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Course 5: Chemistry |
 | | | 5.00-5.4999 | | | 5.50-5.999, plus UROP and Theses | | |  |
5.511 Synthetic Organic Chemistry I
 ( ); second half of term
Prereq: 5.43 and permission of instructor Units: 2-0-4 
Presents and discusses important topics in modern synthetic organic chemistry, with the objective of developing problem-solving skills for the design of synthetic routes to complex molecules. M. Movassaghi 5.512 Synthetic Organic Chemistry II
( ); second half of term
Prereq: 5.511 Units: 2-0-4  Begins Mar 31. Lecture: MW10.30-12 (4-257)
General methods and strategies for the synthesis of complex organic compounds. M. Movassaghi Textbooks (Spring 2025) 5.52 Tutorial in Chemical Biology
()
Prereq: Permission of instructor Units: 2-2-8
Provides an overview of the core principles of chemistry that underlie biological systems. Students explore research topics and methods in chemical biology by participating in laboratory rotations, then present on experiments performed during each rotation. Intended for first-year graduate students with a strong interest in chemical biology. R. Raines 5.53 Molecular Structure and Reactivity
()
Prereq: 5.43, 5.601, and 5.602 Units: 3-0-9
Reaction mechanisms in organic chemistry: methods of investigation, relation of structure to reactivity, and reactive intermediates. A. Radosevich, M. Elkin 5.54[J] Advances in Chemical Biology
()
(Same subject as 7.540[J], 20.554[J]) Prereq: 5.07, 5.13, 7.06, and permission of instructor Units: 3-0-9
Introduction to current research at the interface of chemistry, biology, and bioengineering. Topics include imaging of biological processes, metabolic pathway engineering, protein engineering, mechanisms of DNA damage, RNA structure and function, macromolecular machines, protein misfolding and disease, metabolomics, and methods for analyzing signaling network dynamics. Lectures are interspersed with class discussions and student presentations based on current literature. L. Kiessling, O. Johnson 5.55 NMR Spectroscopy and Biochemical Structure Determination
(); second half of term
Prereq: (5.07 and 5.08) or permission of instructor Units: 2-0-4 Begins Mar 31. Lecture: MW9-10.30 (4-153)
Practical nuclear magnetic resonance (NMR) spectroscopy applied to problems in biochemistry and chemical biology. W. Massefski No textbook information available 5.56 Molecular Structure and Reactivity II
 (); second half of term
Prereq: 5.53 or permission of instructor Units: 2-0-4
Application of physical principles and methods to contemporary problems of interest in organic and polymer chemistry. J. Johnson 5.561 Chemistry in Industry
()Not offered regularly; consult department Prereq: 5.03, 5.13, and (5.07 or 7.05) Units: 2-0-4 [P/D/F]
Examination of recent advances in organic, biological, and inorganic and physical chemical research in industry. Taught in seminar format with participation by scientists from industrial research laboratories. R. Danheiser 5.601 Thermodynamics I
 (, ); first half of term
Prereq: Calculus II (GIR) and Chemistry (GIR) Units: 2-0-4 Ends Mar 21. Lecture: MWF11 (2-105) Recitation: MW1 (4-145) or TR9 (2-147)
Basic thermodynamics: state of a system, state variables. Work, heat, first law of thermodynamics, thermochemistry. Second and third law of thermodynamics: entropy and free energy, including the molecular basis for these thermodynamic functions. Equilibrium properties of macroscopic systems. Special attention to thermodynamics related to global energy issues and biological systems. Combination of 5.601 and 5.602 counts as a REST subject. Fall: S. Peng, B. McGuire Spring: R. Griffin Textbooks (Spring 2025) 5.602 Thermodynamics II and Kinetics
(, ); second half of term
Prereq: 5.601 Units: 2-0-4 Begins Mar 31. Lecture: MWF11 (2-105) Recitation: MW1 (4-145) or TR9 (2-147) +final
Free energy and chemical potential. Phase equilibrium and properties of solutions. Chemical equilibrium of reactions. Rates of chemical reactions. Special attention to thermodynamics related to global energy issues and biological systems. Combination of 5.601 and 5.602 counts as a REST subject. Fall: S. Peng, B. McGuire Spring: S. Peng Textbooks (Spring 2025) 5.611 Introduction to Spectroscopy
