Overview of Computational Chemistry


Computational Chemistry

Overview Materials

  • Computational Science
  • Computational Chemistry
  • Basic Quantum Chemistry
  • Schrodinger's Equation
  • Atomic Units
  • The Born Oppenheimer Approximation
  • The Hartree Fock Approximation

  • Key Points


  • Overview
  • Atomic Orbitals

    Lab Activities

  • Z-matrices
  • Basis Sets
  • Geometry Optimizations
  • Ionization Energies

    Support Materials

  • Interactive Tools
  • Glossary of Terms
  • Quick Guide to DISCO Output File

    Related Links

  • ChemViz
  • Computational Chemistry
  • SUCCEED's Computational Chemistry

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    Key Points


    Chemists have been some of the most active and innovative participants in this rapid expansion of computational science. Computational chemistry is simply the application of chemical, mathematical and computing skills to the solution of interesting chemical problems. It uses computers to generate information such as properties of molecules or simulated experimental results. Some common computer software used for computational chemistry includes:
    • Gaussian xx, Gaussian 94 currently
    • GAMESS
    • MOPAC
    • Spartan
    • Sybyl
    Computational chemistry has become a useful way to investigate materials that are too difficult to find or too expensive to purchase. It also helps chemists make predictions before running the actual experiments so that they can be better prepared for making observations. The Schroedinger equation (explained in another section) is the basis for most of the computational chemistry scientists use. This is because the Schroedinger equation models the atoms and molecules with mathematics. For instance, you can calculate:
    • electronic structure determinations
    • geometry optimizations
    • frequency calculations
    • transition structures
    • protein calculations, i.e. docking
    • electron and charge distributions
    • potential energy surfaces (PES)
    • rate constants for chemical reactions (kinetics)
    • thermodynamic calculations- heat of reactions, energy of activation
    Currently, there are two ways to approach chemistry problems: computational quantum chemistry and non-computational quantum chemistry Computational quantum chemistry is primarily concerned with the numerical computation of molecular electronic structures by ab initio and semi-empirical techniques and non-computational quantum chemistry deals with the formulation of analytical expressions for the properties of molecules and their reactions.

    We just mentioned ab initio and semi-empirical numerical techniques. Definitions of these terms are helpful in understanding the use of computational techniques for chemistry. Scientists mainly use three different methods to make calculations:

    • ab initio, (Latin for "from scratch") a group of methods in which molecular structures can be calculated using nothing but the Schroedinger equation, the values of the fundamental constants and the atomic numbers of the atoms present (Atkins, 1991).
    • Semi-empirical techniques use approximations from empirical (experimental) data to provide the input into the mathematical models.
    • Molecular mechanics uses classical physics to explain and interpret the behavior of atoms and molecules

    The table below attempts to capture the specifics of each of these three methods:

    Method Type Advantages Disadvantages Best for
    Molecular Mechanics
    • uses classical physics
    • relies on force-field with embedded empirical parameters
    • Computationally least intensive - fast and useful with limited computer resources
    • can be used for molecules as large as enzymes
    • particular force field applicable only for a limited class of molecules
    • does not calculate electronic properties
    • requires experimental data (or data from ab initio) for parameters

    • large systems (thousands of atoms)
    • systems or processes with no breaking or forming of bonds
    • uses quantum physics
    • uses experimentally derived empirical parameters
    • uses approximation extensively
    • less demanding computationally than ab initio methods
    • capable of calculating transition states and excited states
    • requires experimental data (or data from ab initio) for parameters
    • less rigorous than ab initio) methods

    • medium-sized systems (hundreds of atoms)
    • systems involving electronic transitions
    Ab Initio
    • uses quantum physics
    • mathematically rigorous, no empirical parameters
    • uses approximation extensively
    • useful for a broad range of systems
    • does not depend on experimental data
    • capable of calculating transition states and excited states
    • computationally expensive

    • small systems (tens of atoms)
    • systems involving electronic transitions
    • molecules or systems without available experimental data ("new" chemistry)
    • systems requiring rigorous accuracy

    To summarize, computational chemistry is:

    • a branch of chemistry that generates data which complements experimental data on the structures, properties and reactions of substances. The calculations are based primarily on Schroedinger's equation and include:

      1. calculation of electron and charge distributions
      2. molecular geometry in ground and excited states
      3. potential energy surfaces
      4. rate constants for elementary reactions
      5. details of the dynamics of molecular collisions

    • particularly useful for:

      1. determination of properties that are inaccessible experimentally
      2. interpretation of experimental data

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