochemical properties, syntheses of nucleosides/nucleotides/oligonucleotides, chemical modification of nucleic acids, methods to manipulate and analyze nucleic acids (e.g., PCR, sequencing, and electrophoresis). Advanced topics include nucleic acid therapeutics (e.g., siRNA, antisense technology, CRISPR, and aptamers) DNA damage and repair and DNA for materials science (e.g., DNA nanotechnology).

CHEM 5636. Statistical Thermodynamics. (3 Hours)

Briefly reviews classical thermodynamics before undertaking detailed coverage of statistical thermodynamics, including probability theory, the Boltzmann distribution, partition functions, ensembles, and statistically derived thermodynamic functions. Reconsiders the basic concepts of statistical thermodynamics from the modern viewpoint of information theory. Presents practical applications of the theory to problems of contemporary interest, including polymers and biopolymers, nanoscale systems, molecular modeling, and bioinformatics.

Prerequisite(s): CHEM 3401 with a minimum grade of C- or CHEM 3421 with a minimum grade of C- or CHEM 3431 with a minimum grade of C- or graduate program admission

CHEM 5638. Molecular Modeling. (3 Hours)

Introduces molecular modeling methods that are basic tools in the study of macromolecules. Is structured partly as a practical laboratory using a popular molecular modeling suite, and also aims to elucidate the underlying physical principles upon which molecular mechanics is based. These principles are presented in supplemental lectures or in laboratory workshops.

CHEM 5640. Biopolymeric Materials. (3 Hours)

Examines the structure, properties, and processing of biomaterials, the forms of matter that are produced by or interact with biological systems. One of the pillars of biomedical engineering is to use naturally derived and synthetic biomaterials to treat, augment, or replace human tissues.

CHEM 5641. Computational Chemistry. (3 Hours)

Introduces basic concepts, methods, techniques, and recent advances in computational chemistry and their relevance to experimental characterizations such as spectroscopy. Topics include electronic structure theory (wave function theory and density functional theory), principles of molecular dynamics simulations, multiscale modeling, machine learning, and quantum computing relevant to computational chemistry. Builds a theoretical foundation for students to properly choose computational methods to solve common research problems in chemistry, biochemistry, and materials science. Also introduces the field of research in computational chemistry. Suitable for advanced undergraduate students and graduate students who plan to conduct research in the field of computational chemistry or plan to utilize computational techniques to complement experimental research in the molecular sciences.

CHEM 5648. Chemical Principles and Application of Drug Metabolism and Pharmacokinetics. (3 Hours)

Offers students an opportunity to obtain a comprehensive grounding in the chemistry of drug metabolism and pharmacokinetics (DMPK) and its application to drug design and optimization. Multiple rounds of chemical synthesis and testing are usually required to discover new drugs with the appropriate balance of properties such as potency and selectivity, efficacy in preclinical models of disease, safety, and pharmacokinetics. Introduces students to modern tools and concepts utilized to screen for favorable DMPK properties, as well as methods to predict human PK from in vitro and preclinical data. Examines the linkage between drug levels in the body, pharmacodynamic response (PK/PD), and drug-drug interactions in the context of the iterative process of chemical drug synthesis.

CHEM 5651. Materials Chemistry of Renewable Energy. (3 Hours)

Studies renewable energy in terms of photovoltaics, photoelectrochemistry, fuel cells, batteries, and capacitors. Focuses on the aspects of each component and their relationships to one another.

Prerequisite(s): ((CHEM 2313 with a minimum grade of C- or CHEM 2317 with a minimum grade of C-) CHEM 3403 with a minimum grade of C-) or graduate program admission

CHEM 5655. Molecular Symmetry and Group Theory. (3 Hours)

Covers symmetry operations point groups and classification of molecules into point groups as well as matrix representation of symmetry operations, orthogonality theorem, and its use in determining irreducible representation spanned by a basis. Studies decomposition of reducible representation and direct products, characters and character tables, and reviews quantum mechanics. Also covers infrared and Raman spectroscopy, normal modes of vibrations, determining symmetry of vibrations, the role of symmetry in selection rules, LCAO MO theory, Hückel method, electronic spectroscopy, and vibronic spectroscopy and symmetry.

CHEM 5660. Analytical Biochemistry. (3 Hours)

Covers the analysis of biological molecules, which include nucleic acids, proteins, carbohydrates, lipids, and metabolites. Discusses isolation, characterization, and quantification of these molecules.

CHEM 5672. Organic Synthesis 2. (3 Hours)

Continues CHEM 5626. Surveys types of organic reactions including stereochemistry, influence of structure and medium, mechanistic aspects, and synthetic applications.

Prerequisite(s): CHEM 5626 with a minimum grade of C-

CHEM 5676. Bioorganic Chemistry. (3 Hours)

Covers host guest complexation by crown ethers, cryptands, podands, spherands, and so forth molecular recognition including self-replication peptide and protein structure coenzymes and metals in bioorganic chemistry nucleic acid structure interaction of DNA with proteins and small molecules including DNA-targeted drug design catalytic RNA and catalytic antibodies.

Prerequisite(s): (CHEM 5626 with a minimum grade of C- CHEM 5627 with a minimum grade of C-) or graduate program admission

CHEM 5688. Principles of Nuclear Magnetic Resonance. (3 Hours)

Presents the physical principles underlying magnetic resonance spectroscopy, including Fourier transform theory, classical and quantum-mechanical treatments of spin angular momentum, the Bloch equations, and spin relaxation. Covers fundamental concepts in time domain magnetic resonance methods, including pulse sequences, selective pulses, phase cycling, coherence pathways, field gradients, and nonuniform sampling. Surveys the NMR methods most commonly applied to chemical structural analysis, including pure shift NMR 2D correlation (COSY, DQF-COSY, TOCSY, HSQC, HMBC) methods and cross-relaxation (NOESY, ROESY) methods.

CHEM 5700. Topics in Organic Chemistry. (3 Hours)

Offers various topics within the breadth of organic chemistry. Intended to meet the needs and interests of students. Topics could range from the physical and material aspects of organic chemistry to the biochemical and biomedical aspects of organic chemistry. Undergraduate students who have completed a second semester of organic chemistry with a grade of at least C– may be admitted with permission of instructor. May be repeated once.

CHEM 5904. Seminar. (1 Hour)

Focuses on oral reports by master of science and PlusOne participants on current research topics in chemistry and chemical biology. May be repeated up to two times.

CHEM 5976. Directed Study. (1-4 Hours)

Offers independent work under the direction of members of the department on a chosen topic. Course content depends on instructor. May be repeated without limit.

CHEM 5984. Research. (1-6 Hours)

Offers an opportunity to conduct research under faculty supervision. May be repeated up to three times for up to 6 total credits.


2: Basic Cell Chemistry - Chemical Compounds and their Interactions - Biology

Chemical bonds are formed when the electrons in an atom interact with the electrons in another atom. This allows for the formation of more complex molecules.

There are 3 types of chemical bonds:

Bond Strength Description Example
Covalent Strong Two atoms share electrons. Bonding of Oxygen and Hydrogen in H2O
Ionic Moderate Oppositely charged ions are attracted to each other. Bond between Na+ and Cl- in salt.
Hydrogen Weak Forms between oppositely charges portions of covalently bonded hydrogen atoms. Bonds between water molecules.

Covalent

These strong bonds form when two atoms share electrons .

Sometimes the electrons in an atom get shared. It's much like when you were a kid and got to sleep over at a friends house. Your friends parents were in charge of you both for one night and the next night you would sleep over at your house and your own parents would be in charge. This sharing of responsibility is functionally similar to the way covalent bonding works.

Normally this sharing is an equal proposition. Sometimes it's not equal (but that gets us into hydrogen bonding discussed below.)

Ionic

Atoms gain or lose electron (opposites attract)

Ions have positive or negative charges. In dating situations, you may know that sometimes opposites attract. In Chemistry, opposites ALWAYS attract . This forms an ionic bond between two atoms.

Hydrogen

Weakest bond between atoms

Occurs in molecules that have covalent bonds . Sometimes the electrons are not equally shared one atom tends to have an electron more often than the other atom. In this situation one atom of the molecule becomes partly negative and the other then becomes partly positive.

Now we have positive and negative things becoming attracted to each other. (remember ionic bonds?) This is especially common between water molecules .


2: Basic Cell Chemistry - Chemical Compounds and their Interactions - Biology

Differential Scanning Calorimetry to Study Lipids and Lipid Membranes

Ruthven N.A.H. Lewis, David A. Mannock, and Ronald N. McElhaney, University of Alberta, Edmonton, Alberta, Canada

Differential scanning calorimetry (DSC) is a relatively rapid direct and nonperturbing thermodynamic technique for studying the thermotropic phase behavior of hydrated lipid dispersions and of reconstituted lipid model and biological membranes. DSC can accurately and reliably determine the temperature, enthalpy, entropy and cooperativity of a wide variety of lipid phase transitions and how these parameters are influenced by variations in hydration, and in the pH and the ionic strength and composition of the aqueous phase. Also, the effects of the presence of membrane-associated sterols, peptides and proteins, as well as toxins, drugs, and other agents, on the thermotropic phase behavior of lipid membranes can be determined. Under appropriate conditions, DSC can also characterize the kinetics of some lipid phase transitions. The thermodynamic data provided by DSC, therefore, can provide valuable information about the phase state and organization of lipid assemblies and about how the structure and physical properties of lipid model and biological membranes are modulated by other membrane constituents and by the environment. However, because DSC is a thermodynamic and not a structural technique, it is most valuable when applied in conjunction with a direct structural technique, such as X-ray diffraction, and with nonperturbing spectroscopic methods, such as nuclear magnetic resonance and Fourier transform infrared spectroscopy.

Biological Background

The central structural feature of almost all biological membranes is a continuous and fluid lipid bilayer that serves as the major permeability barrier of the cell or intracellular compartment (1) and as a scaffold for the attachment and organization of other membrane constituents (2, 3). In particular, peripheral membrane proteins are bound to the surface of lipid bilayers primarily by electrostatic and hydrogen-bonding interactions, whereas integral membrane proteins penetrate into, and usually span, the lipid bilayer, and are stabilized by hydrophobic and van der Waal’s interactions with the lipid hydrocarbon chains in the interior of the lipid bilayer as well as by polar interactions with the glycerol backbone and polar headgroup regions of the host lipid bilayer. In addition to playing a structural role in determining the topology and stabilizing the active conformation of peripheral and integral membrane proteins, the physical properties of the lipid also markedly influence the activity and thus presumably the conformation and dynamics of many membrane proteins (4-8, but see 9). Specifically, the physical state (lamellar gel versus liquid-crystalline), fluidity, hydrophobic thickness, lipid lamellar/nonlamellar phase propensity (lipid shape), surface charge and surface-charge density, as well as various mechanical properties of the lipid bilayer (10), all modulate the thermal stability and activity of many membrane-associated enzymes, transporters and receptors. Therefore, understanding the thermotropic phase behavior and organization and thus the specific functions of the large number of lipid classes and molecular species that comprise biological membranes, remains a major challenge in membrane biology generally. In this brief review, we consider the applications of DSC to lipid model and biological membranes to address in particular the role of lipid fluidity and phase state and to some degree the role of lipid lamellar/nonlamellar phase propensity in membrane structure and function.

Lipid Mesomorphic Phase Behavior

Membrane lipids are invariably polymorphic that is, they can exist in a variety of kinds of organized structures, especially when hydrated. The particular polymorphic form that predominates depends not only on the structure of the lipid molecule itself and on its degree of hydration, but also on such variables as temperature, pressure, ionic strength and pH (see References 11 and 12 and article Lipids, Phase Transitions of). However, under physiologically relevant conditions, most (but not all) membrane lipids exist in the lamellar or bilayer phase, usually in the lamellar liquid-crystalline phase but sometimes in the lamellar gel phase. It is not surprising, therefore, that the lamellar gel-to-liquid-crystalline or chain-melting phase transition has been the most intensively studied lipid phase transition and is also the most biologically relevant. This cooperative phase transition involves the conversion of a relatively ordered gel-state bilayer, in which the hydrocarbon chains exist predominantly in their rigid, extended, all-trans conformation, to a relatively disordered liquid-crystalline bilayer, in which the hydrocarbon chains contain several gauche conformers and exhibit greatly increased rates of intra- and intermolecular motions. The gel-to-liquid-crystalline phase transition is accompanied by a pronounced lateral expansion and a concomitant decrease in the thickness of the bilayer, as well as by a small increase in the total volume occupied by the lipid molecules. Evidence also shows that the number of water molecules bound to the surfaces of the lipid bilayer increases during hydrocarbon chain melting. Thermodynamically, the gel-to-liquid-crystalline phase transition occurs when the entropic reduction in free energy that results from hydrocarbon chain isomerism counterbalances the decrease in bilayer cohesive energy that results from the lateral expansion and from the energy cost of creating gauche rotational conformers in the hydrocarbon chains.

Gel-to-liquid-crystalline phase transitions can be induced by changes in temperature and hydration, as well as by changes in pressure and in the ionic strength or pH of the aqueous phase. In this article, we will concentrate on thermally induced phase transitions because these have been studied most extensively and are of direct biological relevance, particularly for organisms that cannot regulate their own temperature. However, hydration-induced (lyotropic) and pressure-induced (barotropic) phase transitions also occur, and these may also be biologically relevant under special environmental circumstances. Finally, phase transitions induced by alterations in pH and in the nature and quantity of ions in the aqueous phase that surrounds the bilayer are also possible, and these transitions may also be of importance in living cells. However, a detailed discussion of these types of lipid phase transitions is beyond the limited scope of the current article, and interested readers should consult appropriate reviews for detailed information on this topic (11, 12).

Pure synthetic lipids often exhibit gel-state polymorphism, and phase transitions between various forms of the gel-state bilayer can occur. Although we will illustrate this behavior for a common phospholipid, dipalmitoylphosphatidylcholine (DPPC), gel-state transitions will not be emphasized here because with only one known exception (13), they do not seem to occur in the heterogeneous collection of lipid molecular species found in biological membranes. Moreover, certain synthetic or naturally occurring lipid species can exist in liquid-crystalline nonlamellar phases, especially three-dimensional reversed cubic and hexagonal phases. Although the actual existence of nonbilayer lipid phases in biological membranes has never been demonstrated under physiological conditions, the propensity to form such phases likely plays major roles in membrane fusion and other processes (see Reference 14). Moreover, evidence suggests that the relative proportion of bilayer-preferring and nonbilayer-preferring lipids may be biosynthetically regulated in response to variations in temperature and membrane lipid fatty acid composition and cholesterol content in some organisms. Thus, lipid species that in isolation may form nonlamellar phases may have important roles to play in the liquid-crystalline bilayers found in essentially all biological membranes. The transitions between lamellar and nonlamellar lipid phases have been reviewed in detail by us and others elsewhere (see References 14 and 15).

Differential Scanning Calorimetry

As mentioned earlier, the technique of DSC has been of primary importance in studies of lipid phase transitions in model and biological membranes (see References 16-18). The principle of DSC is comparatively simple. A sample and an inert reference (i.e., a material of comparable thermal mass that does not undergo a phase transition within the temperature range of interest) are simultaneously heated or cooled at a predetermined constant rate (dT/dt) in an instrument configured to measure the differential rate of heat flow (dE/dt) into the sample relative to that of the inert reference. The temperatures of the sample and reference may either be actively varied by independently controlled units (power compensation calorimetry) or be passively changed through contact with a common heat sink that has a thermal mass that greatly exceeds the combined thermal masses of the sample and reference (heat conduction calorimetry). For our purposes, the sample would normally be a suspension of lipid or membrane in water or an aqueous buffer, and the reference cell would contain the corresponding solvent alone. At temperatures distant from any thermotropic events, the temperatures of the sample and reference cells change linearly with time, and the temperature difference between them remains zero. The instrument thus records a constant difference between the rates of heat flow into the sample and reference cells, which, ideally, is reflected by a straight, horizontal baseline. When the sample undergoes a thermotropic phase transition, a temperature differential between the sample and reference occurs, and the instrument either actively changes the power input to the sample cell to negate the temperature differential (power compensation calorimetry) or passively records the resulting changes in the rate of heat flow into the sample cell until the temperature differential eventually dissipates (heat conduction calorimetry). In both instances, a change develops in the differential rates of heat flow into the sample and reference cells, and either an exothermic or endothermic deviation from the baseline condition occurs. On completion of the thermal event, the instrument either re-establishes its original baseline condition or establishes a new one if a change in the specific heat of the sample has occurred. The output of the instrument is thus a plot of differential heat flow (dE/dt) as a function of temperature in which the intensity of the signal is directly proportional to the scanning rate (dT/dt).