(); first half of term
Prereq: Calculus II (GIR), Chemistry (GIR), and Physics II (GIR) Units: 2-0-4
Introductory quantum chemistry; particles and waves; wave mechanics; harmonic oscillator; applications to IR, Microwave and NMR spectroscopy. Combination of 5.611 and 5.612 counts as a REST subject. M. Hong 5.612 Electronic Structure of Molecules
(); second half of term
Prereq: 5.611 Units: 2-0-4
Introductory electronic structure; atomic structure and the Periodic Table; valence and molecular orbital theory; molecular structure, and photochemistry. Combination of 5.611 and 5.612 counts as a REST subject. R. Griffin 5.62 Physical Chemistry
()
Prereq: 5.601, 5.602, 5.611, and 5.612 Units: 4-0-8 Lecture: MWF12 (2-131) Recitation: R2 (2-132) +final
Elementary statistical mechanics; transport properties; kinetic theory; solid state; reaction rate theory; and chemical reaction dynamics. S. Ceyer, K. Nelson No textbook information available 5.64[J] Advances in Interdisciplinary Science in Human Health and Disease
()
(Same subject as HST.539[J]) Prereq: 5.13, 5.601, 5.602, and (5.07 or 7.05) Units: 3-0-9
Introduces major principles, concepts, and clinical applications of biophysics, biophysical chemistry, and systems biology. Emphasizes biological macromolecular interactions, biochemical reaction dynamics, and genomics. Discusses current technological frontiers and areas of active research at the interface of basic and clinical science. Provides integrated, interdisciplinary training and core experimental and computational methods in molecular biochemistry and genomics. A. Shalek, X. Wang 5.68[J] Kinetics of Chemical Reactions
()
(Same subject as 10.652[J]) Prereq: 5.62, 10.37, or 10.65 Units: 3-0-6
Experimental and theoretical aspects of chemical reaction kinetics, including transition-state theories, molecular beam scattering, classical techniques, quantum and statistical mechanical estimation of rate constants, pressure-dependence and chemical activation, modeling complex reacting mixtures, and uncertainty/ sensitivity analyses. Reactions in the gas phase, liquid phase, and on surfaces are discussed with examples drawn from atmospheric, combustion, industrial, catalytic, and biological chemistry. W. H. Green 5.697[J] Computational Chemistry
()
(Same subject as 10.437[J]) (Subject meets with 5.698[J], 10.637[J]) Prereq: Permission of instructor Units: 3-0-9
Addresses both the theory and application of first-principles computer simulations methods (i.e., quantum, chemical, or electronic structure), including Hartree-Fock theory, density functional theory, and correlated wavefunction methods. Covers enhanced sampling, ab initio molecular dynamics, and transition-path-finding approaches as well as errors and accuracy in total and free energies. Discusses applications such as the study and prediction of properties of chemical systems, including heterogeneous, molecular, and biological catalysts (enzymes), and physical properties of materials. Students taking graduate version complete additional assignments. Limited to 35; no listeners. H. J. Kulik 5.698[J] Computational Chemistry
()
(Same subject as 10.637[J]) (Subject meets with 5.697[J], 10.437[J]) Prereq: Permission of instructor Units: 3-0-9
Addresses both the theory and application of first-principles computer simulations methods (i.e., quantum, chemical, or electronic structure), including Hartree-Fock theory, density functional theory, and correlated wavefunction methods. Covers enhanced sampling, ab initio molecular dynamics, and transition-path-finding approaches as well as errors and accuracy in total and free energies. Discusses applications such as the study and prediction of properties of chemical systems, including heterogeneous, molecular, and biological catalysts (enzymes), and physical properties of materials. Students taking graduate version complete additional assignments. Limited to 35; no listeners. H. J. Kulik 5.70[J] Statistical Thermodynamics
()
(Same subject as 10.546[J]) Prereq: 5.601 or permission of instructor Units: 3-0-9
