Chemistry
Sterling Chemistry Laboratory, 432.3913
M.S., Ph.D.
Chair
Andrew Hamilton
Director of Graduate Studies
Mark Johnson
Professors
Sidney Altman (Molecular, Cellular & Developmental Biology), Jerome Berson (Emeritus), Gary Brudvig, William Chupka (Emeritus), Robert Crabtree, R. James Cross, Jr., Donald Crothers, John Faller, Gary Haller (Engineering & Applied Science), Andrew Hamilton, John Hartwig, Francesco Iachello (Physics), Mark Johnson, William Jorgensen, Philip Lyons (Emeritus), J. Michael McBride, Peter Moore, Lynne Regan (Molecular Biophysics & Biochemistry), Martin Saunders, Alanna Schepartz, Robert Shulman (Molecular Biophysics & Biochemistry), Oktay Sinanoglu (Emeritus), Dieter Söll (Molecular Biophysics & Biochemistry), Thomas Steitz (Molecular Biophysics & Biochemistry), Julian Sturtevant (Emeritus), John Tully, Patrick Vaccaro, Harry Wasserman (Emeritus), Kenneth Wiberg (Emeritus), John Wood, Frederick Ziegler, Kurt Zilm
Associate Professors
David Austin, Craig Crews (Molecular Biophysics & Biochemistry), Charles Schmuttenmaer, Scott Strobel (Molecular Biophysics & Biochemistry)
Assistant Professors
Victor Batista, J. Patrick Loria, Ann Valentine
Fields of Study
Fields include bio-inorganic chemistry, bio-organic chemistry, biophysical chemistry, chemical physics, inorganic chemistry, organic chemistry, physical chemistry, physical-organic chemistry, synthetic-organic chemistry, and theoretical chemistry.
Special Admissions Requirements
Applicants are expected to have completed or be completing a standard undergraduate chemistry major including a year of elementary organic chemistry, with laboratory, and a year of elementary physical chemistry. Other majors are acceptable if the above requirements are met. The GRE General Test and the Subject Test in Chemistry are required. Students whose native language is not English are required to take the Test of English as a Foreign Language (TOEFL) and the Test of Spoken English (TSE).
Special Requirements for the Ph.D. Degree
A foreign language is not required. Three term courses are required in each of the first two terms of residence, and participation in additional courses is encouraged in subsequent terms. Courses are chosen according to the student's background and research area. To be admitted to candidacy a student must: (1) receive at least two term grades of Honors, exclusive of those for research; (2) pass either three cumulative examinations and one oral examination (organic students) or two oral examinations (nonorganic students) by the end of the second year of study; and (3) submit a thesis prospectus no later than the end of the third year of study. Remaining degree requirements include completing eight cumulative examinations (organic students), a written thesis describing the research, and an oral defense of the thesis. The ability to communicate scientific knowledge to others outside the specialized area is crucial to any career in chemistry. Therefore, all students are required to teach a minimum of two terms at the level of Teaching Fellow 3 or higher.
Master's Degrees
M.S. (en route to the Ph.D.). A student must pass at least five graduate-level term courses in the Chemistry department exclusive of seminars and research. The student must obtain at least one term grade of Honors or three of High Pass in graduate-level courses. One full year of residence is required.
Program materials are available upon request to the Director of Graduate Studies, Department of Chemistry, Yale University, PO Box 208107, New Haven CT 06520-8107.
Courses
CHEM 520u, Advanced Organic Chemistry. Martin Saunders [F], David Austin [Sp]. MWF 9.30–10.20
A discussion of structure and mechanism in organic chemistry. Fall: bonding, structure and strain; carbanions, carbocations, and carbenes. Spring: conjugated systems, aromaticity, orbital symmetry, and pericyclic reactions; free radicals, biradicals, carbonyl group reactions, and photochemistry.
CHEM 522au, Chemical Biology II. Alanna Schepartz. TTh 9–10.15
A comprehensive introduction to the origins and emerging frontiers of chemical biology. This course develops the fundamental chemistry of molecules found in nature, a quantitative description of their interactions with themselves and each other, and subsequent effects on biological function. Topics include protein design, molecular evolution, chemical genetics, metabolic engineering, and methods in genomics and proteomics research.