The variation of excess specific heat (dE/dt) with temperature for a simple two-state, first-order endothermic process, such as the gel-to-liquid-crystalline phase transition of a single, highly pure phosphatidylcholine (PC), is illustrated schematically in Fig. 1. From such a DSC trace, several important parameters can be determined directly. The phase transition temperature, usually denoted Tm, is that temperature at which the excess specific heat reaches a maximum. For a symmetrical curve, Tm represents the temperature at which the transition from the gel-to-liquid-crystalline state is one-half complete. However, for asymmetric traces, which are characteristic of certain pure phospholipids and many biological membranes, the Tm does not represent the midpoint of the phase transition, and a T1/2 value may be reported instead. Once normalized with respect to the scan rate, the peak area under the DSC trace is a direct measurement of the calorimetrically determined enthalpy of the transition, ∆Hcal, usually expressed in kcal/mol. The area of the peak can be determined by planimetry or by the cutting and weighing technique alternatively, the calorimeter output can be digitized, and the Tm and ∆Hcal can be calculated by a computer. Because at the phase transition midpoint temperature the change in free energy (∆G) of the system is zero, the entropy change associated with the transition can be calculated directly from the equation:

where ∆S is normally expressed in cal/K -1 mol -1 .

Figure 1. The variation of excess specific heat with temperature during a two-state, endothermic lipid phase transition. The symbols are explained in the text.

The sharpness or cooperativity of the gel-to-liquid-crystalline phase transition can also be evaluated from the DSC trace. The sharpness of the phase transition is often expressed as the temperature width at half-height, ∆T1/2, or as the temperature difference between the onset or lower boundary of the phase transition, Ts, and the completion or upper boundary, Tl, or ∆T = Tl — Ts. The ∆T1/2values may range from + -trans-gauche - ) sequences. As the melting of the hydrocarbon chains produces a marked increase in cross-section area and effectively shortens the length of the chains, the bilayer expands laterally and thins at the main phase transition. Although the hydrocarbon chains exhibit rapid flexing and rotation in the Lα phase, they are on average oriented normally to the bilayer plane and pack in a loose hexagonal lattice. This increase in the cross-section area per molecule results in an increase in the area available to the polar headgroup, with the result that rotational motion becomes fast on the NMR timescale, and the hydration at the bilayer interface increases, in part because of the partial exposure of more deeply located polar residues, such as the carbonyl oxygens of the fatty acyl chains, to the aqueous phase.

The pattern of thermotropic phase behavior exhibited by an aqueous dispersion of any lipid molecular species will vary considerably, depending on the length and structure of the hydrocarbon chains, the structure and charge of the polar headgroup, the nature of the link (ester or ether) of the hydrocarbon chains to the glycerol or sphingosine backbone, and other chemical features of the lipid under study. Also, the degree of hydration and the pH and ionic composition of the aqueous phase can affect lipid thermotropic phase behavior profoundly. However, even a cursory discussion of this topic is beyond the scope of this article, and the reader is referred to recent reviews for more detailed information (16-18).

Phospholipid mixtures

Although studies of the thermotropic phase behavior of singlecomponent multilamellar phospholipid vesicles are necessary and valuable, these systems are not realistic models for biological membranes that normally contain at least several different types of phospholipids and a variety of fatty acyl chains. As a first step toward understanding the interactions of both the polar and apolar portions of different lipids in mixtures, DSC studies of various binary and ternary phospholipid systems have been carried out. Phase diagrams can be constructed by specifying the onset and completion temperatures for the phase transition of a series of mixtures and by an inspection of the shapes of the calorimetric traces. A comparison of the observed transition curves with the theoretical curves supports a literal interpretation of the phase diagrams obtained by DSC. For a summary of the first high-sensitivity DSC studies of binary phospholipid-phospholipid and phospholipid-cholesterol mixtures and a description of how phase diagrams can be constructed from DSC data, the reader is referred to an early review by Mabrey and Sturtevant (21) for a compilation of the results of later DSC and other studies on other phospholipid mixtures, the reader is referred to Marsh (22).

The effect of cholesterol

The occurrence of cholesterol and related sterols in the membranes of eukaryotic cells has prompted many investigations of the effect of cholesterol on the thermotropic phase behavior of phospholipids (see References 23-25). Studies using calorimetric and other physical techniques have established that cholesterol can have profound effects on the physical properties of phospholipid bilayers and plays an important role in controlling the fluidity of biological membranes. Cholesterol induces an “intermediate state” in phospholipid molecules with which it interacts and, thus, increases the fluidity of the hydrocarbon chains below and decreases the fluidity above the gel-to-liquid-crystalline phase transition temperature. The reader should consult some recent reviews for a more detailed treatment of cholesterol incorporation on the structure and organization of lipid bilayers (23-25).

Recent high-sensitivity DSC studies of cholesterol/PC interactions have revealed a complex picture of cholesterol/DPPC interactions (26). At cholesterol concentrations from 0 to 20-25 mol %, the DSC endotherm consists of two components (see Fig. 3). The sharp component exhibits a phase transition temperature and cooperativity only slightly reduced from those of the pure phospholipid, and the enthalpy of this component decreases linearly with increasing cholesterol content, becoming zero at 20-25 mol %. In contrast, the broad component exhibits a progressively increasing phase transition temperature and enthalpy with a progressively decreasing cooperativity over this same range of cholesterol content. Above cholesterol levels of 20-25 mol %, the broad component becomes progressively less cooperative, the phase transition midpoint temperature continues to increase, and the transition enthalpy continues to decrease, eventually approaching zero only at cholesterol concentrations near 50 mol %. These results suggest that at low cholesterol concentrations, cholesterol-poor and cholesterol-rich domains coexist, with the former decreasing in proportion to the latter as cholesterol concentrations increase. In fact, a cardinal point in the cholesterol/DPPC phase diagram at about 22 mol % had been predicted from the earlier model-building studies, which calculated that the cholesterol molecule could interact with a maximum of 7 adjacent phospholipid hydrocarbon chains (or 3.5 phospholipid molecules) and thus that free phospholipid would exist only at cholesterol concentrations below this value. This model also explains the decreasing enthalpy of the broad component observed above 22 mol % cholesterol because an increasing proportion of phospholipid molecules would interact with more than one cholesterol molecule rather than with the more flexible hydrocarbon chains of adjacent phospholipids and, thus, progressively decrease and eventually abolish the cooperative chain-melting phase transition.

Figure 3. Typical high-sensitivity DSC heating thermograms of multilamellar, aqueous suspensions of DPPC containing various amounts of incorporated cholesterol. The amount of cholesterol present (in mole %) is indicated near each thermogram.

McMullen and coworkers (26) have studied the effects of cholesterol on the thermotropic phase behavior of aqueous dispersions of a homologous series of linear saturated PCs, using high-sensitivity DSC and an experimental protocol that ensures that the broad, low-enthalpy phase transitions at high cholesterol concentrations are accurately monitored. They found that the incorporation of small amounts of cholesterol progressively decreases the temperature and the enthalpy, but not the cooperativity, of the pretransition of all PCs exhibiting such a pretransition and that the pretransition is completely abolished at cholesterol concentrations above 5 mol % in all cases. Moreover, the incorporation of increasing quantities of cholesterol was found to alter the main or chain-melting phase transition of these phospholipid bilayers in both hydrocarbon chain length-dependent and hydrocarbon chain length-independent ways. The temperature and cooperativity of the sharp component are reduced only slightly and in a chain length-independent manner with increasing cholesterol concentration, an observation ascribed to the colligative effect of the presence of small quantities of cholesterol at the domain boundaries. Moreover, the enthalpy of the sharp component decreases and becomes zero at 20-25 mol % cholesterol for all PCs examined. In contrast, the broad component exhibits a chain length-dependent shift in temperature and a chain length-dependent decrease in cooperativity but a chain length-independent relative increase in enthalpy over the same range of cholesterol concentrations. Specifically, cholesterol incorporation progressively increases the phase transition temperature of the broad component in PCs that have hydrocarbon chains of 16 or fewer carbon atoms and decreases the broad-component phase transition temperature in PCs that have hydrocarbon chains of 18 or more carbon atoms, an effect attributed to hydrophobic mismatch between the cholesterol molecule and its host PC bilayer. The best match between the effective length of the cholesterol molecule and the mean hydrophobic thickness of the PC bilayers is obtained with the diheptadecanoyl PC molecule. Moreover, cholesterol decreases the cooperativity of the broad component more rapidly and to a greater extent in the shorter-chain as compared with the longer chain PCs. At cholesterol concentrations above 20-25 mol %, the sharp component is abolished, and the broad component continues to manifest the chain length-dependent effects on the temperature and cooperativity described above. However, the enthalpy of the broad component decreases linearly and reaches zero at about 50 mol % cholesterol, regardless of the chain length of the phosphatidylcholine.

The effect of cholesterol on the thermotropic phase behavior of PC bilayer also varies significantly with the structure, particularly the degree of unsaturation, of the hydrocarbon chains, with more highly unsaturated PCs exhibiting a reduced miscibility with cholesterol and other sterols. Moreover, the structure of the lipid polar headgroup is also important in determining the effect of cholesterol on the host lipid, as is the structure of the sterol molecule itself. For more information on the application of DSC to the biologically important area of lipid-sterol interactions, the reader is referred to recent reviews (23-25).

The effect of small molecules

Several lipid-soluble small molecules, including drugs like tranquilizers, antidepressants, narcotics, and anaesthetics, produce biological effects in living cells. Although some of these compounds are known to produce their characteristic effects by interacting with specific membrane proteins, others seem to interact rather nonspecifically with the lipid bilayer of many biological membranes. The effect on the gel-to-liquid-crystalline phase transition profile of synthetic PCs of over 100 hydrophobic small molecules that produce biological effects have now been studied by DSC (27). At least four different types of modified transition profiles can be distinguished: In so-called type C profiles, the addition of the additive shifts Tm usually (but not always) to a lower temperature while having little or no effect on the cooperativity (∆T1/2) or ∆Hcal of the transition other physical evidence suggests that additives that produce this behavior are usually localized in the central region of the bilayer, which interacts primarily with the C9-C16 methylene region of the phospholipid hydrocarbon chains. Type A profiles are characterized by a shift in Tm usually to a lower temperature, an increase in ∆T1/2, and a relatively unaffected ∆Hcal during the addition of the appropriate small molecules these additives seem to be partially buried in the hydrocarbon core of the bilayer, which interacts primarily with the C2-C8 methylene region of the hydrocarbon chains. In type B profiles, a shoulder emerges on the main transition, the area of which increases in conjunction with a corresponding decrease in the area of the original peak as the concentration of additive increases. The total area of both peaks is relatively unchanged, at least at low additive concentration. Additives that produce type B profiles generally reside at the hydrophobic-hydrophilic interface of the bilayer and interact primarily with the glycerol backbone of the phospholipid molecules. Finally, type D profiles exhibit a discrete a new peak that grows in area at the expense of the parent peak as the additive concentration increases normally, however, the final ∆Hcal and ∆T1/2 values of the new and original peaks are not greatly different. Type D additives usually seem to be located at the bilayer surface and interact with the phosphorylcholine headgroup.

Although this classification is useful, not all small molecules produce one of these four types of DSC profiles. Whether a consistent relationship exists between the type of transition profile produced by a small molecule and its physiological effects remains to be determined.

The effect of transmembrane peptides

DSC has been used to great effect to study the effect of the incorporation of α-helical transmembrane peptides on the thermotropic phase behavior of various phospholipid bilayers. Because most integral membrane proteins contain one or more α-helical transmembrane segments, such studies are relevant to the mechanisms by which the physical properties of the membrane lipid bilayer modulate the structure and activity of such proteins. In this regard, several investigations have been carried out using DSC and many other physical techniques to understand how the presence of such transmembrane peptides effect the organization and dynamics of the host lipid bilayer and vice versa. Such studies have examined the effects of systematic variations in the length and structure of model α-helical transmembrane peptides on lipid bilayer organization and dynamics, and how the effects of such peptides are themselves affected by the hydrophobic thickness and chemical composition of the host phospholipid bilayer. These important studies are ongoing, and the reader should consult recent reviews for more information (28, 29).

The effect of membrane antimicrobial peptides

DSC has also been used to study the effects of a wide variety of antimicrobial peptides on the thermotropic phase behavior of different lipid bilayers. These studies again are highly biologically relevant because the primary mode of action of most antimicrobial peptides is the perturbation and permeabilization of the lipid bilayers of the target membrane, and these agents have considerable promise as antibiotics, especially to treat multiple drug-resistant pathogenic bacteria. Again, the reader should consult recent reviews for more information on this topic (30, 31).

The effect of membrane proteins

Because of their obvious relevance to biological membranes, the effect of several peptides and proteins on the thermotropic phase behavior of single synthetic phospholipids or phospholipid mixtures has been studied by many groups (see 16, 17). It was originally proposed by Papahadjopoulos et al. (32) that polypeptides and proteins could be considered as belonging to one of three types according to their characteristic effects on phospholipid gel-to-liquid-crystalline phase transitions. Type 1 proteins typically produce no change or a modest increase in Tm, a slight increase or no change in ∆T1/2and an appreciable and progressive increase in ∆Hcal as the amount of protein added is increased. These proteins normally do not expand phospholipid monolayers nor alter the permeability of phospholipid vesicles into which they are incorporated. Type 1 proteins are “hydrophilic” proteins that are thought to interact with the phospholipid bilayer exclusively by electrostatic forces and, as such, normally show stronger effects on the phase transitions of charged rather than zwitterionic phospholipids. Type 2 proteins produce a decrease in Tm, an increase in ∆T1/2 and a considerable and progressive decrease in ∆Hcal phospholipid monolayers are typically expanded by such proteins, and these proteins normally increase the permeability of phospholipid vesicles. These proteins, which are also hydrophilic, are believed to interact with phospholipid bilayers by a combination of electrostatic and hydrophobic forces, initially adsorbing to the charged polar headgroups of the phospholipids and subsequently partially penetrating the hydrophilic-hydrophobic interface of the bilayer to interact with a portion of the hydrocarbon chains. Finally, type 3 proteins usually have little effect on the Tm or ∆T1/2 of the phospholipid phase transition, but ∆Hcal decreases linearly with protein concentration. Type 3 proteins are “hydrophobic” proteins that markedly expand phospholipid monolayers and increase the permeability of phospholipid vesicles. These proteins are thought to penetrate deeply into or to span the hydrophobic core of anionic or zwitterionic lipid bilayers and, thus, to interact strongly with the phospholipid fatty acyl chains and essentially to remove them from participation in the cooperative chain-melting transition. It should be noted, however, that some type 3 proteins may also interact electrostatically with phospholipid polar headgroups, particularly with those bearing a net negative charge.

The results of more recent DSC and other studies of lipid-protein model membranes clearly indicate that the classification scheme originally proposed is not completely appropriate for naturally occurring membrane proteins (see Reference 17). Thus, none of the water-soluble, peripheral membrane-associated proteins studied thus far exhibit classical type 1 behavior (no change or a modest increase in Tm, a slight increase in ∆T1/2 and an increase in the AH of the phospholipid phase transition). Therefore, it seems doubtful whether natural membrane proteins ever interact with phospholipid bilayers exclusively by electrostatic interactions. However, a few examples of membrane proteins do exhibit more-or-less-classical type 2 behavior. These examples include the myelin basic protein and cytochrome c, all of which usually reduce the Tm, increase the ∆T1/2 and substantially reduce the AH of the chain-melting transition of anionic phospholipids. Strictly speaking, few if any membrane proteins actually exhibit classical type behavior as originally defined (no change in the Tm or ∆T1/2 and a progressive linear reduction in the ∆H of both neutral and anionic phospholipid phase transitions with increasing protein concentration). This is because, with the advent of high-sensitivity calorimeters and the availability of pure phospholipids, it has become clear that all integral membrane proteins reduce the cooperativity of gel-to-liquid-crystalline phase transitions, as indeed would be expected from basic thermodynamic principles. Moreover, some type 3 proteins exhibit a nonlinear decrease in ∆H with changes in protein levels, whereas others can produce at least moderate shifts in the Tm of phospholipid phase transitions. However, if we relax the original type 3 criteria somewhat, then several integral, transmembrane proteins can be said to exhibit “modified” type 3 behavior.

The classification scheme of Papahadjopoulos et al. (32), appropriately modified for type 3 proteins, is still of some use in studies of lipid-protein interactions, although some proteins, at least under certain conditions, do not fall neatly into any of these three categories. It seems that all naturally occurring membrane proteins studied to date interact with lipid bilayers by both hydrophobic and electrostatic interactions and that different membrane proteins differ only in the specific types and relative magnitudes of these two general classes of interactions. It is also clear that the behavior exhibited by any particular membrane protein can depend on its conformation, method of reconstitution, and relative concentration, as well as on the polar headgroup and fatty acid composition of the lipid bilayer with which it is interacting (see Reference 17).

Although DSC and other physical techniques have made considerable contributions to the elucidation of the nature of lipid-protein interactions, several outstanding questions remain. For example, it remains to be definitively determined whether some integral, transmembrane proteins completely abolish the cooperative gel-to-liquid-crystalline phase transition of lipids with which they are in direct contact or whether only a partial abolition of this transition occurs, as is suggested by the studies of the interactions of the model transmembrane peptides with phospholipids bilayers (see above). The mechanism by which some integral, transmembrane proteins perturb the phase behavior of very large numbers of phospholipids also remains to be determined. Finally, the molecular basis of the complex and unusual behavior of proteins such as the concanavalin A receptor and the Acholeplasma laidlawii B ATPase is still obscure (see Reference 17).

