An Outlook of Computational Chemistry

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An Outlook of 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 does Computational Chemistry Calculate?

• Energy, Structure, and Properties
• Energy
• Equilibrium geometry
• Dipole moment
• Orbital energy levels and electronic excitation
  energy
• Electron distribution (electron density)
• Electrostatic potential and atomic charges
• Vibrational frequencies (IR spectra)
• Ionization energy, electron affinity, and proton
  affinity
• Reaction path, barrier height, and rate constant
• Etc.

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What Tools does 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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What Approximations does Computational Chemistry
Use? (MM)

• Ignore the changes in electronic structure.
• (Replace quantum mechanics by classical Newtonian
  mechanics.)
• Include only two-body effects for intermolecular
  interactions.
• (Many-body effects are accounted for in an
  averaged fashion implicitly through
  parameterization.)
• Use simple math functions for energy
  calculations.
• (Assume parameters are transferable use harmonic
  potentials for stretching and bending
  interactions use Lenard-Jone potential for VDW
  interactions use point charges to represent
  charge distributions negelect polarization
  effects.)

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What Approximations does Computational Chemistry
Use? (QM)
Schrödinger Equation
Electronic Schrödinger Equation
Hartree-Fock Equations
Roothann-Hall Equations
Best Approximated (Lowest) Energy
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What Approximations does Computational Chemistry
Use? (QM-2)
HF Theory
Neglecting Certain Terms in Hamiltonian
Represent Many-electon Wave Function by a Finite
Sum of Slater Determinants
Approximated Exchange Correlation Functionals
Semi-empirical Methods
Electron-correlated Wave Function Methods
Density Functional Theory
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What Approximations does Computational Chemistry
Use? (Propety)

• Use harmonic approximation for vibrational
  analysis and thermodynamic quantity computation.
• Reduce the temperature to 0 K.
• (Use the static structure to represent the
  molecule instead of the ensemble treatment with
  the electric, vibrational, rotational, and
  translational distribution of states at a
  non-zero temperature.)
• Calculate for a small number of particles and a
  short-time scale.
• (Experiments measure macroscopic properties.)
• Use transition state theory to determine rate
  constants.
• (Neglect the variational effects, non-classical
  recrossing, and tunneling.)

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What should I Do?

• Be aware of the merits and drawbacks of the
  methods, select and apply the suitable techniques
  to solve your chemical problems.

Full CI expansion Best many-electron WF
Complete CI expansion Exact solution to
electronic Schrödinger equation
Number of determinants
Complete basis set limit Best one-electron MO
HF
Minimum Basis set
Basis set size
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How could I Do?

• Obtain results as accurate as possible with
  reasonable compuational effort.
• Keep balance between theory and basis sets.
• HF/6-31G(d), B3LYP/6-31G(d,p),
• MP2/6-311G(2df,2pd), CCSD(T)/cc-pVQZ
• Start with low-level theory to get preliminary
  results, and refine the results with increasingly
  higher-level calculations.
• AM1 ? HF ? DFT ? MP2 ? CCSD(T)
• Geometry optimization at a lower level and
  single-point energy calculations at a higher
  level of theory.
• CCSD(T)/cc-pVQZ//MP2/cc-pVTZ
• Test the level of theory on smaller compounds and
  estimate the computational cost for your bigger
  system.
• Check convergency to make sure the numbers are
  meaningful.
• Practise, practise, and practise.

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Outlook

• Higher Accuracy
• Combining several levels of theory with a few
  empirical adjustments
• Design of new density functional models
• Improvement of the quality of basis sets
• Go beyond the Born-Oppenheimer approximation
  (e.g., spin-orbit coupling)
• Advanced dynamic algorithms (e.g., tunneling
  contribution)
• Development of special techniques for a
  particular purpose (e.g., energy conservation in
  molecular dynamics, implicit solvation models).

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Outlook (2)

• Bigger System
• Development of linear-scaling methods
• Development of combined QM/MM algorithms
• Development of efficient algorithms to sample
  hyperspace.
• More Diverse Applications
• Energy, geometry, IR spectrum, NMR shifting, rate
  constants, ...
• Gas-phase, liquid, solid, soft-materials ...
• Organic, inorganic, biological ...
• Environmental, medicinal, industrial, military
  ...
• More user-friendly programs.

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Summary

• Why do we need computational chemistry?
• What does computational chemistry calculate?
• What tools does computational chemistry provide?
• What should I do and how could I do?
• Outlook
• Higher accuracy
• Bigger system
• More diverse applications

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Your Homework

• Prepare for the
• Report for paper analysis (2 4 pages)
• Oral presentation of your project (40 minutes
  including questions)
• Short paper for your project (3 5 pages)

Please turn in two reports on 5/11. Also email me
your power point file between 5/11 and 5/15.
Thank you for attending the class! I hope that
you have enjoyed it. Now I look forward to you
teaching me something next Thursday in your
wonderful presentation!