Chemistry 478

Spring Term 2014

Instructor: Jay Ponder


Syllabus & Schedule [PDF]

Take-Home Final Exam [PDF]


Lecture 1 (Jan 13): Introduction to Molecular Modeling [PDF]

Lecture 2 (Jan 15): Potential Energy Surfaces & Optimization Methods [PDF]

Lecture 3 (Jan 22): ab Initio MO Theory: From the Beginning [PDF]

Lecture 4 (Jan 27): Methods for Electron Correlation [PDF]

Lecture 5 (Jan 29): Semi-Empirical Molecular Orbital Methods [PDF]

Lecture 6 (Feb 3): Density Functional Theory (DFT) [PDF]

Lecture 7 (Feb 5): Frontier Orbital Theory (FMO) [PDF]

Lecture 8 & 9 (Feb 10/12): Introduction to Molecular Mechanics [PDF]

Lecture 10 (Feb 17): Advanced Electrostatics for Force Fields [PDF]

Lecture 11 & 12 (Feb 19/24): Basics of Molecular Dynamics Simulation [PDF]

Lecture 13 (Feb 26): Using Molecular Dynamics to Compute Properties [PDF]

Lecture 14 & 15 (Mar 3/5): Introduction to Monte Carlo Methods [PDF]

Lecture 16 & 17 (Mar 17/19): Electrostatics & Solvation in Biomolecules [PDF]

Lecture 18 & 19 (Mar 24/26): Calculation of Free Energy [PDF]

Lecture 20 (Mar 31): Small Molecular & Protein Docking [PDF]

Lecture 21 (Apr 2): Tutorial & Introduction to AutoDock [PDF]

Lecture 22 (Apr 7): Distance Geometry in NMR Structure Refinement [PDF]

Lecture 23 (Apr 9): Calculation of Rates via Brownian Dynamics [PDF]

Lecture 24 & 25 (Apr 14/16): Protein Structure Prediction & Design [PDF]

Lecture 26 (Apr 21): Quantum Mechanics/Molecular Mechanics (QM/MM) [PDF]

Lecture 27 (Apr 23): Coarse-Grained Modeling Methods [PDF]


Perspectives on Molecular Modeling

Biomolecular Modeling: Goals, Problems, Perspectives,
W. F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen,
X. Daura, P. Gee, D. P. Geerke, A. Glattli, P. H. Hunenberger, M. A. Kastenholz,

Lecture 21 (Apr 2): Tutorial & Introduction to AutoDock [PDF]

C. Oostenbrink, M. Schenk, D. Trzesniak, N. F. A. van der Vegt and H. B. Yu,
Angewandte Chemie International Edition, 45, 4064-4092 (2006) [PDF]

Biomolecular Modeling and Simulation: A Field Coming of Age,
T. Schlick, R. Collepardo-Guevara, L. A. Halvorsen, S. Jung and X. Xiao,
Quarterly Reviews of Biophysics, 44, 191-228 (2011) [PDF]

ab initio Electronic Structure Calculations

Computational Quantum Mechanics & Advanced ab Initio Methods,
Chapters 2 & 3 from Molecular Modeling, 2nd Edition by A. R. Leach [PDF]

Derivation of the Hartree-Fock Equation, Appendix 7
from Quantum Chemistry, 3rd Edition by J. P. Lowe and K. A. Peterson [PDF]

Approximate Molecular Orbital Methods

The Extended Huckel Method, Chapter 10
from Quantum Chemistry, 3rd Edition by J. P. Lowe and K. A. Peterson [PDF]

Basic Theory of the FMO Method, Chapters 2 & 3
from Frontier Orbitals, by N. T. Anh [PDF]

Molecular Dynamics Simulation

Molecular Dynamics, J. Meller,
Encyclopedia of Life Sciences, 1-8 (2001) [PDF]

Introduction to Molecular Dynamics Simulation, M. P. Allen,
Computational Soft Matter, NIC Series, 23, 1-28 (2004) [PDF]

History of the Monte Carlo Method

Equation of State Calculations by Fast Computing Machines, N. Metropolis,
A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller and E. Teller,
Journal of Chemical Physics, 21, 1087-1092 (1953) [PDF]

The Beginning of the Monte Carlo Method,
N. Metropolis, Los Alamos Science, 14, 125-130 (1987) [PDF]