Lipid lamellar/nonlamellar phase transitions

The mixture of lipids present in all biological membranes studied to date seems to exist exclusively in the liquid-crystalline lamellar phase under physiologically relevant conditions of temperature and hydration. However, individual membrane lipids potentially can form a variety of liquid-crystalline normal, lamellar, or reversed phases when dispersed in water, depending primarily on their effective molecular shapes. For these rod-like amphiphilic lipid molecules, the relative effective sizes of their polar and nonpolar regions are important elements in determining their molecular shapes, in particular, the relative cross-section areas occupied by their polar headgroups and nonpolar hydrocarbon chains. The effective cross-section area of a lipid polar headgroup seems to depend primarily on headgroup volume, whereas the effective cross-section area of the hydrocarbon chains depends primarily on the length and degree of unsaturation of the chains. If the effective cross-section area of the polar headgroup exceeds that of the nonpolar region, then the lipid molecule will have a conical shape and will tend to aggregate in water to form normal micelles or related structures. Conversely, if the relative cross-section of the polar headgroup is less than that of the hydrocarbon chains, then the lipid will have an “inverted” conical shape and will tend to aggregate in water to form either a reversed cubic or a reversed hexagonal phase. If, however, the relative areas occupied by the polar headgroup and the hydrocarbon chains are roughly equal, then the molecules will be cylindrical in shape and will tend to form a lamellar or bilayer phase. Because the effective area of the hydrocarbon chains in the liquid-crystalline state increases to a much greater extent with temperature than does that of the polar headgroup, increases in temperature favor the formation of lamellar over normal and reversed over lamellar phases (see Reference 14).

It is relatively straightforward to determine the types of phases formed by aqueous dispersions of individual membrane lipids over a range of temperature and thus to infer something about the lipids’ overall effective shape. In fact, the structures of the various phases formed by the individual lipids of the membrane of A. laidlawii have been studied extensively (see Reference 8). It is difficult, however, to quantitate the relative strengths of the phase preferences of a series of different lipids because the effective shapes of the lipid molecules cannot be directly determined in their various liquid-crystalline phases. However, Epand (33) has shown that small amounts of lipids with small (large) polar headgroups decrease (increase) the liquid-crystalline, lamellar-reversed, hexagonal phase transition temperature (Th) of the host dielaidoylphosphatidylethanolamine bilayer (DEPE), and Janes and coworkers (34) have recently shown that the intrinsic headgroup volumes of seven synthetic dioleoyl glycerolipids correlate well with the ability of these lipids to alter the Th of a 1-palmitoyl-2-oleoyl phosphatidylethanolamine matrix. In fact, both groups have presented evidence that Th probably varies linearly with the effective size of the lipid polar headgroup at the lipid/water interface. This approach thus seems suitable for quantitating the relative phase preferences of any series of lipids based on differences in their effective shapes, which will be determined largely by effective head- group size when the structures of their fatty acyl chains are identical. However, this method would generally not be applicable to the lipids of most biological membranes because the fatty acid compositions of the individual lipids are usually quite different. However, the ability to manipulate the fatty acid composition of the membrane lipids of the simple, cell wall-less prokaryote A. laidlawii B has permitted us to determine the relative effective headgroup sizes and, thus, the relative strength of the phase preferences of all quantitatively significant membrane lipids of this organism by determining the effect of the incorporation of small amounts of these lipids on the Th of a phos- phatidylethanolamine matrix of identical fatty acid composition (35). We found that the incorporation of small amounts of these lipids produced effects ranging from a moderate depression to a marked elevation of the Th of the phosphatidylethanolamine. Thus, although the total membrane lipids from this organism form only lamellar phases under physiological conditions, the individual membrane lipids seem to exhibit a wide range of phase preferences. Phosphatidylglycerol and diglucosyldiacyl-glycerol seem to have relatively strong and weak preferences for the lamellar liquid-crystalline phase, respectively, whereas monoglucosyldiacylglycerol and, especially, acyl polyprenyl glucoside strongly prefer the reversed hexagonal phase. Most notable in this regard is the phase preference of glycerylphos-phoryldiglucosyldiacylglycerol, which strongly destabilizes the reversed hexagonal phase and which actually prefers the normal micellar phase in isolation (36) (see Fig. 4). The presence of normal, lamellar, and reversed phase-preferring lipids in a single membrane has important implications for understanding the physical basis of lipid organization and biosynthetic regulation in this organism and possibly in other organisms. We also showed that the characteristic effect of the individual A. laidlawii membrane lipids on the lamellar/reversed hexagonal phase transition temperature of the phosphatidylethanolamine matrix is not well correlated with their polar head- group intrinsic volumes. This result indicates that the effective cross-section area of the polar headgroups of these lipid species must be strongly influenced by factors such as charge, hydration, orientation, and motional freedom as well as by intrinsic headgroup volume.

The approach discussed above to determine quantitatively the effect of various membrane phospho- and glycolipids on the lamellar/nonlamellar phase behavior of a host phosphatidylethanolamine or similar matrix has been applied to determine the relative shape, and thus the effect on the monolayer curvature of the host bilayer, of several agents, including sterols, peptides, detergents, and drugs (see Reference 14). Such studies can be very useful in providing insight into the function and mechanism of action of these agents on biological membranes.

Figure 4. High-sensitivity DSC heating thermograms of aqueous multilamellar dispersions of DEPE containing (A) 0 mol %, (B) 2.5 mol % > (C) 5.0 mol and (D) 10.0 mol % of the glycerylphosphoryldiglucosyl diacylglycerol from elaidic-acid homogeneous Acholeplasma laidlawii B membranes. Only the lamellar liquid-crystalline (Lα) to liquidcrystalline reversed hexagonal (H||) phase transition is illustrated. Note that the strong upward shift in the Lα/H|| phase transition temperature indicates that this membrane lipid strongly stabilizes the La phase and destabilizes the H|| phase of DEPE, indicating that it has a conical shape with a large polar headgroup volume relative to the volume of the hydrocarbon chains. In fact, this lipid forms a normal micellar phase in water in isolation from the other membrane lipids (31).

DSC Studies of Biological Membranes

The A. laidlawii membrane was used by Steim and colleagues (37) to show for the first time that biological membranes can undergo a gel-to-liquid-crystalline lipid phase transition similar to that previously reported for lamellar phospholipid-water systems. These workers demonstrated that when whole cells or isolated membranes are analyzed by DSC, two relatively broad endothermic transitions are observed on the initial heating scan. The lower-temperature transition is fully reversible, varies markedly in position with changes in the length and degree of unsaturation of the membrane lipid fatty acyl chains, is broadened and eventually abolished by cholesterol incorporation, and exhibits a transition enthalpy characteristic of the mixed-acid synthetic phospholipids. Moreover, an endothermic transition that has essentially identical properties is observed for the protein-free total membrane lipid extract dispersed in excess water or aqueous buffer, which indicates that the presence of membrane proteins has little effect on the thermotropic phase behavior of most membrane lipids. In constrast, the higher-temperature transition is irreversible, is independent on membrane lipid fatty acid composition or cholesterol content, and is absent in total membrane lipid extracts, which indicates that the higher temperature transition results from an irreversible thermal denaturation of the membrane proteins. A comparison of the enthalpies of transition of the lipids in the membrane and in water dispersions indicates that at least 75% of the total membrane lipids participate in this transition. Evidence was also presented that the lipids must be predominantly in the fluid state to support normal growth. These results were later confirmed and extended by Reinert and Steim (38) and by Melchior et al. (39), who showed that the gel-to-liquid-crystalline lipid phase transition is a property of living cells and that about 85-90% of the lipid participates in the gel-to-liquid-crystalline phase transition. These studies provided strong, direct experimental evidence for the hypothesis that lipids are organized as a liquid-crystalline bilayer in biological membranes, a basic feature of the currently well-accepted fluid-mosaic model of membrane structure.

Representative high-sensitivity DSC initial heating scans of viable cells, isolated membranes, and total membrane lipid dispersions are shown in Fig. 5 in this instance, cells, membranes, and lipids were made nearly homogeneous in elaidic acid (13). The fully reversible gel-to-liquid-crystalline lipid phase transitions observed in cells and membranes essentially have identical phase transition temperatures, enthalpies, and degrees of cooperativity, which suggests that membrane lipid organization in these two samples is very similar or identical. In contrast, the midpoint of the chain-melting transition of the membrane lipid dispersion is shifted to a higher temperature, exhibits a greater enthalpy, and is considerably less cooperative than in cells or membranes, which suggests that native membrane lipid organization has been perturbed during extraction and resuspension of the membrane lipids in water. The thermal denaturation of the proteins in the cells and membranes has absolutely no effect on the peak temperature or cooperativity of the lipid phase transition. However, about 15% of the lipids do not participate in the cooperative gel-to-liquid-crystalline phase transition in both the native and heat-denatured membranes, presumably because their cooperative phase behavior is abolished by interaction with the transmembrane regions of integral membrane proteins. Alternatively, a larger proportion of the membrane lipids may interact with the membrane proteins but have their cooperative melting behavior only partially perturbed, which thereby leads to the 15% reduction in the transition enthalpy observed. The fact that the gel-to-liquid-crystalline lipid phase transition in cells and membranes exhibits a similar temperature maximum and a higher cooperativity than does the membrane lipid dispersion favors the former interpretation.

Figure 5. High-sensitivity DSC heating scans of Acholeplasma laidlawii B elaidic acid-homogeneous intact cells, isolated membranes and extracted total membrane lipids dispersed as multilamellar vesicles in water.

The presence of high levels of cholesterol in many eukaryotic membranes, particularly plasma membranes, abolishes a discrete cooperative gel-to-liquid-crystalline membrane lipid phase transition in these systems. Thus, no lipid phase transitions could be detected by DSC in the cholesterol-rich erythrocyte (40) or myelin (41) membranes. The thermotropic behavior of rat liver microsomal membranes, which contain moderate levels of cholesterol, has been studied by DSC. An early study using conventional DSC revealed a single reversible, broad phase transition occurring between — 15°C and +5°C in both intact membranes and isolated lipids (42). A more recent high-sensitivity DSC study confirmed the absence of a reversible phase transition above 0°C (43). Rat liver mitochondrial membranes, which are low in cholesterol, have been studied by several groups using DSC and other techniques. The earliest work with whole mitochondrial revealed a reversible broad gel-to-liquid-crystalline phase transition centered at 0° C in mitochondrial membranes and in extracted lipids (42). A later study of both intact mitochondria and of isolated inner and outer membranes confirmed these results, except that the outer membrane transition seemed to occur at a slightly lower temperature than did the inner membrane transition (44). However, a more recent study of the rat liver inner mitochondrial membrane reported a narrower membrane lipid transition centered near +10°C by artificially increasing cholesterol content some 10-fold to about 30 mol %, the inner membrane gel-to-liquid-crystalline phase transition could be lowered and broadened, and its ∆Hcal reduced to less than one tenth that of the native membrane (45). It has also been reported that in beef heart mitochondrial inner membranes, a broad reversible endothermic phase transition centered at —10 ° C occurs.

DSC has been used to study the individual protein components of biological membranes of relatively simply protein composition and the interaction of several of these components with lipids and with other proteins. The red blood cell membrane, which has been most intensively studied, exhibits five discrete protein transitions, each of which has been assigned to a specific membrane protein. The response of each of these thermal transitions to variations in temperature and pH as well as to treatment with proteases, phospholipases, specific labelling reagents, and modifiers and inhibitors of selected membrane activities, has provided much useful information on the interactions and functions of these components in the intact erythrocyte membrane (46-49). Similar approaches have been applied to the bovine rod outer segment membrane (50) and to the spinach chloroplast thylakoid membrane (51).

Research performed in the authors’ laboratory has been supported by operating and major equipment grants from the Canadian Institutes of Health Research, operating grants from the Natural Sciences and Engineering Research Council of Canada, and by major equipment and personnel support grants from the Alberta Heritage Foundation for Medical Research.

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Abstract

CDC25 phosphatases are key cell cycle regulators and represent very attractive but challenging targets for anticancer drug discovery. Here, we explored whether fragment-based screening represents a valid approach to identify inhibitors of CDC25B. This resulted in identification of 2-fluoro-4-hydroxybenzonitrile, which directly binds to the catalytic domain of CDC25B. Interestingly, NMR data and the crystal structure demonstrate that this compound binds to the pocket distant from the active site and adjacent to the protein–protein interaction interface with CDK2/Cyclin A substrate. Furthermore, we developed a more potent analogue that disrupts CDC25B interaction with CDK2/Cyclin A and inhibits dephosphorylation of CDK2. Based on these studies, we provide a proof of concept that targeting CDC25 phosphatases by inhibiting their protein–protein interactions with CDK2/Cyclin A substrate represents a novel, viable opportunity to target this important class of enzymes.


Chemistry Notes Form 2

When scientists started exploring matter, they realised that matter can be divided into smaller and still smaller particles.

They called the smallest particle an 'atom’.

The name 'atom' was derived from the Greek word 'atomos', meaning 'indivisible’.

They discovered that the 'atom' maintains its chemical identity through all chemical and physical changes.

Dalton's Atomic Theory

John Dalton provided a simple theory of matter to provide theoretical justification to the laws of chemical combinations in 1805. The basic postulates of the theory are:

At present we know that the atom is the smallest particle of an element.

It is made up of sub-atomic particles like electrons, protons and neutrons.

Atoms of one type of element differ from those of the other due to different number of sub-atomic particles.

The protons and neutrons are in the nucleus (centre) of the atom and the electrons orbit round the outside in shells (energy levels or layers).

The picture below represents an atom of lithium. Lithium has 3proton, 4 neutrons and 3 electrons as shown.

Notice that the number of electrons and that of electrons are always equal in neutral atoms.

Summary of sub-atomic particles

The electrons revolve rapidly around the nucleus in fixed circular paths called energy levels or shells.

The 'energy levels' or 'shells' or 'orbits' are represented in two ways: either by the numbers 1, 2, 3, 4, 5 and 6 or by letters K, L, M, N, O and P.

The energy of the K shell is the least while those of L, M, N and O shells increases progressively. The energy levels are counted from centre outwards.

2nd energy level is L shell. It has a maximum of 8 electrons

3rd energy level is M shell. has a maximum of 8 electrons

4th energy level is N shell and so on. The 19th and 20th electrons go into the 4th shell

Electronic configuration of an element

The arrangement of electrons in the various shells/orbits/energy levels of an atom of the element is known as electronic configuration.

Important Rules: Number of electrons in a shell

Maximum number of electrons in 1 st energy level = 2n 2

Maximum number of electrons in the 2nd energy level = 2n 2

Maximum number of electrons in the 3rd energy level = 2n 2

Maximum number of electrons in the 4th energy level = 2n 2

Maximum number of electrons(2n 2 ) 2 x (1) 2

2 x 22 2x(3)2 2x(4)2 Total 2 8 18 32

This is a very important rule and is also called the Octet rule.

The presence of 8 electrons in the outermost shell makes the atom very stable.

Geometric Representation of Atomic Structure

Example 1: Magnesium atom

Atomic number of potassium is 19 and its electronic configuration is

Atomic number of calcium is 20 and its electronic configuration is

This abnormal behaviour can be explained as follows:

It is found that shells have sub shells. The smaller sub shells are termed s, p, d and f.

The maximum number of electrons that can go into these are 2, 5, 10 and 14 respectively.

These sub shells can overlap, resulting in energies that may differ from that predicted purely on the basis of n=1, 2, 3 etc.

Therefore when electrons start filling, they may go to a new outer shell even before the inner shell is filled to capacity.

Atomic Number and Mass Number

The nuclei of atoms are made up of protons and neutrons.

These two components of the nucleus are referred to as nucleons.

The electrons occupy the space outside the nucleus.

Since an atom is electrically neutral, the number of protons in the nucleus is exactly equal to the number of electrons.

This number is the atomic number given by the symbol Z.

Atomic number represents the number of protons in an atom.

As atoms are electrically neutral, an atom contains as many electrons as it has protons.

The total number of protons and neutrons present in one atom of an element is known as its mass number.

Mass number (A) = number of protons (Z) + number of neutrons (n)

Mass number (A) = atomic number (Z) + number of neutrons (n)

The mass number (A) is written as a superscript on the top-left corner of the symbol of the atom. The atomic number(Z) is written as a subscript on the bottom-left corner.

The symbol represents an atom of sodium whose atomic mass is 23 and atomic number is 11. Calculate the number of protons, electrons and neutrons.

It is interesting to note that atoms of a given atomic number can have different number of neutrons.

Atoms of elements having the same atomic number with different mass numbers are called isotopes

Some examples are listed below:

Hydrogen atom (Z=1) has no neutrons.

It has been reported that the hydrogen element has atoms with mass number 2 and 3 also i.e.

Nuclear composition of isotopes of chlorine:

Nuclear composition of isotopes of carbon:

Table of some elements that exist as mixtures of isotopes

The relative atomic mass (Ar) is the average mass of an element, taking account of its natural isotopes and their percentage abundance.

The strict definition of relative atomic mass is that Ar = average mass of all the isotopic atoms present in the element compared to 1/12th the mass of a carbon-12 atom.

Example: chlorine consists of 75% chlorine-35 and 25% chlorine-37.

So the relative atomic mass of chlorine is 35.5 or Ar (Cl) = 35.5

By the loss or gain of electrons a neutral atom is changed to an ion. Ions are charged atoms or a group of atoms.

