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 semiempirical 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