Scientific Uses of the MANIAC, H. L. Anderson,
Journal of Statistical Physics, 43, 731-748 (1986) [PDF]

Monte Carlo Theory and Algorithms

Progress and Outlook in Monte Carlo Simulations, D. N. Theodorou,
Industrial & Engineering Chemistry Research, 49, 3047-3058 (2010) [PDF]

Monte Carlo Simulations, D. J. Earl and M. W. Deem,
Methods in Molecular Biology, 443, 25-36 (2008) [PDF]

Monte Carlo Codes, Tools and Algorithms, D. Dubbledam, A. Torres-Knoop
and K. S. Walton, Molecular Simulation, 39, 1253-1292 (2013) [PDF]

Biomolecular Electrostatics and Solvation

Computational Methods for Biomolecular Electrostatics, F. Dong,
B. Olsen and N. A. Baker, Methods in Cell Biology, 84, 843-870 (2008) [PDF]

Classical Electrostatics for Biomolecular Simulations, G. A. Cisneros,
M. Karttunen, P. Ren and C. Sagui, Chemical Reviews, 114, 779-814 (2014) [PDF]

Biomolecular Electrostatics and Solvation: A Computational Perspective,
P. Ren, J. Chun, D. G. Thomas, M. J. Schnieders, M. Marcho, J. Zhang
and N. A. Baker, Quarterly Reviews of Biophysics, 45, 427-491 (2012) [PDF]

Free Energy Calculations

Free Energy Calculations in Structure-Based Drug Design, M. R. Shirts,
D. L. Mobley and S. P. Brown, Chapter 5 from Drug Design: Structure- and
Ligand-Based Approaches, by K. M. Merz Jr., D. Ringe and C. H. Reynolds [PDF]

Efficient Estimation of Free Energy Differences from Monte Carlo Data,
C. H. Bennett, Journal of Computational Physics, 22, 245-268 (1976) [PDF]

Molecular Docking Methods

A Critical Assessment of Docking Programs and Scoring Functions,
G. L. Warren, C. W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde,
M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger,
G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff and M. S. Head,
Journal of Medicinal Chemistry, 49, 5912-5931 (2006) [PDF]

Challenges and Advances in Computational Docking: 2009 in Review, E. Yurlev,
M. Agostino and P. A. Ramsland, Journal of Molecular Recognition, 24, 149-164 (2011) [PDF]

Protein-Ligand Docking in the New Millennium - A Retrospective of 10
Years in the Field, S. F. Sousa, A. J. M Ribeiro, J. T. S. Coimbra,
R. P. P. Neves, S. A. Martins, N. S. H. N. Moorthy, P. A. Fernandes and
M. J. Ramos, Current Medicinal Chemistry, 20, 2296-2314 (2013) [PDF]

AutoDock Search and Scoring Methodology

Automated Docking Using a Lamarckian Genetic Algorithm and an
Empirical Binding Free Energy Function, G. M. Morris, D. S. Goodsell,
R. S. Halliday, R. Huey, W. E. Hart, R. K. Belew and A. J. Olsen,
Journal of Computational Chemistry, 19, 1639-1662 (1998) [PDF]

A Semiempirical Free Energy Force Field with Charge-Based Desolvation,
R. Huey, G. M. Morris, A. J. Olsen and D. S. Goodsell,
Journal of Computational Chemistry, 28, 1145-1152 (2007) [PDF]

Brownian Dynamics Simulation

Diffusion and Association Porcesses in Biological Systems: Theory,
Computation and Experiment, P. Mereghetti, D. Kokh, J. A. McCammon
and R. C. Wade, BMC Biophysics, 4, 2 (2011) [PDF]

Browndye: A Software Package for Brownian Dynamics, G. A. Huber and
J. A. McCammon, Computer Physics Communications, 181, 1896-1905 (2010) [PDF]

References for Final Exam - DFT

A Fast Doubly Hybrid Density Functional Method Close
to Chemical Accuracy Using a Local Opposite Spin Ansatz,
I. Y. Zhang, Y. Jung and W. A. Goddard III,
Proceedings of the National Academy of Sciences of the USA,
108, 19896-19900 (2011) [PDF]

Long-Range Corrected Double-Hybrid Density Functionals,
J.-D. Chai and M. Head-Gordon,
Journal of Chemical Physics, 131, 174105 (2009) [PDF]