In other words, ions are particles formed by atoms by the donation or acceptance of electrons.

Listed below are some elements that attain the octet configuration of Noble gases. Let us see how this happens. Study the given table:

Na, Mg, K, Ca g lose electrons

S, O, F, Cl g gain electrons

Most of these atoms try to attain the configurations of either neon (2,8) or argon (2,8,8).

Differences between atoms and ions

Let us consider the example of a sodium atom and the sodium ion.

Differences between sodium atom and sodium ion

Ionization potential (or ionization energy) is the amount of energy required to remove one or more electrons from the outermost shell of an isolated atom in the gaseous state.

Atom(g) + IE Positive ion(g) + electron(g)

Thus, the ionization energy gives the ease with which the electron can be removed from an atom.

The smaller the value of the ionization energy, the easier it is to remove the electron from the atom.

An electron is held in an atom by the electrostatic force of the positively charged protons in the nucleus and the negative charge of the electrons.

By supplying enough energy, it is possible to remove an electron from an atom.

The element is first brought into the vapour state.

Then the electron is removed by supplying energy equivalent to the ionization potential.

Factors affecting ionization energy

a) The inert gases have very high ionization energy, due to the stability of the outer shell. Helium has the highest ionization energy.

b) Within a group, the ionization energy generally decreases with increasing atomic number.

Increasing atomic number results in increasing atomic radii.

Thus, the electrons of the outer shell are further away than those of the previous element and can be removed easily.

c) Ionization energy decreases down the group because of increase in the number of shells.

The effective nuclear charge decreases as atomic size increases.

Thus it is easier to pull one electron from the outermost shell of the atom.

This is the enthalpy change when 1 mole gaseous atoms gains 1 mole of electrons under standard conditions.

The elements in group 7 have the highest electron affinities, they form negative ions easily, as go down the group the electron affinity decreases so reactivity decreases.

The second electron affinity is the energy needed to to add an electron to 1 mole of gaseous 1- ions to form 1 mole of gaseous 2- ions under standard conditions (where standard conditions are 100kpa and 298K).

This process involves adding a negatively charged electron to a negative ion - naturally this process is endothermic since energy needs to be supplied to overcome the repulsive forces between the negative ion and the negative incoming electron.

Characteristics of isotopes

The densities, melting points and boiling points etc., are slightly different.

1. The table shows the number of protons, neutrons and electrons in a chlorine atom.

(i) Complete the table to show the number of these particles in the chloride ion, Cl–, formed from this atom.

(ii) What is the arrangement of electrons in a chlorine atom?

2. The element bromine exists as a mixture of two isotopes.

(i) Complete the table to show the number of protons and neutrons in the nuclei

Deduce the percentage abundance of the two isotopes in bromine.

3. The table below shows some information about the isotopes of chlorine.

(a) Use information from the periodic table to help you complete the table.

(ii) What is the relative molecular mass of a chlorine molecule?

(c) Draw a dot and cross diagram for a molecule of chlorine, showing outer electrons only.

4. Atoms are made of electrons, neutrons and protons.

(a) Complete the table to show the relative mass and charge of an electron, neutron and proton.

(ii) What is the atomic number of this element?

5. The electronic structures (configuration) of elements represented by letters P, Q, R and S are:

Which element a) forms a singly charged anion

b) forms a soluble carbonate

c) reacts most vigorously with water

6. The table below shows the elements in the same group of the periodic table and their average atomic radii, measured in the usual atomic measurements.

The symbols do not represent the actual symbols of elements.

(b) Using the letters given, which element has the highest ionisation energy? Give a reason for your answer

1.3 The Periodic Table

Dmitri Mendeleev is credited as being the Father of the modern periodic table.

In 1869 he arranged the 50 or so known elements in order of atomic number, Z, putting elements with similar properties in the same vertical group, and leaving gaps for unknown elements, yet to be discovered.

When the elements were later discovered, they were found to have the properties predicted by Mendeleev's table.

Elements in the same period have the same number of shells, but the number of electrons occupying the last shell increase from left to right i.e. from one to eight.

The number of shells increases down a group.

However, the number of electrons in the last shell of each element is the same.

Elements in a given group in the periodic table share many similar chemical and physical properties.

The modern periodic table is very useful for giving a summary of the atomic structure of all the elements.

Some of the Groups have Names and some have Numbers.

A Group is a vertical column of chemically and physically similar elements. The alkali metals are in group 1 on the left of the periodic table.

The elements in this group are Hydrogen (H), Lithium (Li), Sodium (Na), Potassium (K), Rubidium (Rb), Cesium (Cs) and Francium (Fr) They have all only one electron in their outermost shells.

Since the atomic number, hence number of shells increases down the group, the atomic radius increases down the group.

From one element to the next, an extra shell of electrons is added. This increases the electron 'bulk' and the outer electrons are increasingly less strongly held .

The radii of the adjacent Group 2 atom is smaller than Group 1 atom on the same period, because the nuclear charge has increased by one unit (L to R ), but is attracting electrons in the same shell.

Similarly the radii of Group 2 M2+ ion is smaller than the adjacent Group 1 M+ ion on the same period, because the nuclear charge has increased by one unit (L to R ), but is attracting the same number of electrons in the same shells.

The alkali metals are all highly reactive, losing their one outer electron to form a 1+ ion with non-metals. They give up 1 electron easily as losing 1 is easier than gaining 7 to complete the octet.

They are unusually soft, and can easily be cut with a knife.

When freshly cut, they rapidly tarnish by reaction with oxygen to form an oxide layer, which is why they are stored under oil.

The first three members, lithium, sodium and potassium, are unique in being the only metals which are less dense than water (they float!).

This is the energy required to remove one mole of electrons from the outermost shell of an atom to form a positively charged ion.

This process can be repeated again to give the second ionisation energy.

This is more difficult than the first ionisation energy because we are removing a negative electron from a positive ion.

It is possible to continue in this way until al of the electrons on an atom have been removed.

As you go down the group from one element down to the next, the atomic radius gets bigger due to an extra filled electron shell.

The outer electrons are further and further from the nucleus and are also shielded by the extra full electron shell of negative charge.

Therefore the outer electrons are less and less strongly held by the positive nucleus and so less and less energy is needed to remove them.

Successive ionisation energies always increase e.g. . 3rd > 2nd > 1st, because the same nuclear charge is attracting fewer electrons and on average closer to the nucleus.

BUT note the 2nd IE for Group 1, and the 3rd IE for Group 2, show a particularly significant increase in IE compared to the previous ionisation energy or energies.

This is due to removing an electron from an electronically highly stable full inner shell and puts an upper limit on the chemically stable oxidation state.

Why reactivity increases down the group

When an alkali metal atom reacts, it loses an electron to form a singly positively charged ion e.g. Na Na+ + e- (in terms of electrons 2.8.1 2.8 and so forming a stable ion with a noble gas electron arrangement).

As you go down the group from one element down to the next the atomic radius gets bigger due to an extra filled electron shell.

The outer electron is further and further from the nucleus and is also shielded by the extra full electron shell of negative charge.

Therefore the outer electron is less and less strongly held by the positive nucleus.

This combination of factors means the outer electron is more easily lost, the M+ ion more easily formed, and so the element is more reactive as you go down the group.

The reactivity argument mainly comes down to increasingly lower ionisation energy down the group.

Summary of the Reactivity Trend of Alkali Metals

1. Common salt from sea water or underground deposits is sodium chloride and is the raw material for making sodium, hydrogen, chlorine and sodium chloride by electrolysis.

2. Sodium hydrogen carbonate (NaHCO3) Used in baking soda, pharmaceutical products like indigestion tablets and fire extinguishers.

3. Sodium hydroxide (NaOH) Used in the manufacture of soaps, detergents, salts of acids, paper and ceramics.

The Alkaline Earth Metals - Group 2 - Properties.

The second group (group II A) has Beryllium (Be), Magnesium (Mg), Calcium (Ca), Strontium (Sr), Barium (Ba) and Radium (Ra).

They have two electrons in their last shell and their valence is +2 as they give up two electrons to form compounds.

The elements in group II A are not as metallic as the alkali metals.

They form oxides easily and are known as alkali earth metals.

Group 2 Alkaline Earth Metals

From calcium going down the group, they have to be stored under oil, or they react with oxygen in the air. They are less reactive than the alkali metals (Group 1).

Calcium and magnesium are fourth and fifth in the reactivity series.

They all have the common properties of metals, being silvery-grey in colour, and good conductors of heat and electricity.

They are less soft than the alkali metals, and it is difficult to cut them with a knife.

The only two of the group which are studied at KCSE are magnesium and calcium.

Strontium, barium and radium are all too reactive or unstable to be used.

All you need to know about these three is that they have the same chemical properties as magnesium and calcium.

Beryllium is odd and is not studied at KCSE.

It would be expected to lose its two outer electrons like the rest of Group 2 but beryllium is so small that it doesn't like to lose two electrons.

Its compounds have covalent character! As we proceed to group III and further, we will notice that the number of valence electrons increases by one in each subsequent group.

Trend in first ionization energy down group 2

The first ionisation energy is the enthalpy change when one mole of gaseous atoms forms one mole of gaseous ions with a single positive charge. It is an endothermic process, i.e. is positive.

A general equation for this enthalpy change is:

Ionisation energy is governed by:

• The charge on the nucleus,

• The amount of screening by the inner electrons,

• The distance between the outer electrons and the nucleus.

How does the first ionisation energy change going down the group?

The outer electrons are held in their shells by the attractive force of the positive protons in the nucleus, the nuclear attraction.

As more and more electron shells are added this force gets weaker because

1. the distance between the outer electrons and the nucleus is increasing

2. The inner electrons shield the nuclear electrons from the outer electrons, electronic shielding.

The lower the ionisation energy the easier it is to remove electrons from the outermost shell of the atom.

As you go down a group the ionisation energy decreases.

This also explains why metals get more reactive as you go down a group.

It gets easier for them to give up electrons to form bonds.

As the number of protons in the nucleus increases going down Group 2, you might expect the first ionisation energy to increase because the nuclear charge increases.

This does not happen, because the factors described above have a greater influence on the value of the first ionisation energy.

There are more filled energy levels between the nucleus and the outer electrons, therefore the outer electrons are more shielded from the attraction of the nucleus So the electrons in the outer energy levels are further from the nucleus and the atomic radius increases.

As the number of protons in the nucleus increases going down Group 2, you might expect the atomic radius to decrease because the nuclear charge increases.

This does not happen, because although the electrons in the inner energy levels become closer to the nucleus, the factors described above have a greater influence on the atomic radius overall.

Magnesium burns vigorously with a bright white flame when strongly heated in air/oxygen to form a white powder of magnesium oxide.

Magnesium + oxygen magnesium oxide

2Mg(s) + O2(g) 2MgO(s) Calcium burns quite fast with a brick red flame when strongly heated in air/oxygen to form the white powder calcium oxide.

Calcium + oxygen calcium oxide

1. Magnesium will not react with cold water. Even finely powdered magnesium reacts only very slowly. Magnesium will react with gaseous water (steam) to form magnesium oxide and hydrogen. Magnesium + steam magnesium oxide + hydrogen.

Magnesium oxide is a base. It will not dissolve in water.

In fact magnesium is so reactive, it will even burn in carbon dioxide, the products being white magnesium oxide powder and black specks of elemental carbon!

Magnésium + carbon dioxide ==> magnesium oxide + carbon 2Mg(s) + CO2(g) ==> 2MgO(s) + C(s)

2. Calcium (and the metals below calcium in group 2) will react with cold water. They will sink as they react, unlike the group 1 metals which float.

Calcium + water calcium hydroxide + hydrogen. Ca(s) + 2H2O(l) Ca(OH)2(s) + H2(g)

Calcium hydroxide is called slaked lime and will dissolve a little in water to form lime water

Magnesium is very reactive with dilute hydrochloric acid forming the colourless soluble salt magnesium chloride and hydrogen gas.

Magnesium + hydrochloric acid ==> magnesium chloride + hydrogen Mg(s) + 2HCl(aq) ==> MgCl2(aq) + H2(g)

Magnesium is very reactive with dilute hydrochloric acid forming the colourless soluble salt calcium chloride and hydrogen gas.

Calcium + hydrochloric acid ==> calcium chloride + hydrogen

Ca(s) + 2HCl(aq) ==> CaCl2(aq) + H2(g)

Not very reactive with dilute sulphuric acid because the colourless calcium sulphate formed is not very soluble and coats the metal inhibiting the reaction, so not many bubbles of hydrogen.

Calcium + sulphuric acid ==> calcium sulphate + hydrogen

Reaction With Halogens

They occur in nature only in compounds because of their high reactivity.

They are less reactive than group 1 elements due to higher IE.

They react with elements in group 7 to give the general formula MX2(M is the metal and X represents any members of group 7.

Summary of the Reactivity Trend of Alkali Earth Metals

When 2 electrons have been removed from the gaseous atom, the remaining electrons are arranged like a noble gas, which is a very stable electron configuration.

The Halogens - Group 7.

The halogens are all in group 7 on the right of the periodic table. This group consists of elements like Fluorine (F), Chlorine (Cl), Bromine (Br), Iodine (I), Astatine (At).

The Halogens are typical non-metals and form the 7th Group in the Periodic Table 'Halogens' means 'salt formers' and the most common compound is sodium chloride which is found from natural evaporation as huge deposits of 'rock salt' or the even more abundant as 'sea salt' in the seas and oceans.

• Typical non-metals with relatively low melting points and boiling points.

• The melting points and boiling increase steadily down the group (so the change in state at room temperature from gas => liquid => solid), this is because the inter molecular attractive forces increase with increasing size of atom or molecule.

• They are all coloured non-metallic elements.

• The colour of the halogen gets darker down the group.

• They are all poor conductors of heat and electricity - typical of non-metals.

• When solid they are brittle and crumbly e.g. iodine.

• The size of the atom gets bigger as more inner electron shells are filled going down from one period to another.

The atoms all have 7 outer electrons, this outer electron similarity, as with any Group in the Periodic Table, makes them have very similar chemical properties eg

They gain one negative electron (reduction) to be stable and this gives a surplus electric charge of -1.

These ions are called the halide ions, two others you will encounter are called the bromide Br- and iodide I- ions.

• The reactivity decreases down the group.

• They are all TOXIC elements.

• Astatine is very radioactive, so difficult to study but its properties can be predicted using the principles of the Periodic Table and the Halogen Group trends!

These elements are gaseous in nature and have valence -1, they borrow electrons to stabilize their electronic configuration.

The formulae are F2, Cl2, Br2, I2, (see structure of chlorine).

All of the halogens will either.

1) Gain one electron from a metal to form an ionic bond, or

2) share one electron with a non-metal to form a covalent bond

Reactions with Metals.

The halogens will gain one electron to form an ionic bond with metals. The halogens will react with

• Alkali metals burn very exothermically and vigorously when heated in chlorine to form colourless crystalline ionic salts eg NaCl or Na + Cl - .

This is a very expensive way to make salt! Its much cheaper to produce it by evaporating sea water!

eg sodium + chlorine ==> sodium chloride

• The sodium chloride is soluble in water to give a neutral solution pH 7, universal indicator is green.

The salt is a typical ionic compound ie a brittle solid with a high melting point.

Similarly potassium and bromine form potassium bromide KBr, or lithium and iodine form lithium iodide LiI.

Again note the group formula pattern.

Iron + bromine iron (III) bromide.

Iron + chlorine iron(III) chloride.

2Fe(s) + 3Cl2(g) 2FeCl3(s) All of the compounds with metals are ionic salts which form a giant structure.

They are called metal halides because they are formed from a metal and a halogen.

Halide ions undergo a series of unique reactions that allow an unknown solid or aqueous sample to be tested for the presence of chloride, bromide or iodide ions.

Aqueous silver ions react with halide ions to produce individually coloured precipitates. These precipitates have different solubilities in ammonia solution and so further differentiation can be achieved, see the table below,

(Typically, metals have low electro negativity, little ability to attract electrons, while non-metals have high electro negativity, greater ability to attract electrons).

The reactivity of Group VII elements is related to the element's ability to attract electrons, so the greater the electro negativity, the more reactive the Halogen.

So, chemical reactivity of Group VII elements decreases down the Group, from the most reactive (Fluorine) to the least reactive (Iodine).

Similarly there is a gradation in physical appearance at STP, from gas to liquid to solid, as the elements become more metallic in nature.

1. Chlorine by itself is used as bleach and in the manufacture of sodium chlorate, which can be used as bleach and a herbicide.

2. Water purification also relies on chlorine to kill bacteria in the water, after the impure water has passed through various filtration stages.

3. Chlorine is also used in the production of chlorofluorocarbons, commonly called CFC's, used in the past as refrigerant gases and propellants for aerosol cans.

Both these uses have now been banned by international law, in the developed world at least.

4. The problem these chemicals cause is that when they reach the high atmosphere the molecules break apart to release chlorine atoms.

These chlorine atoms then react with molecules of ozone, O 3 , turning them into molecules of oxygen. One chlorine atom can destroys thousands of molecules of ozone.