Develops classical equilibrium statistical mechanical concepts for application to chemical physics problems. Basic concepts of ensemble theory formulated on the basis of thermodynamic fluctuations. Examples of applications include Ising models, lattice models of binding, ionic and non-ionic solutions, liquid theory, polymer and protein conformations, phase transition, and pattern formation. Introduces computational techniques with examples of liquid and polymer simulations. B. Zhang, J. Cao 5.72 Statistical Mechanics
(); second half of term
Prereq: 5.70 or permission of instructor Units: 2-0-4
Principles and methods of statistical mechanics. Classical and quantum statistics, grand ensembles, fluctuations, molecular distribution functions, and other topics in equilibrium statistical mechanics. Topics in thermodynamics and statistical mechanics of irreversible processes. J. Cao, B. Zhang 5.73 Introductory Quantum Mechanics I
()
Prereq: 5.611, 5.612, 8.03, and 18.03 Units: 3-0-9
Presents the fundamental concepts of quantum mechanics: wave properties, uncertainty principles, Schrodinger equation, and operator and matrix methods. Includes applications to one-dimensional potentials (harmonic oscillator), three-dimensional centrosymetric potentials (hydrogen atom), and angular momentum and spin. Approximation methods include WKB, variational principle, and perturbation theory. M. Bawendi 5.74 Introductory Quantum Mechanics II
()
Prereq: 5.73 Units: 3-0-9 Lecture: WF9.30-11 (2-132)
Time-dependent quantum mechanics and spectroscopy. Topics include perturbation theory, two-level systems, light-matter interactions, relaxation in quantum systems, correlation functions and linear response theory, and nonlinear spectroscopy. K. Nelson, G. Schlau-Cohen No textbook information available 5.78 Biophysical Chemistry Techniques
 ()
(Subject meets with 7.71) Prereq: 5.07 or 7.05 Units: 2-0-4 Lecture: MWF1.30-3 (56-191)
Presents principles of macromolecular crystallography that are essential for structure determinations. Topics include crystallization, diffraction theory, symmetry and space groups, data collection, phase determination methods, model building, and refinement. Discussion of crystallography theory complemented with exercises such as crystallization, data processing, and model building. Meets with 7.71 when offered concurrently. Enrollment limited. C. Drennan, T. Schwartz No textbook information available 5.80 Advanced Topics of Current Special Interest
(, )
Prereq: None Units arranged TBA.
Advanced topics of current special interest. Fall: Staff Spring: Staff No textbook information available 5.81[J] United States Energy Policy: Lessons Learned for the Future
(); second half of term
(Same subject as 15.029[J]) (Subject meets with 5.811[J], 15.0291[J]) Prereq: None Units: 2-0-4
Compares the US policy responses, from the Nixon administration to the current administration, on issues ranging from oil import dependence to nuclear nonproliferation. Examines what lessons were learned from these issues and how they have shaped the country's current climate change policy. Prepares students to be informed and effective participants in policy deliberations that require difficult decisions and trade-offs. Addresses both domestic and international policy aspects. Students taking graduate version complete additional assignments. J. Deutch 5.811[J] United States Energy Policy: Lessons Learned for the Future
(); second half of term
(Same subject as 15.0291[J]) (Subject meets with 5.81[J], 15.029[J]) Prereq: None Units: 2-0-4
Compares the US policy responses, from the Nixon administration to the current administration, on issues ranging from oil import dependence to nuclear nonproliferation. Examines what lessons were learned from these issues and how they have shaped the country's current climate change policy. Prepares students to be informed and effective participants in policy deliberations that require difficult decisions and trade-offs. Addresses both domestic and international policy aspects. Students taking graduate version complete additional assignments. J. Deutch 5.812[J] Principles of Innovation
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| | | 5.00-5.4999 | | | 5.50-5.999, plus UROP and Theses | | | |
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