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Introduction to Computational Chemistry

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Title: Introduction to Computational Chemistry


1
Introduction to Computational Chemistry
Computational Chemistry 5510 Spring 2006 Hai Lin
2
Biological 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
3
What is Computational Chemistry?
  • Use of Computers to Help Solving Chemical
    Problems

Chemical Problems
Computer Programs
Math formulas
Physical Models
4
What 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?

5
What 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)

6
What 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

7
What 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
8
Levels 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.

9
Levels 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.

10
Exploring 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

11
Computational 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, ...

12
Computational 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)

13
Computational 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
14
Units
  • 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)

15
Computers 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...

16
Literature
  • 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.
17
Literature (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.
18
WWW
  • 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.
19
How 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.
20
Summary
  • 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?

21
Your Homework
  • Further reading
  • Syllabus
  • Textbook
  • Preface
  • 1 Introduction
  • Appendix C
  • Please read the materials that I assigned, and
    take notes when you read.
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