Ozone traps UV light from the sun, preventing it hitting the surface of the Earth, and with a depletion of ozone more UV light gets through, which increases occurrences of skin cancer in humans.

5. Fluorine is used as fluoride salts in toothpaste or added to domestic water supplies to strengthen teeth enamel helping to minimise tooth decay. (eg potassium fluoride).

6. Bromine and iodine are both used in 'halogen' car headlamps.

7. Iodine is used in hospitals in the mild antiseptic solution 'tincture of iodine'.

The Noble Gases - Group 0.

In this group, we have Helium (He), Neon (Ne), Argon (Ar), Krypton (Kr), Xenon (Xe) and Radon (Rn).

These elements are therefore chemically non-interacting and inert. They are therefore gaseous in nature.

They are Noble gases or inert gases.

Monatomic means that they exist as single atoms. The forces between the atoms are very weak (and so they are gases).

Going down the group from helium to radon, the density increases.

The melting and boiling point increases because the atoms become heavier (bigger) and require more energy to melt or boil.

• The "Noble Gases" are the last group in the Periodic Table i.e. they form the last elements at the end of a period.

• They are all non-metallic elements and all are colourless gases at room temperature and pressure with very low melting points and boiling points.

• They form 1% of air, and most of this is argon. All the noble gases, except radon, are separated by the fractional distillation of liquified air.

Helium can also be obtained from natural gas wells where it has accumulated from radioactive decay (alpha particles become atoms of helium gas when they gain two electrons).

• They are very unreactive elements because the highest occupied electron level is complete, meaning they have a full shell of outer electrons!

They have no 'wish' electronically to share electrons to form a covalent bond or to lose or gain electrons to form an ionic bond. In other words, they are electronically very stable.

• They exist as single atoms, i.e. they are monatomic He Ne Ar etc.

(NOT diatomic molecules as with many other gases).

• Their very inertness is an important feature of their practical uses.

• Down the Group with increasing atomic number:

Variation of Atomic Radius Down the Group

As we move down the group, the atoms get bigger as more electron shells are added. One full shell i.e. a set of 8 electrons is added from one element to the next.

This means that the atomic number and mass number both increase as we move down the group.

We can observe here that all the group member elements have the same valence electrons and display same valencies.

On going down a particular group, the properties of elements get enhanced. For example, the figure below shows group I A, the alkali metal elements.

As the atomic radii increases in the alkali metal elements, the last electron is farther away from the attractive forces of the nuclear charge.

So it is relatively easy for the element to give up its last electron.

And hence show more metallicity.

To say it in terms of electro positive character of elements, we can say that the electro positive character increases as we go down the group I.

Now if we see the behaviour of elements in the group VII or the halogen elements, we see that the electro negative character reduces as we go down the group.

This means that fluorine (F) is more reactive than chlorine (Cl).

The reason for this is that the orbit where the extra electron is captured is closer to the nucleus in F than in Cl.

Thus the extra electrons get attracted into the F-atom in a stronger manner than that in Cl.

As far as chemical reactivity is concerned, we can see that in group I, the reactivity increases as we go down the group.

On the other hand, in the other extreme, in group VII A, the reactivity decreases as we go down the group.

Also group VIII A consisting of noble gases is completely unreactive.

• The atomic numbers are not consecutive.

• The number of valence electrons in the elements is same in a group.

• The elements of the same group have the same valencies. The atomic radii increase while going from top to bottom in a group.

• Metallic character increases while going from top to bottom in a group for metallic groups.

For non-metallic groups, the non-metallic nature decreases while going from top to bottom

• Chemical reactivity increases while going from top to bottom in a group for metallic groups.

For non-metallic groups, the chemical reactivity decreases while going from top to bottom.

: Characteristics of periods

The first period starts with hydrogen (H) and ends with helium (He). It has just two elements H (Z=1) and He (Z = 2).

H has one electron in the first-shell. He has 2 electrons in the first-shell.

As we have seen in the chapter on the structure of atoms, the first-shell can hold only 2 electrons.

Thus the first period is complete.

It has to be borne in mind that the place of hydrogen is unique in the periodic table.

It has been placed above the alkali elements starting with Li in group 1A.

This is because H has valency 1 just as the other alkali elements.

But the properties of hydrogen otherwise are very different from the other group 1A alkali elements Li, Na, K, Cs, etc.

The second period starts with Li (Z=3), where the first-shell is filled and the next shell is starting to fill. After Li the next element is beryllium (Be, Z=4).

Its first-shell is complete and it has 2 electrons in the second shell. The maximum number of electrons held in the second shell is 8.

So the period has 8 elements, in which each element’s second shell is getting filled.

The last element in the period is neon (Ne, Z=10).

Neon’s both first and the second shell are completely filled.

A similarly situation occurs for the third period.

Here the next shell after second shell or the third shell is getting filled.

The maximum number of electrons in the third shell is 8.

Thus across the period, starting with element sodium (Na, Z=11) the third-shell has 1 electron and the period ends with argon (Ar, Z= 18) which has 2 electrons in the first, 8 electrons in the second shell and 8 electrons in the third shell.

Trends Across Period 3

Now let us look at some of the chemical and physical properties in a particular period. What we will learn from one period, will hold true for all the other periods.

Consider the third period.

The figure below shows how the electronic configuration is changing as we go from left to right in the period.

The number of valence electrons is increasing in an integral fashion.

The change in the valency is according to the tendency to give up or borrow electrons.

Thus elements in the same period have consecutive atomic numbers and different valencies.

Now let us consider the metallic character of the elements in the third period. Figure below shows the same.

We have proper metals in the first and the second places: sodium (Na) and magnesium (Mg) are alkali and alkaline-earth metals.

They give up the electrons in the last shell very easily.

They are shiny in colour and conduct electricity.

After Mg comes aluminum (Al).

Al has 3 electrons in its outermost shell and behaves like a metal.

The next element is silicon (Si).

It has 4 electrons in its outermost shell.

It thus needs to borrow four electrons or give up all its four electrons to form a stable shell.

Si does not do any of these, instead it binds tetrahedrally most of the time.

Thus Si behaves neither like a metal nor like a non-metal.

Hence it is called as a metalloid. After Si, come three elements: phosphorus (P), sulphur (S) and chlorine (Cl).

All the three are non-metals.

Thus while moving from left to right in the period, the metallicity decreases.

Also the chemical reactivity first decreases and then increases.

As discussed before, the chemical reactivity depends on how easily the outermost orbit gives off or borrows electrons to make a stable orbit.

The two extremes of the third period, namely Na and Cl are very reactive.

But Na is very electro-positive in nature, where as Cl is very electro-negative in nature.

The next oxide, namely magnesium oxide is also basic in nature.

At the other extreme, chlorine oxide, sulphur oxides and phosphorus oxides are acidic in nature.

The mid-elements like Al, Si have their oxides behave in both acidic and basic manner, depending on the oxidation conditions.

Such oxides are said to be amphoteric in nature.

First Ionisation Energy Across Period 3

First ionisation energy generally increases going across Period 3.

However, it needs more detailed consideration than the trend in Group 2 because:

• The first ionisation energy drops between magnesium and aluminium before increasing again.

• The first ionisation energy drops between phosphorus and sulphur before increasing again.

Table of physical data

General increase across the period

The first ionisation energy is the enthalpy change when one mole of gaseous atoms forms one mole of gaseous ions with a single positive charge.

It is an endothermic process, i.e. is positive.

A general equation for this enthalpy change is:

• there are more protons in each nucleus so the nuclear charge in each element increases .

• therefore the force of attraction between the nucleus and outer electron is increased, and .

• there is a negligible increase in shielding because each successive electron enters the same energy level .

• so more energy is needed to remove the outer electron.

Trend in atomic radius of Period 3 elements

Atomic radius decreases going across Period 3.

Table of physical data

• the number of protons in the nucleus increases so .

• the nuclear charge increases .

• there are more electrons, but the increase in shielding is negligible because each extra electron enters the same principal energy level .

• therefore the force of attraction between the nucleus and the electrons increases .

• So the atomic radius decreases.

As the number of electrons in each atom increases going across Period 3, you might expect the atomic radius to increase.

This does not happen, because the number of protons also increases and there is relatively little extra shielding from electrons in the same principal energy level.

Trend in electrical conductivity

Electrical conductivity increases going across Period 3 from sodium to aluminium, then decreases to silicon.

The remaining elements have negligible conductivity.

Table of physical data

For an element to conduct electricity, it must contain electrons that are free to move.

In general, metals are good conductors of electricity and non-metals are poor conductors of electricity.

Sodium, magnesium and aluminium

Sodium, magnesium and aluminium are all metals.

They have metallic bonding, in which positive metal ions are attracted to delocalised electrons.

The delocalised electrons are free to move and carry charge. Going from sodium to aluminium:

• the number of delocalised electrons increases .

• there are more electrons which can move and carry charge .

• So the electrical conductivity increases.

Silicon is a metalloid (an element with some of the properties of metals and some of the properties of non-metals).

Silicon has giant covalent bonding. It has a giant lattice structure similar to that of diamond, in which each silicon atom is covalently-bonded to four other silicon atoms in a tetrahedral arrangement.

This extends in three dimensions to form a giant molecule or macromolecule.

Silicon is called a semiconductor because:

• the four outer electrons in each atom are held strongly in covalent bonds .

• few electrons have enough energy at room temperature to enter the higher energy levels so there are few delocalised electrons and silicon is a poor conductor . but .

• at higher temperatures more electrons are promoted to the higher energy levels .

• so there are more delocalised electrons to move and carry charge.

The remaining elements in Period 3 do not conduct electricity:

• in phosphorus, sulphur and chlorine, the outer electrons are not free to move and carry charge because they are held strongly in covalent bonds .

• in argon (which exists as single atoms) the outer electrons are not free to move and carry charge because they are held strongly in a stable third energy level.

Trends in melting and boiling points

The trends in melting points and boiling points going across Period 3 are not straightforward, and need more detailed consideration than the trends in Group 2:

• Melting points generally increase going from sodium to silicon, then decrease going to argon (with a “bump” at sulphur).

• Boiling points generally increase going from sodium to aluminium, then decrease to argon (again with a “bump” at sulphur).

Table of physical data

When a substance melts, some of the attractive forces holding the particles together are broken or loosened so that the particles can move freely around each other but are still close together.

The stronger these forces are, the more energy is needed to overcome them and the higher the melting temperature.

When a substance boils, most of the remaining attractive forces are broken so the particles can move freely and far apart.

The stronger the attractive forces are, the more energy is needed to overcome them and the higher the boiling temperature.

Sodium, magnesium and aluminium

Sodium, magnesium and aluminium are all metals.

They have metallic bonding, in which positive metal ions are attracted to delocalised electrons.

Going from sodium to aluminium:

• the charge on the metal ions increases from +1 to +3 (with magnesium at +2) .

• the number of delocalised electrons increases .

• so the strength of the metallic bonding increases and .

• the melting points and boiling points increase.

Silicon is a metalloid (an element with some of the properties of metals and some of the properties of non-metals).

Silicon has giant covalent bonding.

It has a giant lattice structure similar to that of diamond, in which each silicon atom is covalently-bonded to four other silicon atoms in a tetrahedral arrangement.

This extends in three dimensions to form a giant molecule or macromolecule.

Silicon has a very high melting point and boiling point because:

• All the silicon atoms are held together by strong covalent bonds .

• Which need a very large amount of energy to be broken.

Phosphorus, sulphur, chlorine and argon

These are all non-metals, and they exist as small, separate molecules.

Phosphorus, sulphur and chlorine exist as simple molecules, with strong covalent bonds between their atoms.

Argon exists as separate atoms (it is monatomic).

Their melting and boiling points are very low because when these four substances melt or boil, it is the van der Waal’s forces between the molecules which are broken.

These bonds are very weak bonds so little energy is needed to overcome them.

Sulphur has a higher melting point and boiling point than the other three because:

• phosphorus exists as P4 molecules

• sulphur exists as S8 molecules

• chlorine exists as Cl2 molecules

• argon exists individual Ar atoms

• the strength of the van der Waal’s forces decreases as the size of the molecule decreases

• so the melting points and boiling points decrease in the order S8 > P4 > Cl2

Summary of the characteristics of elements in a period:

The reactivity on the left extreme is most electro-positive whereas on the extreme right it is most electro-negative.

Oxides of elements in the centre are amphoteric.

1. In 1829 Dobereiner suggested that some elements could be put into groups of three because they had similar chemical properties.

(a) Use the information in this table to explain why these elements are placed in the same group.

(i) What is the atomic number of R?

(ii) In which group of the periodic table is R found?

(iii) Find R in the periodic table.

Give the name of a more reactive element in the same group as R.

(iv) Although R is a very reactive element, it does not react with krypton, the element immediately before it in the periodic table.Suggest a reason for this failure to react.

3. A small piece of sodium is dropped into a large beaker of water.

It reacts to form sodium hydroxide solution and a gas.

(a) Describe three things you would see in this experiment.

(b) Give the name of the gas formed by this reaction.

(c) Sodium hydroxide solution has a pH of 14.

Complete the sentence using a word from the box.

Sodium hydroxide solution is …………………. ……………..

(d) The reaction between sodium and water is exothermic.

How would the temperature of the water change during the reaction?

(c) The experiment was repeated with a piece of potassium of the same size.

Give two observations that would be different in this experiment.

4. Part of the periodic table is shown.

The letters used are not the symbols of the elements.

Each letter may be used once, more than once, or not at all.

(iii) a solid at room temperature

(v) a gas at room temperature

7. (a) Noble gases are used in advertising signs and in light bulbs.

(i) Name a noble gas used in one of these ways.

(ii) Explain why it is chosen for this use.

(b) The table gives the boiling points of the noble gases.

(ii) Using the data, calculate the relative atomic mass of neon.

(iii) Explain why the noble gases are unreactive.

8.0.0. Structure and Bonding

Ionic (Electrovalent) Bonding

Noble gases like neon or argon have eight electrons in their outer shells (or two in the case of helium).

These noble gas structures are thought of as being in some way a "desirable" thing for an atom to have.

When other atoms react, they try to organise electrons such that their outer shells are either completely full or completely empty.

Chemical reactions occur so that atoms attain inert gas configuration by either losing valency electrons as in the case of metals, or gaining electrons as in the case of non metals.

Ionic bonding in sodium chloride

Sodium (2,8,1) has 1 electron more than a stable noble gas structure (2,8). If it gave away that electron it would become more stable.

Chlorine (2,8,7) has 1 electron short of a stable noble gas structure (2,8,8).

If it could gain an electron from somewhere it too would become more stable.

If a sodium atom gives an electron to a chlorine atom, both become more stable.

Because it has one more proton than electron, it has a charge of 1+.

If electrons are lost from an atom, positive ions are formed.

Positive ions are sometimes called cations because they move to the cathode during electrolysis.

The chlorine has gained an electron, so it now has one more electron than proton.

It therefore has a charge of 1-.

If electrons are gained by an atom, negative ions are formed.

A negative ion is sometimes called an anion since it drifts to the anode during electrolysis.

The nature of ionic bond

The sodium ions and chloride ions are held together by the strong electrostatic attractions between the positive and negative charges.

You need one sodium atom to provide the extra electron for one chlorine atom, so they combine together 1:1. The formula is therefore NaCl.

The ionic bonding is stronger than in sodium chloride because this time you have 2+ ions attracting 2- ions.

The greater the charge, the greater the attractive force. The formula of magnesium oxide is MgO.

• Electrons are transferred from one atom to another resulting in the formation of positive and negative ions.

• The electrostatic attractions between the positive and negative ions hold the compound together.

Properties of ionic compounds

Covalent Bonding - Single Bonds

As well as achieving noble gas structures by transferring electrons from one atom to another as in ionic bonding, it is also possible for atoms to reach these stable structures by sharing electrons to give covalent bonds.

Depending on the number of electron pairs shared between atoms which participate in bonding, covalent bonds are classified as follows:

For example, two chlorine atoms could both achieve stable structures by sharing their single unpaired electron as in the diagram.

The fact that one chlorine has been drawn with electrons marked as crosses and the other as dots is simply to show where all the electrons come from. In reality there is no difference between them.

The reason that the two chlorine atoms stick together is that the shared pair of electrons is attracted to the nucleus of both chlorine atoms.

Hydrogen atoms only need two electrons in their outer level to reach the noble gas structure of helium.

Oxygen atom has six electrons in the outer shell, while each of the two hydrogen atoms has one each.

After bonding, oxygen has 8 electrons while each hydrogen atom has two as shown by the molecule.

Each nitrogen atom has five electrons in the outer shell. Each needs 3 electrons to complete the outer shell.

In the formation of the molecule, each nitrogen atom contributes three electrons and a triple bond is formed

Each oxygen atom has six electrons in the outer shell. Each atom donates two electrons for sharing.

After the covalent double bond is formed, each atom has 8 electrons around it as shown.

1) Covalent compounds consist of molecules and not ions. The molecules do not have any electric charge on them. The molecules are held together by weak forces called Van der Waal's forces.

2) Covalent compounds are gases, volatile liquids or soft solids. As there are weak, Van der Waal's forces between the molecules, they are not held in rigid position.

The state depends on the bond energy. If the bond energy is very low, they stay as gases, if it is appreciable they are volatile liquids. If very high, they exist as soft solids.

