Chemistry 6440 / 7440

Computational Chemistry

and Molecular Modeling

Course Goals

• To provide an introduction to some current methods in molecular modeling

• To provide hands-on experience with various molecular modeling software packages

• To provide some background on the theoretical and computational methods use in molecular modeling

• To provide some understanding of the capabilities, limitations and reliability of various molecular modeling methods

Prerequisites

• CHM5440 (undergrad PChem) or the equivalent• CHM7470 (Intro to Quantum Chemistry)

desirable but not required (we will go over the basics of molecular orbital theory)

• Will try to keep the math on the light side, but need some math to present the modeling methods and underlying theory

• Familiarity with Mac, Windows and Unix desirable but not required (we will go over the basics)

Lectures and Labs• H. B. Schlegel – 371 / 379 Chemistry

– hbs@chem.wayne.edu– chem.wayne.edu/schlegel

• Lectures and computer labs - Rm 9 Chemistry

• Syllabus, announcements and assignments will be posted on BlackBoard

• Grades will be based on the assignments, a midterm and a final project

• Undergrads should be registered for Chm6440, grads for Chm7440

Assignments and Final Project

• Computational assignments - use various molecular modeling packages to investigate selected chemical problems

• Reading assignments – provide a one page summary of selected articles from the current literature involving molecular modeling

• Final project and presentation– Select a computational chemistry problem related to your current

research– Discuss the computational strategy with HBS– Carry out the study during the second half of the course– 10 – 15 min presentation of your problem, computational

methods and results during the last few lectures of the course

Text and Materials for Course

• No one text covers the many aspects of molecular modeling that will be discussed in this course

• Numerous hand-outs will be provided

• Some texts will be recommended

• Various websites will provide additional information

Some useful texts

• Computational Chemistry (Oxford Chemistry Primer) G. H. Grant and W. G. Richards (Oxford University Press)

• Molecular Modeling – Principles and Applications, A. R. Leach (Addison Wesley Longman)

• Introduction to Computational Chemistry, 2nd eddition, F. Jensen (Wiley)

• Essentials of Computational Chemistry – Theories and Models, 2nd edition, C. J. Cramer (Wiley)

• Exploring Chemistry with Electronic Structure Methods, J. B. Foresman and A. Frisch (Gaussian Inc.)

– HBS will place a group order for this book

Types of Molecular Models

• Wish to model molecular structure, properties and reactivity

• Range from simple qualitative descriptions to accurate, quantitative results

• Costs range from trivial to months of supercomputer time

• Some compromises necessary between cost and accuracy of modeling methods

Plastic molecular models

• Assemble from standard parts• Fixed bond lengths and coordination geometries• Good enough from qualitative modeling of the

structure of some molecules• Easy and cheap to use• Provide a good feeling for the 3 dimensional

structure of molecules• No information on properties, energetics or

reactivity

Molecular mechanics

• Ball and spring description of molecules• Better representation of equilibrium geometries than

plastic models• Able to compute relative strain energies• Cheap to compute• Lots of empirical parameters that have to be carefully

tested and calibrated• Limited to equilibrium geometries• Does not take electronic interactions into account • No information on properties or reactivity• Cannot readily handle reactions involving the making

and breaking of bonds

Semi-empirical molecular orbital methods

• Approximate description of valence electrons• Obtained by solving a simplified form of the

Schrödinger equation• Many integrals approximated using empirical

expressions with various parameters• Semi-quantitative description of electronic

distribution, molecular structure, properties and relative energies

• Cheaper than ab initio electronic structure methods, but not as accurate

Ab Initio Molecular Orbital Methods

• More accurate treatment of the electronic distribution using the full Schroedinger equation

• Can be systematically improved to obtain chemical accuracy

• Does not need to be parameterized or calibrated with respect to experiment

• Can describe structure, properties, energetics and reactivity

• Expensive

Molecular Modeling Software

• Many packages available on numerous platforms

• Most have graphical interfaces, so that molecules can be sketched and results viewed pictorially

• Will use a few selected packages to simplify the learning curve

• Experience readily transferred to other packages

Modeling Software, cont’d• Chem3D

– molecular mechanics and simple semi-empirical methods

– available on Mac and Windows– easy, intuitive to use– most labs already have copies of this, along

with ChemDraw

• Tinker – dynamics with molecular mechanics– available on Mac and Windows

Modeling Software, cont’d

• Gaussian – semi-empirical, density functional and ab initio

molecular orbital calculations– available on Mac, Windows and Unix

• GaussView– graphical user interface for Gaussian

Modeling Software, cont’d

• Amber– marcomolecular modeling and molecular

dynamics

• VMD– graphical display of macromolecular modeling

results