Welcome to CBE 422, an introductory course on computational chemistry and molecular simulation methods.  

Time and place: The course meets on Tuesdays and Thursdays from 1:30 - 2:50 in A224 (EQuad).

Books: A recommended textbook is A. Hinchliffe, "Molecular Modelling for Beginners," 2nd ed., Wiley (2008). Other potentially useful books: B. Smit and D. Frenkel, "Understanding Molecular Simulation," 2nd ed., Academic Press (2002) and A. R. Leach, "Molecular Modelling: Principles and Applications" 2nd ed., Prentice-Hall (2001).

Grading: There will be 6 biweekly assignments (65%) and a final project (35%). Assignments are submitted electronically on BlackBoard.

Staff: Prof. Thanos Panagiotopoulos, A317 EQuad., x8-4591 (azp@princeton). Office hour: Wed. 3-4 pm.
Dr. Anirban Mondal, G107 EQuad, x8-0206 (anirbanm@princeton) Office hours: Mon. and Thu. 3-4 pm.

Web Site: The current class schedule is on the course web site, http://paros.princeton.edu/CBE422.

Tentative Course Syllabus: 12/5/2018

Lec.#

Date

Topic(s)

 Reading Assignment
1 Tue 2/5 Introduction and Intermolecular Forces Ch. 1  
2 Thu 2/7 Intermolecular Forces (cont.) Ch. 2  
3 Tue 2/12 Molecular Mechanics Ch. 3,4
4 Thu 2/14 Energy Minimization, Intro to Hyperchem Ch. 5,6
5 Tue 2/19 Conformational Search, Sampling from Probability Distributions Ch. 6,7 # 1
6 Thu 2/21 Excel and Matlab Programming Files  
7 Tue 2/26 Statistical Mechanical Ensembles Ch. 8, Notes  
Thu 2/28 Statistical Mechanical Ensembles (cont.) Notes # 2
8 Tue 3/5 Monte Carlo Ch. 9
9 Thu 3/7 Grand Canonical and constant-pressure MC mVT, NPT  
10 Tue 3/12 Periodic Boundaries DNT # 3
11 Thu 3/14 Analysis of Results, Gibbs Ensemble MC AZP  
12 Tue 3/26 Molecular Dynamics; Hyperchem MD Ch. 10  
13 Thu 3/28 Constant-temperature MD, measuring diffusion
14 Tue 4/2 Interfacial simulations, Gibbs-Duhem MS, DK # 4
15 Thu 4/4 Quantum Modeling Ch. 11,13  
16 Tue 4/9 Quantum Modeling (cont.) and Na example Ch. 14  
17 Thu 4/11 Hartree-Fock approach Ch. 16,17
18 Tue 4/16 Basis Sets and Correlations Ch. 18
19 Thu 4/18 Density Functional Theory and AIMD Ch. 19,20 # 5
20 Tue 4/23 Computation of properties from QM
21 Thu 4/25 Free Energies LK, JL  
22 Tue 4/30 Crystal Structures VN, MP Project definition
23 Thu 5/2 Multiscale methods, Dissipative Particle Dynamics (DPDf, BDf, DPDu, BDu) Ch. 24, R, G, S # 6 [5/3]
Tue 5/14 Dean's Day Project