3) Covalent compounds generally have low melting and boiling points.

As Van der Waal's forces are weak, a very small amount of energy is required to break the bond between the molecules corresponding to low melting point and boiling point.

4) Covalent compounds dissolve in organic solvents. As they do not contain ions, solvation does not take place when water is added to the compound. Hence they do not dissolve in water.

5) Covalent compounds are bad conductors of electricity.

They do not contain ions in the fused state, nor do ions migrate on application of an electric potential. Hence, there is no conduction of current.

6) Covalent compounds are less dense when compared to water.

Very weak Van der Waal's forces hold the molecules together, hence there are large inter molecular spaces.

Consequently less number of molecules per unit volume, which means mass per unit volume is also less. Hence they have a low density.

Giant Covalent Structures

The giant covalent structure of diamond Carbon has an electronic arrangement of 2, 4.

In diamond, each carbon shares electrons with four other carbon atoms - forming four single bonds.

In the diagram some carbon atoms only seem to be forming two bonds (or even one bond), but that's not really the case. We are only showing a small bit of the whole structure.

It is not a molecule, because the number of atoms joined up in a real diamond is completely variable - depending on the size of the crystal.

The physical properties of diamond

• Has a very high melting point (almost 4000°C).

Very strong carbon-carbon covalent bonds have to be broken throughout the structure before melting occurs.

This is again due to the need to break very strong covalent bonds operating in 3-dimensions.

• Doesn’t conduct electricity.

All the electrons are held tightly between the atoms, and aren't free to move.

• Is insoluble in water and organic solvents.

There are no possible attractions which could occur between solvent molecules and carbon atoms which could outweigh the attractions between the covalently bound carbon atoms.

The giant covalent structure of graphite

Graphite has a layer structure which is quite difficult to draw convincingly in three dimensions.

The diagram below shows the arrangement of the atoms in each layer, and the way the layers are spaced.

Each carbon atom uses three of its electrons to form simple bonds to its three close neighbours.

That leaves a fourth electron in the bonding level.

These "spare" electrons in each carbon atom become delocalised over the whole of the sheet of atoms in one layer.

They are no longer associated directly with any particular atom or pair of atoms, but are free to wander throughout the whole sheet.

The important thing is that the delocalised electrons are free to move anywhere within the sheet - each electron is no longer fixed to a particular carbon atom.

There is, however, no direct contact between the delocalised electrons in one sheet and those in the neighbouring sheets.

The atoms within a sheet are held together by strong covalent bonds - stronger, in fact, than in diamond because of the additional bonding caused by the delocalised electrons.

So what holds the sheets together?

In graphite you have the ultimate example of van der Waals dispersion forces.

As the delocalised electrons move around in the sheet, very large temporary dipoles can be set up which will induce opposite dipoles in the sheets above and below - and so on throughout the whole graphite crystal.

The physical properties of graphite

• Has a high melting point, similar to that of diamond. In order to melt graphite, it isn't enough to loosen one sheet from another.

You have to break the covalent bonding throughout the whole structure.

• Has a soft, slippery feel, and is used in pencils and as a dry lubricant for things like locks.

You can think of graphite rather like a pack of cards - each card is strong, but the cards will slide over each other, or even fall off the pack altogether.

When you use a pencil, sheets are rubbed off and stick to the paper.

• Has a lower density than diamond. This is because of the relatively large amount of space that is "wasted" between the sheets.

• Is insoluble in water and organic solvents - for the same reason that diamond is insoluble.

Attractions between solvent molecules and carbon atoms will never be strong enough to overcome the strong covalent bonds in graphite.

• Conducts electricity. The delocalised electrons are free to move throughout the sheets. If a piece of graphite is connected into a circuit, electrons can fall off one end of the sheet and be replaced with new ones at the other end.

The structure of silicon dioxide, SiO2

Silicon dioxide is also known as silicon (IV) oxide.

The giant covalent structure of silicon dioxide

There are three different crystal forms of silicon dioxide. The easiest one to remember and draw is based on the diamond structure.

Crystalline silicon has the same structure as diamond.

To turn it into silicon dioxide, all you need to do is to modify the silicon structure by including some oxygen atoms.

The physical properties of silicon dioxide

• Has a high melting point - varying depending on what the particular structure is (remember that the structure given is only one of three possible structures), but around 1700°C.

Very strong silicon-oxygen covalent bonds have to be broken throughout the structure before melting occurs.

• Is hard. This is due to the need to break the very strong covalent bonds.

• Doesn’t conduct electricity. There aren't any delocalised electrons. All the electrons are held tightly between the atoms, and aren't free to move.

• Is insoluble in water and organic solvents.

There are no possible attractions which could occur between solvent molecules and the silicon or oxygen atoms which could overcome the covalent bonds in the giant structure.

i) Quartz glass is used for manufacturing optical instruments.

ii) Colored quartz is used for manufacturing gems.

iii) Sand is used in manufacture of glass, porcelain, sand paper and mortar etc.

iv) Sand stone is used as a building material.

Co-ordinate (Dative Covalent) Bonding

Co-ordinate (dative covalent) bonding

A covalent bond is formed by two atoms sharing a pair of electrons.

The atoms are held together because the electron pair is attracted by both of the nuclei.

In the formation of a simple covalent bond, each atom supplies one electron to the bond - but that doesn't have to be the case.

A co-ordinate bond (also called a dative covalent bond) is a covalent bond (a shared pair of electrons) in which both electrons come from the same atom.

The reaction between ammonia and hydrogen chloride

If these colourless gases are allowed to mix, a thick white smoke of solid ammonium chloride is formed. Ammonium ions, NH4 + , are formed by the transfer of a hydrogen ion from the hydrogen chloride to the lone pair of electrons on the ammonia molecule.

The hydrogen's electron is left behind on the chlorine to form a negative chloride ion.

Once the ammonium ion has been formed it is impossible to tell any difference between the dative covalent and the ordinary covalent bonds.

Although the electrons are shown differently in the diagram, there is no difference between them in reality.

Intermolecular Bonding - Van Der Waals Forces

Intermolecular attractions are attractions between one molecule and a neighbouring molecule.

The forces of attraction which hold an individual molecule together (for example, the covalent bonds) are known as intramolecular attractions.

All molecules experience intermolecular attractions, although in some cases those attractions are very weak.

Even in a gas like hydrogen, H2, if you slow the molecules down by cooling the gas, the attractions are large enough for the molecules to stick together eventually to form a liquid and then a solid.

Helium's intermolecular attractions are even weaker - the molecules won't stick together to form a liquid until the temperature drops to (-269°C).

Polar molecules, such as water molecules, have a weak, partial negative charge at one region of the molecule (the oxygen atom in water) and a partial positive charge elsewhere (the hydrogen atoms in water).

The force of attraction, shown here as a dotted line, is called a hydrogen bond. Each water molecule is hydrogen bonded to four others.

The hydrogen bonds that form between water molecules account for some of the essential — and unique — properties of water.

• The attraction created by hydrogen bonds keeps water liquid over a wider range of temperature than is found for any other molecule its size.

• The energy required to break multiple hydrogen bonds causes water to have a high heat of vaporization that is a large amount of energy is needed to convert liquid water, where the molecules are attracted through their hydrogen bonds, to water vapor, where they are not.

Liquid Water and Hydrogen Bonding

Why water is a liquid?

In many ways, water is a miracle liquid. Since the hydrogen and oxygen atoms in the molecule carry opposite (though partial) charges, nearby water molecules are attracted to each other like tiny little magnets.

Hydrogen bonding makes water molecules "stick" together.

This makes water have high melting and boiling points compared to other covalent compounds such as ammonia (NH3) which have similar molecular mass but are gases

Ice and Hydrogen Bonding

The structure that forms in the solid ice crystal actually has large holes in it.

Therefore, in a given volume of ice, there are fewer water molecules than in the same volume of liquid water.

In other words, ice is less dense than liquid water and will float on the surface of the liquid.

As we just discussed, neighboring water molecules are attracted to one another.

Molecules at the surface of liquid water have fewer neighbors and, as a result, have a greater attraction to the few water molecules that are nearby.

This enhanced attraction is called surface tension.

It makes the surface of the liquid slightly more difficult to break through than the interior.

The partial charge that develops across the water molecule helps make it an excellent solvent.

Water dissolves many substances by surrounding charged particles and "pulling" them into solution.

For example, common table salt, sodium chloride, is an ionic substance that contains alternating sodium and chlorine ions.

When table salt is added to water, the partial charges on the water molecule are attracted to the Na+ and Cl- ions.

Ethanol, CH3CH2-O-H, and methoxymethane, CH3-O-CH3, both have the same molecular formula, C2H6O.

They have the same number of electrons, and a similar length to the molecule.

The van der Waals attractions (both dispersion forces and dipole-dipole attractions) in each will be much the same.

However, ethanol has a hydrogen atom attached directly to oxygen - and that oxygen still has exactly the same two lone pairs as in a water molecule.

Hydrogen bonding can occur between ethanol molecules, although not as effectively as in water.

The hydrogen bonding is limited by the fact that there is only one hydrogen in each ethanol molecule with sufficient + charge.

In methoxymethane, the lone pairs on the oxygen are still there, but the hydrogens aren't sufficiently + for hydrogen bonds to form.

Except in some rather unusual cases, the hydrogen atom has to be attached directly to the very electronegative element for hydrogen bonding to occur.

The boiling points of ethanol and methoxymethane show the dramatic effect that the hydrogen bonding has on the stickiness of the ethanol molecules:

ethanol (with hydrogen bonding) 78.5°C methoxymethane (without hydrogen bonding) -24.8°C The hydrogen bonding in the ethanol has lifted its boiling point about 100°C.

It is important to realise that hydrogen bonding exists in addition to van der Waals attractions.

For example, all the following molecules contain the same number of electrons, and the first two are much the same length.

The higher boiling point of the butan-1-ol is due to the additional hydrogen bonding.

Metal atoms have relatively few electrons in their outer shells. When they are packed together, each metal atom loses its outer electrons into a ‘sea’ of free electrons (or mobile electrons).

Having lost electrons, the atoms are no longer electrically neutral.

They become positive ions because they have lost electrons but the number of protons in the nucleus has remained unchanged.

Therefore the structure of a metal is made up of positive ions packed together.

These ions are surrounded by electrons, which can move freely between the ions.

These free electrons are delocalized (not restricted to orbiting one positive ion) and form a kind of electrostatic ‘glue’ holding the structure together.

In an electrical circuit, metals can conduct electricity because the mobile electrons can move through the structure carrying charge.

His type of bonding (called metallic boding) is present in alloys as well. Alloys, for example solder and brass, will conduct electricity.

This strong bonding generally results in dense, strong materials with high melting and boiling points.

Usually a relatively large amount of energy is needed to melt or boil metals.

a. Metals are good conductors of electricity because these 'free' electrons carry the charge of an electric current when a potential difference (voltage!) is applied across a piece of metal.

b. Metals are also good conductors of heat. This is also due to the free moving electrons.

Non-metallic solids conduct heat energy by hotter more strongly vibrating atoms, knocking against cooler less strongly vibrating atoms to pass the particle kinetic energy on.

In metals, as well as this effect, the 'hot' high kinetic energy electrons move around freely to transfer the particle kinetic energy more efficiently to 'cooler' atoms.

c. Typical metals also have a silvery surface but remember this may be easily tarnished by corrosive oxidation in air and water.

d. Unlike ionic solids, metals are very malleable, they can be readily bent, pressed or hammered into shape.

1. The table shows some properties of diamond and graphite.

colorless, transparent crystals black shiny solid

hardest natural substance known flakes easily

non-conductor of electricity conductor of electricity

(a) Why might you expect diamond and graphite to have the same properties?

(b) Explain why diamond and graphite do not have the same properties.

(c) Explain why diamond does not conduct electricity but graphite does.

(d) Write a balanced equation, including state symbols, for the reaction which occurs when graphite burns in excess air.

2. Carbon dioxide, CO2, and silicon dioxide, SiO2, both occur widely in nature.

They also have some similar physical properties for example both are electrical insulators.

(a) (i) In what way are the electron arrangements of a carbon atom and a silicon atom the same?

(ii) Suggest why carbon dioxide and silicon dioxide have some similar properties.

(b) (i) Suggest the type of bonding present in carbon dioxide and silicon dioxide. Give a reason for your answer.

(ii) Suggest the type of structure present in silicon dioxide.

. Give a reason for your answer.

(iii) Describe the structure of solid carbon dioxide.

3. A hydrogen chloride molecule, HCl, is covalent.

(a) (i) Draw a dot and cross diagram of one molecule of hydrogen chloride.

Show the outer electrons only.

(ii) Explain why liquid hydrogen chloride has a low boiling point.

(b) When dissolved in water, hydrogen chloride forms hydrogen ions (H+) and chloride ions (Cl–).

(i) Draw a diagram of a chloride ion, showing the outer electrons only.

(ii) Electrolysis of this solution produces hydrogen.

Write the equation showing the formation of hydrogen from hydrogen ions.

4. The formula for a molecule of water is H2O.

(a) How many atoms are there in one molecule of water?

(b) Draw a dot and cross diagram to show the arrangement of outer shell electrons in one molecule of water. What type of bond is present in water molecules?

5. (a) The dot and cross diagrams show how a sodium atom bonds with a chlorine atom to form sodium chloride.

Compounds with ionic bonding usually have high melting points.

(i) What do the dots and crosses in the diagrams represent?

(ii) What is the name of the negative ion present in sodium chloride?

(iii) What does the high melting point of sodium chloride suggest about the strength of the ionic bonds in sodium chloride?

(b) Two chlorine atoms can bond together as shown in the diagram below.

Describe how a covalent bond is formed between two chlorine atoms.

(c) Hydrogen bonds with chlorine to form the compound hydrogen chloride, HCl.

(i) Suggest the type of bonding present in hydrogen chloride.

Give a reason for your answer.

(ii) The relative atomic mass of hydrogen is 1.0.

Use the periodic table to find the relative atomic mass of chlorine.

General Preparation of Salts

Salts are generally ionic compounds formed by the reaction of an acid with a base.

The preparation of these salts involves the treating of different metals and non-metals and their compounds with various acids, bases etc.

However, some of them can be prepared by direct combination of the concerned elements or also by indirect routes.

Precipitation is the reaction in which a solid is formed by the action between two or more fluids, e.g., calcium carbonate is precipitated when carbon dioxide is passed through limewater.

1. (a) A solution of zinc chloride can be prepared by adding excess zinc carbonate to dilute hydrochloric acid.

At the end of the reaction, the remaining zinc carbonate is removed by filtration.

(i) Explain why excess zinc carbonate is used.

(ii) State ONE other zinc compound which reacts with dilute hydrochloric acid to form zinc chloride solution.

(b) Silver chloride can be made by reacting silver nitrate solution with hydrochloric acid.

(i) Write the ionic equation, including state symbols, for this reaction.

(ii) Explain why pure silver chloride could NOT be made by adding silver carbonate to hydrochloric acid.

3. Two students made the insoluble salt, lead sulphate, and wrote these notes about the experiment.

‘We took 25 cm 3 of lead nitrate solution and slowly added 25cm3 of acid to it.

The mixture turned cloudy white. We stirred the mixture and filtered it to obtain the solid lead sulphate.’

(a) Describe one safety precaution which the students should take during this experiment.

(b) (i) Which acid was added to lead nitrate solution to make lead sulphate?

(ii) Draw, and name, the piece of apparatus that should be used to measure 25 cm 3 of the acid.

3. Lead chloride can be prepared from dilute hydrochloric acid and lead nitrate solution.

The steps to be used are listed below.

They are not in the correct order.

B Measure out 25 cm3 dilute hydrochloric acid and 25 cm 3 lead nitrate solution.

C Wash the lead chloride with distilled water.

D Mix the dilute hydrochloric acid with lead nitrate solution.

(a) Put the steps in the correct order, using the letters, A, B, C, D and E.

(b) (i) What can be used to measure 25 cm 3 of dilute hydrochloric acid?

(ii) What safety precaution should be taken when measuring out the acid?

(c) When dilute hydrochloric acid is mixed with lead nitrate solution, lead chloride forms.

The lead chloride forms as a solid because it does not dissolve in water.

What is the general name for any solid formed by mixing solutions?

(d) Name two pieces of apparatus required to filter the mixture.

(e) How can the wet solid lead chloride be dried?

4. Table salt contains sodium chloride. ‘Lo-salt’ is an alternative to table salt. It contains potassium chloride.

(a) (i) What element is found in both sodium chloride and potassium chloride?

(ii) Give the symbol for an atom of this element.

(b) (i) In which group of the periodic table is sodium found?

(ii) In which group of the periodic table is potassium found?

(iii) Why would you expect sodium chloride and potassium chloride to have similar properties?

(c) Potassium chloride is soluble in water.

What do you see when a small amount of solid potassium chloride is stirred in a large volume of water?

10.0.0 Effect of an Electric Current on Substances

In any chemical reaction, the existing chemical bonds are broken and new chemical bonds are formed.

Hence, all chemical reactions are fundamentally electrical in nature since electrons are involved in some way or the other in all types of chemical bonding.

Many chemical reactions utilize electrical energy, whereas others can be used to produce electrical energy.