CHEM 523u, Synthetic Methods in Organic Chemistry. David Austin [F], John Wood [Sp]. MWF 10.30–11.20
Modern methods of design in synthetic organic chemistry with an emphasis on natural products. Structural-type recognition, stereochemistry, mechanism and function group transformations in multifunctional group molecules are covered.
CHEM 525bu, Spectroscopic Methods of Structure Determination. Martin Saunders. TTh 10.30–11.20, 1 HTBA
A discussion of the use of nuclear magnetic resonance spectroscopy, vibrational spectroscopy, optical spectroscopy, electron-spin resonance spectroscopy, and other physical techniques to determine structural and dynamic properties of organic molecules.
CHEM 526au, Computational Chemistry and Biochemistry. William Jorgensen. TTh 9–10.15
An introduction to modern computational methods employed for the study of chemistry and biochemistry, including molecular mechanics, quantum mechanics, statistical mechanics, and molecular dynamics. Special emphasis on the hands-on use of computational packages for current applications ranging from organic reactions to protein-ligand binding and dynamics.
CHEM 530bu, Statistical Methods and Thermodynamics. Victor Batista. MWF 9.30–10.20
The fundamentals of statistical mechanics are developed and used to elucidate gas phase and condensed phase behavior, as well as to establish a microscopic derivation of the postulates of thermodynamics. Topics include ensembles; Fermi, Bose, and Boltzmann statistics; density matrices; mean field theories; phase transitions; chemical reaction dynamics; time-correlation functions; Monte Carlo and molecular dynamics simulations.
[CHEM 535a, Chemical Dynamics.]
CHEM 540u, Molecules and Radiation I. Kurt Zilm. MWF 8.30–9.20
The basic quantum mechanics of spectroscopy including the use of angular momentum operators, matrix methods, and time-dependent quantum mechanics. Applications from magnetic resonance.
CHEM 542bu, Molecules and Radiation II. Mark Johnson. MWF 10.30–11.20
An extension of the material covered in CHEM 540a to atomic and molecular spectroscopy, including rotational, vibrational, and electronic spectroscopy, as well as an introduction to laser spectroscopy.
CHEM 547b, Electron Paramagnetic Resonance. Gary Brudvig. TTh 10.30–11.45
A quantum mechanical treatment of magnetic resonance aimed at providing an understanding of the fundamentals of EPR spectroscopy. Topics include solution and solid-state measurements of radicals and spin labels, triplet states, transition metals, pulsed and double-resonance methods, and applications to biological systems.
[CHEM 548b, Nuclear Magnetic Resonance in Liquids.]
CHEM 549bu, Biophysical Chemistry. Peter Moore. TTh 9–10.15
Discussion of several important experimental techniques used to study the properties of biological macromolecules, such as calorimetry, optical spectroscopy, X-ray scattering and diffraction, and sedimentation. Emphasis is on the physical chemistry that underlies both the execution of such experiments and the interpretation of the resulting data. This course is intended primarily for first-year graduate students and capable advanced undergraduates. Prerequisites: physical chemistry (CHEM 330a&b or CHEM 332a&b) and at least one term of biochemistry.
CHEM 550bu, Theoretical and Inorganic Chemistry. John Faller. TTh 9–10.15
Covers the major physical methods used in the determination of molecular structure, bonding, and physical properties of metal complexes. Aimed at advanced undergraduate and first-year graduate students. Students should be familiar with both inorganic coordination chemistry and physical chemistry.
CHEM 552au, Organometallic Chemistry. Robert Crabtree. TTh 9–10.15
A general introduction to organometallic chemistry, mostly of the transition metal elements. Topics include bonding, structure, and reactivity of transition metal organometallic compounds, ligand substitution reactions, oxidative addition/reductive elimination reactions, insertion reactions, reactions of coordinated ligands, applications to catalytic processes, and organic synthesis.
CHEM 553b, Main Group Chemistry. Robert Crabtree. TTh 10.30–11.45
Main group chemistry has influenced heavily inorganic, organic, and industrial chemistry and is assuming increasing importance in biochemistry. The basic principles are discussed including periodic trends, hypervalency, and the distinctions between electron-deficient, electron-precise, and electron-rich elements. Examples of useful or interesting applications are considered, such as silicones, alumoxanes, MOCVD routes to materials, and nanoparticles. Organolithium, organomagnesium, and organoboron reagents are discussed in relation to their utility in organic chemistry as well as the structural puzzles they pose. Main group clusters are considered in relation to multicenter bonding and Wades' rules. Interactions between main group and transition elements are covered. Finally, bioinorganic applications are discussed, such as neutron capture therapy, Si biochemistry, and bone mineralization.
