Chemistry 6440 / 7440

1. Chemistry 6440 / 7440 Computational Chemistry and Molecular Modeling

2. 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

3. 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)

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. Modeling Software, cont’d • Amber • marcomolecular modeling and molecular dynamics • VMD • graphical display of macromolecular modeling results