As electrical energy involves the flow of electrons, these reactions are concerned with the transfer of electrons from one substance to the other.

Conductors and insulators

The ability to conduct electricity is the major simple distinction between elements that are metals and non-metals.

A conductor is a material that conducts electricity but is not chemically changed in the process.

All metals and graphite are conductors of electricity.

An insulator is a material that does not conduct electricity. Such materials have no free electrons.

Summary of Common Electrical Conductors

These materials carry an electric current via freely moving electrically charged particles, when a potential difference (voltage) is applied across them, and they include:

1) All metals (molten or solid) and the non-metal carbon (graphite).

This conduction involves the movement of free or delocalised electrons (e- charged particles) and does not involve any chemical change.

2) Any molten or dissolved material in which the liquid contains free moving ions is called the electrolyte.

Ions are charged particles e.g. Na + sodium ion, or Cl - chloride ion, and their movement or flow constitutes an electric current, because a current is moving charged particles.

The movement of opposite charges during electrolysis is due to the attracting in the electric field produced by the potential difference (the voltage).

Liquids that conduct must contain freely moving ions to carry the current and complete the circuit.

You can't do electrolysis with an ionic solid! The ions are too tightly held by chemical bonds and can't flow from their ordered situation! When ionically bonded substances are melted or dissolved in water the ions are free to move about.

However some covalent substances dissolve in water and form ions. e.g. hydrogen chloride HCl, dissolves in water to form 'ionic' hydrochloric acid H+Cl-(aq).

Electrolytes and Non-electrolytes

However, if the compound is unable to ionise it does not conduct electricity it is called a non-electrolyte.

In general, the extent to which an electrolyte can break up into ions categorises an electrolyte.

This gives a measure of the degree of dissociation (a) of an electrolyte.

Based on this degree the electrolytes can be classified as strong or weak electrolyte and non-electrolyte.

A strong electrolyte, such as a solution of sodium chloride dissociates or ionises completely or almost completely to form free mobile ions in the solution or molten form.

The more the availability of free mobile ions in an electrolyte, the greater is its capacity to carry or conduct current i.e. the stronger the electrolyte.

The ability to conduct current can be observed by setting up a cell as shown in figure 4.4.

But the ions are not mobile so it does not conduct electricity and the bulb does not light.

Pure sulphuric acid exists mostly in the form of molecules.

But when mixed with water, it almost completely breaks up into free mobile ions.

A weak electrolyte ionises or dissociates only partially to form free mobile ions.

Most of the electrolyte remains as un-ionised molecules.

For example in acetic acid, the number of its dissociated ions (the acetate and hydrogen ions) is less compared to the total amount of acetic acid molecules present.

Similarly in ammonium hydroxide the number of its dissociated ions (the ammonium and hydroxyl ions) are less compared to the total amount of the molecules present.

When the number of mobile ions is less in an electrolyte, the lesser is its capacity to carry or conduct current i.e. the weaker is the electrolyte.

This is observed by setting up the cell as shown in figure 4.5. The bulb glows less brightly.

A non-electrolyte does not provide ions in a solution and therefore current does not flow through such solution.

The bulb in the given set up does not glow (Fig.4.6).

Some examples of non-electrolytes are: alcohol, carbon tetrachloride, carbon disulphide.

The process of conversion of a neutral atom into charged ions to complete its octet is known as ionization.

In this process, the neutral atom loses or gains electrons.

The particle that loses electrons gains positive charge equal to the number of electrons lost, while the particle that gains electrons gains negative charge equal to the number of electrons gained.

When atoms from metallic elements combine with those from non-metals, they do so by transfer of electrons from one atom to another, forming compounds having "ionic or electrovalent" bonds.

The neutral atom that loses an electron becomes a cation and the neutral atom that acquires an electron becomes an anion.

For e.g., when a sodium atom combines with a chlorine atom to form sodium chloride, the sodium atom loses one electron and becomes positively charged ion.

The chlorine atom gains the electron and it becomes negatively charged ion.

Electrovalent substances are made up of ions in the solid state.

The oppositely charged ions are held together by strong electrostatic force of attraction.

Due to these forces the ions cannot move.

Thus the break up of an electrovalent compound into free mobile ions when dissolved in water or when melted, is called electrolytic dissociation

Theory of Electrolytic Dissociation

The main ideas of the ionic theory or theory of electrolytic dissociation are as follows:

Electrolysis Splits a Compound:

When substances which are made of ions are dissolved in water, or melted material, they can be broken down (decomposed) into simpler substances by passing an electric current through them.

This process is called electrolysis.

Since it requires an 'input' of energy, it is an endothermic process.

They are known as anions because they drift towards the anode.

In the electrolyte (solution or melt of free moving ions), Positive metal or hydrogen ions move to the negative electrode (cations attracted to cathode), e.g. in the diagram, sodium ions Na+, move to the -ve electrode, and negatively charged ions move to the positive electrode (anions attracted to anode), e.g. in the diagram, chloride ions Cl-, move to the +ve electrode.

During electrolysis, gases may be given off, or metals dissolve or are deposited at the electrodes.

In summary, the following substances are electrolytes:

Metallic conductivity:

Electrolytic conductivity:

There are two ion movements in the electrolyte flowing in opposite directions.

Positive cations e.g. Na + attracted to the negative cathode electrode. Negative anions e.g. Cl- attracted to the positive anode electrode.

No electrons flow in the solution.

They only flow in metal wires or carbon (graphite) electrodes of the external circuit.

The molten or dissolved materials (electrolytes) are usually acids, alkalis or salts and their electrical conduction is usually accompanied by chemical changes e.g. decomposition.

Electrolysis can’t be performed with an ionic solid.

This is because the ions are too tightly held by chemical bonds and can't flow.

When ionically bonded substances are melted or dissolved in water, the ions are free to move about.

However some covalent substances dissolve in water and form ions. Hydrogen chloride (HCl) is covalent.

However it dissolves in water to form 'ionic' hydrochloric acid H+Cl-(aq)

Cathode reactions (reduction)

(-) negative cathode where reduction of the attracted positive cations is by electron gain (reduction) to form metal atoms or hydrogen [from Mn+ or H+, n = numerical charge].

The electrons come from the positive anode.

Hydrogen ions are reduced to hydrogen gas molecules.

Electrolysis of many dilute salts or acid solutions make hydrogen gas by reduction as shown.

Copper (II) ions are reduced to copper atoms in the electrolytic purification or electroplating using copper (II) sulphate solution.

Silver ions reduced to silver atoms in silver electroplating

Anode reactions (oxidation)

Positive anode is where the oxidation of the atom or anion is by electron loss. Non-metallic negative anions are attracted and may be oxidised to the free element.

For example, in the electrolysis of molten chloride salts or their concentrated aqueous solution or conc. hydrochloric acid ,chloride ion oxidised to chlorine gas molecules.

2Cl - (l/aq) Cl2(g) + 2e - In the electrolysis of molten oxides eg anode reaction in the extraction of aluminium from molten bauxite, oxide ion oxidised to oxygen gas molecules. 2O2 - (l) O2(g) + 4e- The electrons released by this process travel round the circuit and are donated to the cations (reduction).

Electrolysis of many salt solutions such as sulphates, sulphuric acid etc. gives oxygen.

Hydroxide ions oxidised to oxygen gas molecules.

Factors That Determine Products of Electrolysis

The ions that are successfully released (or discharged) at the electrodes depend on three factors:

1. The position of the ion in the electrochemical series

2. The concentration of the ion in the solution

3. The nature of the electrode

1. The position of the ion in the electrochemical series

This is probably better expressed as the position of the ions in the electrochemical series.

The ions that are lower in the electrochemical series get discharged in preference to the ones above them.

For e.g., if a solution has potassium ions and copper ions, the copper ions will accept electrons, and get discharged as copper atoms first. The potassium ions will not be affected.

When two ions with similar reactivity are in competition then the relative concentration of the two ions becomes an important factor.

If an electrolyte contains a higher concentration of ions, which are higher in the electrochemical series than those that are lower, then these ions get discharged in preference to the lower ones.

For e.g., a solution of sodium chloride in water contains two types of anions i.e., the chloride (Cl-) ions and the hydroxyl (OH-) ions.

Hydroxyl ions are lower in the electrochemical series than chloride ions.

But if the concentration of chloride ions is much higher than that of the hydroxyl ions then the chloride ions get discharged first.

Electrolysis of NaCl Solution at different Concentration

Usually inert electrodes such as graphite or platinum are used for electrolysis.

These electrodes do not interfere with the reactions occurring at the surface of the electrode they simply act as a point of connection between the electrical circuit and the solution.

However, if metal electrodes are used in same metal ion solutions, they can get involved in the reactions by dissolving as ions leaving their electrons behind.

Example: Electrolysis of sodium chloride solution

The ions present in the solution are:

The positive ions are attracted to the negative cathode.

There is competition between the sodium ions and the hydrogen ions.

As the hydrogen ion hydrogen ion is lower in the electrochemical series than the sodium ion sodium, the hydrogen ions are preferentially reduced and hydrogen gas is produced at the electrode (bubbles are seen)

There is competition between the negative ions at the positive anode.

The chloride ions compete with the hydroxide ions to release their electrons to the anode.

If the solution is fairly concentrated the chloride ions preferentially lose electrons to become chlorine atoms (and then molecules).

Ions remaining in solution

The ions that are removed from the solution, then, are the hydrogen ions and the chloride ions.

This means that the sodium ions and the hydroxide ions remain in the solution - i.e. sodium hydroxide is also produced.

Note: When the solution of chloride ions is dilute then OH, ions are preferentially released at the anode.

Electrolysis of dilute sulphuric acid (electrolysis of water)

Water is a poor conductor of electricity.

However, it can be made to decompose if some dilute sulphuric acid is added.

A Hofmann voltammeter below can be used to keep the gases produced separate.

After a while, the volume of gas in each arm can be measured and tested.

Oxygen collects at the anode. The ratio of volumes is about 2:1 for hydrogen and oxygen respectively.

Effectively, this experiment is the electrolysis of water.`

Example: Electrolysis of copper II sulphate solution

The ions present in the solution are:

The positive ions are attracted to the negative cathode.

There is competition between the copper ions and the hydrogen ions.

As the hydrogen ion appears higher in the electrochemical series than the copper ion, copper ions are preferentially reduced and copper metal is deposited at the electrode (pink layer is observed).

There is competition between the negative ions at the anode.

The sulphate ions compete with the hydroxide ions to release their electrons to the anode.

The hydroxide ions are lower in the series and are preferentially released as oxygen gas (bubbles are seen) and water.

Oxidation Is Loss, Reduction Is Gain (of electrons)

Oxidising agents are easily reduced.

Reducing agents are easily oxidized.

Ions remaining in solution

The ions that are removed from the solution, then, are the copper ions and the hydroxide ions, this means that the hydrogen ions and the sulphate ions remain in the solution - i.e.

sulphuric acid is also produced. The solution changes colour from blue to colourless.

Electroplating is a process of depositing a thin layer of a fine and superior metal (like chromium, zinc, nickel, gold etc.)

over the article of a baser and cheaper metal (like iron, copper, brass), with the help of electric current.

Electroplating is very useful because of the following reasons:

Repair of finer machine parts.

The process of electroplating involves the following steps:

The anode dissolves, depositing the metal ions from the solution on the article in the form of a metallic coating.

The passage of low current is continued for a long time to ensure an even coating.

Electrolysis of copper 11 sulphate solution using copper electrodes

The ions present in the solution are:

The positive ions are attracted to the negative cathode. There is competition between the copper ions and the hydrogen ions.

As the hydrogen ions are higher in the electrochemical series, the copper ions are preferentially reduced and copper metal is deposited at the electrode (a pink layer is observed)

In this case the electrode is made of copper and it is easier for the copper to dissolve leaving its electrons behind on the anode than for any other ion to be released.

Ions remaining in solution

Copper is deposited at the cathode and is dissolved at the anode.

Consequently the concentration of copper ions in solution remains constant.

This can be used as a method of purification of copper as only pure copper is deposited at the cathode.

Basic rules for electroplating an object metal M are as follows:

Electrolysis of Lead Bromide.

Lead bromide must be heated until it is molten before it will conduct electricity.

Electrolysis separates the molten ionic compound into its elements.

The reactions at each electrode are called half equations.

The half equations are written so that the same number of electrons take part in each equation.

Pb 2+ + 2e - Pb (lead metal at the (-) cathode).

2Br - Br2 + 2e - (bromine gas at the (+) anode).

Lead ions gain electrons (reduction) to form lead atoms.

Bromide ions lose electrons (oxidation) to form bromine atoms.

The bromine atoms combine to form molecules of bromine gas.

The overall reaction is

Reactive metals (more reactive than hydrogen) are never deposited during electrolysis of aqueous solutions.

If the metal ion comes from a metal more reactive than hydrogen then hydrogen gas is liberated at the cathode.

Halide ions (chloride, bromide, and iodide) are released preferentially and if these are not present then the hydroxide ions from the water are released at the anode.

11.0.0 Carbon and Some of Its Compounds

Carbon occurs in nature in large quantities in coal, petroleum and carbonates, notably in limestone CaCO3.

Charcoal is almost pure carbon, but this form of carbon does not have a well defined crystalline form, and is classed as amorphous carbon. Other forms of amorphous carbon are carbon black and lamp black.

Allotropy is the existence of the same chemical in different physical forms.

Allotropes of carbon with different crystalline forms exist. These are diamond, graphite.

Carbon is a chemical element in the periodic table that has the symbol C and atomic number 6.

It is an abundant nonmetallic, tetravalent element, and has several allotropic forms:

Diamond is the purest form of natural carbon. It occurs as small crystals embedded in rocks.

These are supposed to have been formed by the crystallization of carbon under extreme pressure and temperature in the interior of the earth.

Nowadays, synthetic industrial diamonds are being manufactured by subjecting graphite to very high temperatures and pressures.

Carbon atoms in diamond have tetrahedral structure.

Each atom of carbon is surrounded by four other atoms that together forms the tetrahedral structure, as shown in the figure 10.1.

1. Diamond is the purest form of carbon.

2. It is the densest of all allotropes of carbon.

3. Diamond's tetrahedral structure, makes it the hardest naturally occurring substance. It is brittle and transparent.

4. Pure diamond is colourless.

5. Diamond has very high refractive index. When properly cut and polished, it allows the light to undergo total internal reflection that makes it very brilliant.

6. It is transparent to light and X-rays. This property is used to identify a real diamond from a fake one, e.g., glass can be made to shine as brilliantly as diamond but it is opaque to X-rays.

7. Due to catenation there are no free electrons that can move in the structure of diamond. Hence it is a non-conductor of electricity, but extremely good conductor of heat.

8. It is insoluble in all known solvents.

Chemical Properties of Diamond

1. Diamond is chemically very inert. It does not react with any substance at ordinary temperatures.

2. When heated in oxygen to about 800oC, it completely burns to form carbon dioxide. This shows that diamond is pure form of carbon.

3. When heated in the absence of air to 1500oC, the atoms get rearranged to form graphite.

4. Diamond is affected slowly by molten sodium carbonate, forming carbon monoxide.

5. When heated with concentrated sulphuric acid and potassium dichromate it gets oxidised to carbon dioxide.

1. Diamond is used as a gem (except the black variety) due to its brilliance.

2. Black variety of diamond is use for cutting glass, as drilling bits for industrial drills, for polishing other diamonds etc.

Unlike the tetrahedral arrangement of atoms in diamond, the carbon atoms in graphite are arranged in the form of hexagonal rings in layers (Fig.10.2).

Each carbon is bonded to only three other carbon atoms in that layer.

Different layers of graphite are held together by rather weak forces. Hence they can slide over one another.

This is one reason why graphite scales off easily and can mark impressions on substrates.

Because of this property, it is also used as a lubricant.

1. Graphite is greyish black crystalline substance.

2. It has a soft and greasy texture, but has a metallic luster.

3. The specific gravity of graphite is only 2.2 g cm-3.

4. Due to the presence of a free valence electron, it is a good conductor of electricity.

5. It is also one of the stable forms of carbon.

6. The structure of graphite has hexagonal rings arranged in layers.

Chemical Properties of Graphite

1. Graphite is inactive and inert to almost all chemicals.

2. It does not burn in air, even if heated to high temperature. But if heated in oxygen, it burns completely to form only carbon dioxide.

1. Graphite is used in making the 'lead' of pencils.

2. It is used in the production of refractory crucibles, which can withstand very high temperature.

3. Graphite being a conductor of electricity finds application in making electrodes.

4. It is used in making polishes and paints.

5. Graphite is used as lubricant in machines, which have to be operated at high temperatures.

All such machines cannot be lubricated with oils, grease, etc. as they vaporize immediately at the high temperature.

6. It is used for making electrotypes for printing

7. Graphite is extensively used in nuclear reactors, to absorb neutrons.

This helps in moderating the nuclear reaction.

Apart from diamond and graphite, which are crystalline forms of carbon, all other forms of carbon are amorphous allotropes of carbon.

Coke is the amorphous allotrope of carbon, which is derived from coal.

When coal undergoes destructive distillation, it yields two allotropes of carbon, namely coke and gas carbon.