CHEM 554b, Bio-Inorganic Chemistry. Ann Valentine. MWF 11.30–12.20
An advanced introduction to biological inorganic chemistry. Important topics in metallo-protein chemistry are illustrated. Objective is to define and understand function in terms of structure. Topics include catalysis with and without electron transfer, and carbon, oxygen, and nitrogen metabolism.
CHEM 555a, Transition Metal Reaction Mechanisms. John Hartwig. MW 9–10.15
A discussion of contemporary mechanistic problems in transition metal chemistry. The course presents fundamental physical organic principles, such as reaction kinetics, isotope effects, substituent effects, solvent effects, acidity, and their application to problems in coordination chemistry, bioorganic chemistry, and organometallic chemistry.
CHEM 556a, Biochemistry Rates and Mechanims. Patrick Loria. MWF 9.30–10.20
The fundamental basis of and methods for studying enzyme function. Topics include transition state theory, pre-steady-state and steady-state enzyme kinetics, and allosterism. The physical principles underlying enzymatic rate enhancements are discussed using examples from the primary literature.
CHEM 557au, Modern Coordination Chemistry. Ann Valentine. TTh 11.30–12.45
The structure of the atom, molecular topologies, ionic bonding, covalent bonding, chemical forces, reaction pathways; fundamental concepts for transition metal complexes; coordination chemistry; structural aspects, isomerism, electron transfer reactions, substitution reactions, molecular rearrangements, and reactions of coordinated ligands; transition metal clusters, multiple bonding between transition metal atoms.
CHEM 560L, Advanced Physical Methods in Molecular Science. Patrick Vaccaro [F], Charles Schmuttenmaer [Sp]. F 3–4
A laboratory course introducing physical chemistry tools used in the experimental and theoretical investigation of large and small molecules. Modules include machining materials, electronics, vacuum technology, magnetic resonance, optical spectroscopy and lasers, computational aids, and molecular modeling.
CHEM 562L, Laboratory in Instrument Design and the Mechanical Arts. Kurt Zilm, David Johnson.
Familiarization with modern machine shop practices and techniques. Use of basic metalworking machinery and instruction in techniques of precision measurement and properties of commonly used metals, alloys, and plastics.
CHEM 564L, Advanced Mechanical Instrumentation. Kurt Zilm, David Johnson.
A course geared for both the arts and sciences that goes beyond the basic introductory shop courses, offering an in-depth foundation study utilizing "hands-on" instructional techniques that must be learned from experience. Prerequisite: CHEM 562L.
[CHEM 565a, Computational Chemistry.]
[CHEM 567au, Topics in Chemical Biology.]
[CHEM 568a, Applications of Molecular Orbital Theory.]
[CHEM 569a, Molecular Modeling.]
CHEM 570au, Introductory Quantum Chemistry. Victor Batista. TTh 9–10.15
The elements of quantum mechanics developed and illustrated with applications to chemical problems. Suitable for first-year graduate students in chemistry who have had some exposure to quantum mechanics as part of an undergraduate chemistry course.
[CHEM 572bu, Advanced Quantum Mechanics.]
[CHEM 580bu, Bio-Organic Chemistry.]
CHEM 600–670, Research Seminars. Faculty.
Presentation of a student's research results to his/her adviser and fellow research group members. Extensive discussion and literature review are normally a part of the series.
CHEM 700, Laboratory Rotation for First-Year Biophysical Graduate Students. Gary Brudvig.
CHEM 720, Current Topics in Organic Chemistry.
A seminar series based on invited speakers in the general area of organic chemistry.
CHEM 730, Molecular Science Seminar.
A seminar series based on invited speakers in the areas of physical, inorganic, and biological chemistry.
CHEM 990, Research. Faculty.
Individual research for Ph.D. degree candidates in the Department of Chemistry, under the direct supervision of one or more faculty members.
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