Title: Introduction to Computational Chemistry
1Introduction to Computational Chemistry
Computational Chemistry 5510 Spring 2006 Hai Lin
2Biological Chemical Processes
Therapeutics Biotechnology
Na,K-ATPase
Bio-nano Device
Mechanism Dynamics
Energy
Influenza Virus
(Science 2004, 304, 1944)
New Drugs
Progress of Reaction
http//www.rkm.com.au/VIRUS/
HY EY
Experiment
Theory/Computation
3What is Computational Chemistry?
- Use of Computers to Help Solving Chemical
Problems
Chemical Problems
Computer Programs
Math formulas
Physical Models
4What does Computational Chemistry Calculate?
- Energy, Structure, and Properties
- What is the energy for a given geometry?
- How does energy vary when geometry changes?
- Which geometries are stable?
- How do atoms rearrange to form new molecules?
- How does energy change w/r extenal perturbation?
- How do stucture, energy, and properties change
over time?
5What does Computational Chemistry Calculate? (2)
- Examples
- Energy (enthalpy of formation)
- Equilibrium geometry
- Dipole moment
- Orbital energy levels (HOMO, LUMO, others)
- Electron distribution (electron density)
- Electrostatic potential
- Vibrational frequencies (IR spectra)
6What does Computational Chemistry Calculate? (3)
- Examples
- Ionization energy (HOMO energy)
- Electron affinity (LUMO energy)
- Proton affinity
- Electronic excitation energy (UV-Vis spectra)
- NMR chemical shifts and coupling constants
- Reaction path and barrier height
- Reaction rate
7What Tools do Computational Chemistry Provide?
- Molecular Visualization (Graphic Representation)
- Molecular Mechanics (Classical Newtonian Physics)
- Semi-empirical Molecular Orbital Theory
- Ab Initio Molecular Orbital Theory
- Density Functional Theory
- Geometry Optimization
- Molecular Dynamics
Quantum Mechanical Methods
8Levels of Calculations
- Molecular Mechanics (MM)
- Empirical energy functions parameterized against
experimental data - Fast, simple, generally not very accurate (gt 104
atoms) - Semi-empirical Molecular Orbital Methods
- Can treat moderate sized molecules (gt 102 atoms).
- Accuracy depends on parameterization.
9Levels of Calculations (2)
- Ab initio Molecular Orbital Methods
- Computationally demanding (gt 10 atoms)
- Accuracy can be systematically improved.
- Density Functional Theory (DFT)
- More efficient than ab initio calculations (gt 10
atoms) - Accuracy varies, however, there is no
systematical way to improve the accuracy.
10Exploring Potential Energy Surface
- Geometry Optimization
- Finding stable structures and transition states
- Efficient in finding local minima, but global
minimum not guaranteed - Molecular Dynamics (MD)
- Providing a time-dependent movie for the
movements of the molecules - Usually by solving Newtons equations of motion
11Computational Cost
- Measured as CPU time needed w/r the Size of
System (e.g., the number of atoms, N) - Typical Scaling behavior
- Molecular mechanics N2
- Semi-empirical MO methods N3
- Density functional theory N4
- Ab initio MO methods N4, N5, N6, ...
12Computational Cost (2)
- Example of Estimation for CPU time
- Supposed N 10, and a semi-empirical MO
calculation ( N3) uses 1000 sec 17 min (a cup
of coffee) - Density functional theory ( N4) would use 10,000
sec 2.8 hour (a French dinner) - MP2 (Møller-Plesset Perturbation Theory with 2nd
order corrections, N5), 100,000 sec (more
than one day)
13Computational Cost vs. Accucary
Accuracy
Linear Scaling Methods N
?
Quantum Mechanical Methods
Molecular Mechanics
Number of Atoms
1000
10,000
10
100
Atom and Small Molecules
Large Compounds and Nano-clusters
Proteins, DNA, RNA
14Units
- Distance
- In Angstroms (1Ã… 10 -10 m 100 pm) and in Bohr
(1 Bohr 0.539 Ã…) - Most bond lengths are of 1 to 2 Ã….
- Angles and Dihedral
- In degrees
- Potential Energy
- In kcal/mol (1 kcal/mol 4.184 kJ/mol) and in
Hartree (1 Hartree 627.5 kcal/mol)
15Computers and Programs
- Unix/Linux vs MS_Windows/Mac
- Computation vs Visualization
- Serial vs Parallel
- Popular Programs
- Gamess, Gaussian, NWChem, MOPAC, Spartan...
- Amber, CHARMM, Tinker...
- InsightII, VMD...
16Literature
- Books
- F. Jensen, Introduction to Computational
Chemistry, Wiley, 1999 (our textbook) - A. R. Leach, Molecular Modelling, 2nd Ed.,
Prentice Hall, 2001 - C. J. Cramer, Essentials of Computational
Chemistry, 2nd Ed., Wiley, 2004
There are more, but these three should be good at
the beginning.
17Literature (2)
- Journals
- Chemical Physics Letters
- Journal of Chemical Physics
- Journal of Chemical Theory and Computation
- Journal of Computational Chemistry
- Journal of Molecular Structure Theochem
- Journal of Physical Chemistry A B
- Molecular Physics
- Reviews in Computational Chemistry
- Theoretical Chemistry Accounts
Computational chemistry papers are also published
by Angw. Chem., Biochemistry, JACS, JOC, PCCP,
and other journals.
18WWW
- Computational Chemistry List (CCL)
http//www.ccl.net/ - Protein Data Bank (PDB) http//www.pdb.org/
- Computational Chemistry at CU-Denver
http//carbon.cudenver.edu/hlin/www-group/Index.h
tml - UNIX Tutorial for Beginners http//www.ee.surrey.a
c.uk/Teaching/Unix/ - Spartan http//www.wavefun.com/
- Tinker http//dasher.wustl.edu/tinker/
- VMD http//www.ks.uiuc.edu/Research/vmd/
There are numerous web sites about computational
chemistry. Go to CCL and you can get more
information.
19How do we do Computational Chemistry?
- Understand the language and culture of
computational chemistry (read the textbook,
attend the class). - Understand the tools (take the lab, practise as
much as you can). - Understand the chemical problem you want to solve
(computers do not solve problems, people do). - Understand the results (be critical on what you
get).
If you do as I suggested above, I do not see any
reasons that you will not get a good
grade...unless you do not do the course work.
20Summary
- What is Computational Chemistry?
- What does Computational Chemistry Calculate?
- What Tools do Computational Chemistry Provide?
- Levels of Calculations
- Exploring Potential Energy Surface
- Computational Cost vs. Accucary
- Units
- Computers and Programs, Literature, and WWW
- How do we do Computational Chemistry?
21Your Homework
- Further reading
- Syllabus
- Textbook
- Preface
- 1 Introduction
- Appendix C
- Please read the materials that I assigned, and
take notes when you read.