Introduction to Computational Chemistry

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Introduction to Computational Chemistry
Computational Chemistry 5510 Spring 2006 Hai Lin
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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
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What is Computational Chemistry?

• Use of Computers to Help Solving Chemical
  Problems

Chemical Problems
Computer Programs
Math formulas
Physical Models
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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?

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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)

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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

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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
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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.

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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.

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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

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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, ...

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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)

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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
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Units

• Distance
• In Angstroms (1Å 10 -10 m 100 pm) and in Bohr
  (1 Bohr 0.539 Å)
• Most bond lengths are of 1 to 2 Å.
• 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)

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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...

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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.
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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.
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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.
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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.
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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?

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Your Homework

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