The M06 Suite of Density Fuctionals for Main Group Thermochemistry,
Thermochemical Kinetics, Noncovalent Interactions, Excited States, and
Transition Elements: Two New Functionals and Systematic Testing of Four
M06-Class Functionals and 12 Other Functionals, Y. Zhao and D. G. Truhlar,
Theoretical Chemistry Accounts, 120, 215-241 (2008) [PDF]

References for Final Exam - MC vs. MD

Monte Carlo vs Molecular Dynamics for Conformational Sampling,
W. L. Jorgensen and J. Tirado-Rives,
Journal of Physical Chemistry, 100, 14508-14513 (1996) [PDF]

Monte Carlo vs Molecular Dynamics for All-Atom Polypeptide Folding
Simulations, J. P. Ulmschneider, M. B. Ulmschneider and A. Di Nola,
Journal of Physical Chemistry B, 110, 16733-16742 (2006) [PDF]

References for Final Exam - Protein Design

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy,
B. Kuhlman, G. Dantas, G. C. Ireton, G. Varani, B. L. Stoddard and D. Baker,
Science, 302, 1364-1368 (2003) [PDF]

Computational Design of Ligand-Binding Proteins with High Affinity and
Selectivity, C. E. Tinberg, S. D. Khara, J. Dou, L. Doyle, J. W. Nelson,
A. Schena, W. Jankowski, C. G. Kalodimos, K. Johnsson, B. L. Stoddard
and D. Baker, Nature, 501, 212-216 (2013) [PDF]


Linux Information

Useful Unix Tools [HTML]

Avogadro Molecular Editor

Avogadro Install Kit for Macintosh [DMG}

Avogadro Documentaton [HTML}

VMD: Visual Molecular Dynamics

VMD 1.9.1 User's Guide [PDF}

Tutorial: Using VMD [PDF}

Spartan Molecular Modeling (Q-Chem)

Spartan Student Overview [PDF}

Spartan '10 Manual [PDF}

Q-Chem 4.1 Manual [PDF}

Gaussian Quantum Chemistry

Gaussian 09 Online Manual [HTML}

GaussView 5 Online Manual [HTML}

TINKER & Force Field Explorer


TINKER Web Site for Downloads [HTML]

Force Field Explorer Manual [PDF}

APBS Poisson-Boltzmann Solver

APBS Documentation [HTML]

PDB2PQR Documentation [HTML]

Tutorial: Lysozyme pKa Calculation [HTML]

Tutorial: Visualizing APBS Results in VMD [HTML]

AutoDock4 (also Python Molecular Viewer & AutoDock Tools)

AutoDock Version 4.2 User Guide [PDF]

AutoDock 4 Seminar Handout [PDF]

Python Molecular Viewer (PMV) Tutorial [PDF]

Files Used for PMV Tutorial [Files]

AutoDock Tutorial [PDF]

Files Used for AutoDock Tutorial [Files]

Autodock Binaries for Mac OSX [TAR]

Molecular Graphics Laboratory (MGL) Tools for Mac OSX [TAR]

SDA7 (Simulation of Diffusional Association, V7)

SDA7 Documentation [HTML]

SDA7 Binaries and Examples for Mac OSX [TAR]


Suggested Lab Report Format [PDF]

Lab 1 (Jan 17): Computing the Rotational Barrier in Hydrazine [Files]

Lab 2 (Jan 24): Structures & Stabilities of meta-Cyclophanes [Files]

Lab 3 (Jan 31): Gas Phase & Aqueous Acidity/Basicity of Organic Molecules [Files]

Lab 4 (Feb 7): Frontier Orbital Analysis of Regioselectivity [Files]

Lab 5 (Feb 14): Conformational Analysis of Alanine Dipeptide [Files]

Lab 6 (Feb 21 & 28): Liquid Properties via Molecular Dynamics Simulation [Files]

Lab 7 (Mar 7): Global Optimization of a Polyalanine Octapeptide [Files]

Lab 8 (Mar 21): Poisson-Boltzmann Calculation on Lysozyme Using APBS [Files]

Lab 9 (Mar 28): Relative Hydration Free Energy of Monovalent Ions [Files]

Lab 10 (Apr 4): Docking Indinavir to HIV Protease Using AutoDock [Files]

Lab 11 (Apr 11): Diffusional Association of the Barnase-Barstar Complex [Files]