Chemistry

Sterling Chemistry Laboratory, 432.3913
M.S., Ph.D.

Chair
Andrew Hamilton

Director of Graduate Studies
Gary Brudvig [F] (SCL 122, 432.5202, gary.brudvig@yale.edu)
TBA [Sp]

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 Soell (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
Charles Schmuttenmaer, Scott Strobel (Molecular Biophysics & Biochemistry)

Assistant Professors
David Austin, 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. William Jorgensen. Mon/Wed/Fri 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 523u, Synthetic Methods in Organic Chemistry. John Wood. Mon/Wed/Fri 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. Tues/Thurs 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 530bu, Statistical Methods and Thermodynamics. Victor Batista. Mon/Wed/Fri 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. Mon/Wed/Fri 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. Charles Schmuttenmaer. Mon/Wed/Fri 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.]

CHEM 548b, Nuclear Magnetic Resonance in Liquids. Patrick Loria.
A theoretical treatment of solution NMR spectroscopy with emphasis on applications to proteins and biological macromolecules. This includes a classical and quantum mechanical description of NMR, product operator formalism, multidimensional NMR, phase cycling and gradient selection, relaxation phenomena, and protein resonance assignments.

CHEM 550bu, Theoretical and Inorganic Chemistry. John Faller.
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. Tues/Thurs 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 554b, Bio-Inorganic Chemistry. Ann Valentine. Tues/Thurs 10.30-11.45
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, Advanced Topics in Inorganic Chemistry. John Hartwig.
A discussion of contemporary mechanistic problems in transition metal chemistry. The course shows how fundamental physical organic principles have been used to address problems in transition metal systems relevant to coordination, bioinorganic, organometallic, and synthetic organic chemistry.

CHEM 557au, Modern Coordination Chemistry. John Faller. Tues/Thurs 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 558a, Research Topics in Biophysics. Donald Crothers. Tues/Thurs 2-3.30
An advanced treatment of the fundamental physical properties that dictate the behavior of biological molecules. Taught with participation of a number of biophysics faculty and extends to their current research specialties. Also MB&B 658a.

CHEM 560L, Advanced Physical Methods in Molecular Science. Patrick Vaccaro [F], R. James Cross [Sp]. Friday 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. David Austin. Tues/Thurs 9-10.15
Chemical biology is a broad discipline encompassing the many fields of and all chemical aspects of biological processes. This course focuses on developing an understanding of the fundamental chemical species found in nature, their interaction with biological macromolecules, and their subsequent effect on biological function. Topics include natural products and chemical ecology, affinity chromatography for protein discovery, small molecule/receptor interactions, cellular signaling and signal transduction, functional genomics and proteomics, protein design, and chemical biological applications to drug development.

[CHEM 568a, Applications of Molecular Orbital Theory.]

[CHEM 569a, Molecular Modeling.]

CHEM 570au, Introductory Quantum Chemistry. Victor Batista. Tues/Thurs 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. John Tully.
Topics in quantum mechanics that are essential for understanding modern chemistry, physics, and biophysics. Topics include the interaction of radiation with matter, using quantized radiation fields, and may include time-dependent quantum theory, scattering, semiclassical methods, angular momentum, density matrices, and electronic structure methods. Prerequisite: CHEM 570 or the equivalent.

[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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