Destructive distillation is a chemical process, which involves is the breaking up of a complex substance by heating it in the absence of air.

It is a very good fuel and when ignited it burns almost with no smoke.

It is a non-conductor of heat and electricity.

It acts as a good reducing agent and is extensively used in the production of producer gas, water gas and hydrogen.

Sugar charcoal can be obtained by dehydrating cane sugar, either by treating it with concentrated sulphuric acid or by heating it in the absence of air.

It is the purest form of the amorphous variety of carbon.

It is used in the preparation of artificial diamonds.

Wood charcoal is obtained by the destructive distillation of wood. The chief products formed are wood charcoal.

Wood charcoal is black, porous, brittle and soft.

Though denser than water it can float on water, as it contains plenty of air bubbles trapped in the pores.

Wood Charcoal is not a conductor of electricity.

It is prepared by the destructive distillation of bones of animals.

It is porous and can adsorb colouring matter.

It is mostly used in sugar industry to decolourise sugar.

Chemical properties of carbon

1. The combustion of carbon:

Carbon reacts with oxygen to form two oxides, carbon dioxide, CO2, and carbon monoxide CO.

The proportions of these two oxides formed during combustion depend on the conditions.

At about 500 ºC, carbon dioxide is produced almost exclusively, provided that oxygen is in excess:

At higher temperatures, or when the supply of oxygen is restricted, carbon monoxide is the main product.

2. Reaction with acids

Carbon reacts with concentrated sulphuric acid and concentrated nitric acid.

Nitric acid is a powerful oxidizing agent. Both acids oxidize carbon to carbon dioxide gas.

Carbon + sulphuric acid carbon dioxide + sulphur dioxide +water

Carbon + nitric acid carbon dioxide + Nitrogen (IV) oxide + water

3. Reducing action of carbon

When carbon is mixed with iron (III) oxide and heated strongly, pure iron metal is produced.

Carbon monoxide + iron (III) oxide carbon dioxide + iron.

Carbon dioxide is easily prepared by the action of dilute hydrochloric acids on metal carbonates (normally calcium carbonate or marble).

Vigorous effervescence occurs as bubbles of carbon dioxide are liberated.

Since carbon dioxide is 1.53 times as heavy as air, it usually collected by upward displacement of air.

In this case, it is collected by downward displacement of water.

Properties of carbon (IV) oxide

Carbon dioxide is a colourless gas with a faint pungent smell.

It does not burn or support combustion, except in extreme cases, and is not poisonous (it is the gas in fizzy cool drinks).

It can however cause death by suffocation, when it is present in sufficient concentrations.

Carbon dioxide is a linear molecule. The gas condenses to a liquid at 0 ºC under a pressure of 35 atm.

At normal pressure, carbon dioxide condenses directly to a solid at -78.5 ºC.

This solid, known as dry ice, is widely used as cooling agent.

Solid carbon dioxide does not melt under conditions of normal atmospheric pressure, but passes directly into the gas phase, a process known as sublimation.

When carbon dioxide is dissolved in water, carbonic acid, H2CO3, is produced in small quantities:

CO2 (g) + H2O (l) H2CO3 (aq) Carbonic acid is a weak diprotic acid which gives rise to salts known as carbonates, which contain the carbonate anion CO3 2- .

2. Reaction with limewater

Limewater is a clear colourless solution of calcium hydroxide (slaked lime).

Calcium carbonate is precipitated when carbon dioxide is passed through a clear solution of calcium hydroxide in water.

The lime water turns milky serving as a test for carbon dioxide liberation.

Carbon dioxide is slightly acidic. It turns blue litmus paper red.

During rainy season, blue litmus paper kept open in the laboratory slowly turns red, due to the presence of carbon dioxide in air.

Carbon dioxide is neither combustible, not a supporter of combustion.

A burning splinter or a burning candle gets put off, but metals like potassium, sodium, magnesium etc. continue to burn in carbon dioxide.

Ignite a ribbon of magnesium, and introduce it in the jar of carbon dioxide. The magnesium ribbon continues to burn in carbon dioxide.

Deposits of carbon can be seen on the inner sides of the jar.

7. Action on heated carbon

When carbon dioxide is passed over red-hot carbon in the form of coke charcoal, the carbon dioxide loses one of its two atoms of oxygen.

As a result, carbon dioxide gets reduced and becomes carbon monoxide. At the same time the hot carbon also gets converted to carbon monoxide.

a) Carbon dioxide is used in photosynthesis by green plants to produce carbohydrates.

b) To induce natural breathing.

2. To extinguish fires

Soda-acid fire extinguishers produce carbon dioxide to put out fires.

Solid carbon dioxide called "Dry ice" can provide temperatures as low as -109.3o F.

It is superior to ordinary ice, for the following reasons:

i) It provides much lower temperature than ice.

iv) It does not wet the food being chilled, as it sublimes directly into gaseous state.

4. Manufacture of fertilizer

Carbon dioxide is used extensively in the manufacture of urea, an important in nitrogenous fertilizer.

5 In the baking industry

Baking powder is used in all the food preparations. The addition of baking powder during baking produces carbon dioxide which makes the dough "rise".

The small pores in a loaf of bread are the spaces in which carbon dioxide was formed .

It produces carbon dioxide by anaerobic respiration.

Baking powder contains starch, sodium hydrogen carbonate and an acid forming ingredient, such as tartaric acid of calcium hydrogen phosphate [Ca(H2PO4)2] or alum [Na2SO4.Al2(SO4)3.24 H2O].

A mixture of 97% oxygen and 3% carbon dioxide, called carbogen is used to revive persons affected by carbon monoxide poisoning, pneumonia, asphyxiation etc.

7. Manufacture of aerated drinks

Carbon dioxide is extensively used in aerated drinks.

Increasing the pressure increases the solubility of the gas.

The fizz in the drink is due to carbon dioxide being liberated when the pressure is reduced.

It is use to fill silos (storage bins) and containers, that are used for storing food grains.

After the silos are packed with the food grains, carbon dioxide is pumped into the silos from the top.

The gas being heavier then air, slowly sinks down, pushing out the air in between the grains.

This prevents the growth of bacteria, fungus, etc. on the grains.

Dry ice is used to create artificial clouds as special effects, for stage shows, films, discotheques etc.

Dry ice is dropped into water absorbing heat from the water, the solid carbon dioxide sublimes, carrying with it a lot of water vapor.

These two together form thick white 'clouds'.

But unlike real clouds, which are formed above due to the low vapor density of water vapor, the artificial cloud fills the floor of the stage, as the vapor density of carbon dioxide is 22.

So while the lower part of the body of the artist is covered by 'cloud', the upper half is visible.

Carbon (II) oxide (Carbon monoxide):

Carbon monoxide is an odourless, tasteless and colourless gas, which is insoluble in water.

It is extremely poisonous.

Under no circumstances must the gas be inhaled or smelled.

It is not usually prepared in a school laboratory.

If need be, the gas should be prepared in a fume chamber.

Preparation of carbon monoxide

1.By dehydrating oxalic acid with hot concentrated sulphuric acid

Carbon monoxide is prepared with the help of oxalic acid and concentrated sulphuric acid as shown below.

The product left behind due to this reaction, is a molecule of carbon dioxide and a molecule of carbon monoxide.

The carbon dioxide can be removed by passing it through a concentrated solution of potassium hydroxide.

2. Preparation of carbon monoxide by dehydrating formic acid

Formic acid has the formula HCOOH. Formic acid can also be dehydrated in a similar way by hot concentrated sulphuric acid.

Sulphuric acid removes two atoms of hydrogen and one atom of oxygen as a molecule of water from it, and leaves behind one molecule of carbon monoxide.

For this reason, it is found in the exhaust gases of motor vehicles, as well as in cigarette smoke. Indoor fireplaces can be a serious hazard if ventilation is poor.

Industrial preparation

It is prepared industrially (mixed with hydrogen) by passing steam over coke at temperatures above 900 ºC. The resulting gas mixture is known as water gas, and it is used as a fuel:

Carbon monoxide is a neutral oxide. It is neither acidic nor basic.

It is very stable and cannot be decomposed by heat.

It is a combustible gas. It burns well in air or oxygen to form carbon dioxide. The formation of carbon dioxide is tested by passing it through a solution of lime water.

Carbon monoxide is a powerful reducing agent.

When CO is passed over heated metallic oxides, it takes away the oxygen to form carbon dioxide and reduces the oxides to their respective metals.

Popularly known as washing soda or soda ash, sodium carbonate is a commercially important compound.

In earlier days, it was obtained from the ash of plants and from natural deposits in India and Egypt.

Manufacture of Sodium Carbonate

The first step in the manufacture of sodium carbonate is to generate carbon dioxide. This can be got by heating limestone.

Saturation of Brine With Ammonia

Brine solution is pumped into the ammonia absorber.

From the ammonia recovery tower, ammonia mixed with a little carbon dioxide enters the absorber and saturates brine.

Impurities of calcium and magnesium present in brine are precipitated as carbonates.

These impurities can be removed by pumping the liquid through the filter press and then passed through cooling pipes.

Ammoniacal brine next enters the carbonating tower from the top.

This tower is partitioned using horizontal plates that have a central hole and covered with a perforated plate.

The ammoniated brine meets the rising stream of carbon dioxide to form crystals of sodium bicarbonate and ammonium chloride, which remains in the solution.

The viscous milky liquid from the carbonating tower is filtered using a rotary vacuum filter.

The solid sodium bicarbonate left on the filter cloth can be periodically scrapped.

The filtrate is pumped to the top of the ammonia recovery tower.

Sodium bicarbonate is then heated strongly to form anhydrous sodium carbonate or soda ash.

To get washing soda (Na2CO3.10H2O) from soda ash, anhydrous sodium carbonate is dissolved in water and recrystallized.

NaO 2 CO 3 + 10H 2 O -> NaO 2 CO 3 .10H 2 O

The calcium oxide or quick lime formed in the lime kiln is changed to slaked lime [Ca(OH)2] and pumped into the ammonia recovery tower.

This then reacts with the filtrate from step 3 (filtration) to regenerate ammonia.

Properties of Washing Soda

Efflorescence is the loss of water of crystallization from a hydrated salt, when exposed to air.

The cyclic changes that carbon undergoes in nature is referred to as the Carbon cycle.

Carbon in the form of carbon dioxide gets added to the air and gets removed from the air constantly.

This addition and subtraction is so well balanced that the percentage of carbon dioxide remains remarkable steady at 0.03 to 0.04

1. By the respiration of living organisms.

2. By the combustion of carbon present in carbon compounds, such as wood, coal, coke, petroleum oil, vegetable oil, alcohol etc.

3. By the decay of organic matter, like the dead bodies of animals and plants.

4. From chemical industry such as, heating of limestone, fermentation of molasses to form alcohol, in beer and wine making processes etc.

Removal of carbon dioxide from air

Green plants take in carbon dioxide to synthesize carbohydrates.

The carbohydrates formed are consumed by animals, digested, absorbed and used in respiration.

During respiration, the carbohydrate is oxidised to carbon dioxide, which is released into the air.

Carbon dioxide of the air dissolves in water, forming a very dilute solution of carbonic acid.

This reaction is an unstable one and depends upon water temperature.

If water gets warmer, some of the dissolved carbon dioxide gets released into the air.

(b) (i) (0.75 × 37) + (0.25 × 35) = 35.5

4. (a) negligible/(approximately) [not zero]

It has a smaller radius, so the attraction of the electrons to the nucleus is stronger.

It has fewer shells so less screening of the outer electrons from the nucleus, stronger attraction to the nucleus.

1. (a) An explanation to include two from:

1. all the elements react with sodium in the same way (to form similar compounds)

2. form similar coloured halides / compounds with silver

3. all silver halides / compounds insoluble in water

4. all silver halides affected by light

(iv) noble gas unreactive element

3. (a) A description to include three from:

plus 1 communication mark for presenting relevant information in a form that suits its purpose

(ii) glows with colour / inert

(b) Boiling point increases as the atomic number increases

(c) (i) (atoms of same element with) different number of neutrons

(ii) A calculation to include:

(iii)An explanation to include:

1. full / complete outer shell

2. atoms do not share / lose / gain electrons

1. (a) both (forms of) carbon/giant covalent

(b) An explanation to include:

[Accept appropriate relevant statements for 1 mark each]

(c) An explanation to include two from: diamond

1. all electrons involved in bonding/four bonds per atom

2. no delocalised/spare electrons graphite

2. delocalized/spare electrons

[To gain the second mark, electrons must be mentioned]

2. (a) (i) 4 electrons/same number of electrons in outer shell

(ii) A suggestion to include:

• carbon and silicon both in group 4/same group/same number of electrons in outer shell

• compounds of elements in same group have similar properties

• stated property is similar

Reason - between non-metallic elements/both electrical

insulators/unlikely to gain/lose four electrons

(ii) Structure - giant/(lattice) structure

Reason - high melting point

(iii) A description to include:

• in regular pattern/lattice

[Deduct 1 mark for incorrect inner electrons]

(ii) weak forces between molecules

[No mark if incorrect inner electrons]

[Allow H + + e- -> H for 1 mark]

(b) one electron on each hydrogen atom

six outer electrons on oxygen atom

(ii) shared pair identified

(b) shared (pair of) electrons

reject other particles for second mark

(between) non-metal (atoms) [Must clearly imply both]

1. (a) (i) to neutralise all the acid

(b) (i) Ag + (aq) + Cl - (aq)  AgCl(s)

(ii) An explanation to include:

1. silver chloride insoluble

2. no reaction/silver carbonate insoluble in acid

2. (a) Either use safety glasses/wear apron/tie back hair

or avoid contact with lead compounds/acid

(ii) diagram of measuring cylinder/pipette/burette

(b) (i) measuring cylinder/burette/pipette

(e) put in warm place e.g. oven, radiator etc

(iii) both (compounds of) group 1 / alkali metals / (metals) in same group

(c) solid disappears / dissolves / (colourless) solution formed

KCSE Revision Notes Form 1 - Form 4 All Subjects

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2: Basic Cell Chemistry - Chemical Compounds and their Interactions - Biology


This lesson will introduce you the student to basic chemistry principles. An understanding of this basic information will allow you to learn the more advanced topics in your course lectures.

This lesson focuses on a number of areas related to basic Chemistry. You should review each page in order as they build upon one another. Many of these topics will be review. Others may be new to you. Either way you will learn the fundamentals of chemistry needed in this course.

Atoms are the basic unit of chemistry. They consist of 3 smaller things:

  • Protons - these are positively charged (+)
  • Electrons - these are negatively charged (-)
  • Neutrons - these have no charge

These 3 smaller particles are arranged in a particular way. In the center is the Nucleus where you find the positive Protons and neutral Neutrons.

In orbit around the nucleus are the Electrons. These are found in a series of orbits (depending on the atom) with differing numbers of electrons as seen below.

Interaction of Atoms

It's the electrons in orbit around the nucleus that allow one atom to interact with other atoms so they can be linked together.

For example, H2O consists of an Oxygen atom linked to 2 Hydrogen atoms. The linkage or interaction between the electrons of the Hydrogen and Oxygen atoms is called a Chemical Bond. More on these later.

Atoms in the Human Body

The human body is made up of a couple dollars worth of chemicals.

The 12 most useful atoms for you to know about are listed below:

Sometimes atoms gain or lose electrons. The atom then loses or gains a "negative" charge. These atoms are then called ions.

  • Positive Ion - Occurs when an atom loses an electron (negative charge) it has more protons than electrons.
  • Negative Ion - Occurs when an atom gains an electron (negative charge) it will have more electrons than protons.

The following image shows Na losing an electron and Cl gaining an electron


Abstract

Dynamin is required for clathrin-mediated endocytosis (CME). Its GTPase activity is stimulated by phospholipid binding to its PH domain, which induces helical oligomerization. We have designed a series of novel pyrimidine-based “Pyrimidyn” compounds that inhibit the lipid-stimulated GTPase activity of full length dynamin I and II with similar potency. The most potent analogue, Pyrimidyn 7, has an IC50 of 1.1 μM for dynamin I and 1.8 μM for dynamin II, making it among the most potent dynamin inhibitors identified to date. We investigated the mechanism of action of the Pyrimidyn compounds in detail by examining the kinetics of Pyrimidyn 7 inhibition of dynamin. The compound competitively inhibits both GTP and phospholipid interactions with dynamin I. While both mechanisms of action have been previously observed separately, this is the first inhibitor series to incorporate both and thereby to target two distinct domains of dynamin. Pyrimidyn 6 and 7 reversibly inhibit CME of both transferrin and EGF in a number of non-neuronal cell lines as well as inhibiting synaptic vesicle endocytosis (SVE) in nerve terminals. Therefore, Pyrimidyn compounds block endocytosis by directly competing with GTP and lipid binding to dynamin, limiting both the recruitment of dynamin to membranes and its activation. This dual mode of action provides an important new tool for molecular dissection of dynamin’s role in endocytosis.


Watch the video: ΧΗΜΕΙΑ Α ΛΥΚΕΙΟΥ ΧΗΜΙΚΗ ΑΝΤΙΔΡΑΣΗ 2 ΑΠΛΗΣ ΑΝΤΙΚΑΤΑΣΤΑΣΗΣ (September 2022).


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