Overview of Molecular Modelling

Molecular modelling is a very diverse subject, ranging from the acquisition and subsequent display of molecular coordinates through to highly accurate (i.e. better than experiment) numerical simulation using theoretically derived functions. Depending on the context and the rigour, the subject itself is also often referred to as "molecular graphics", "molecular visualisation", "computational chemistry", "computational quantum chemistry" or "theoretical chemistry". A related area known as "molecular simulation" relates the use of molecular modelling techniques to describing and understanding the statistical behaviour and properties of collections of molecules on a "macroscopic" scale. "Molecular dynamics" deals with those time-dependent properties of collections of molecules, and uses many of the techniques of molecule modelling and statistical mechanics. Both these last two methods are beyond the scope of this lecture course.

Six Characteristic Features and Classifications

  1. Five Molecular Scales. Molecular modelling spans an enormous range of molecule size.
    1. Solutions of the Quantum Mechanical (QM) Schroedinger equation which predict properties at least as accurate as can be measured by experiment are only available for molecules with up to ~8 atoms (rather more with symmetry)
    2. Acceptably accurate "QM" solutions are nowadays available for molecules with perhaps 250 atoms if large-scale computational resources are available (see DNA).
    3. The "macromolecular" region of up to 10,000 atoms can be treated using semi-empirical (SE) QM methods, giving approximate chemical accuracy.
    4. Beyond this, in the region up to about 50,000 atoms, non-quantum mechanical solutions based on "Molecular Mechanics" (MM) methods can be used.
    5. For larger systems (the "Mesoscopic" region), the "atom" is replaced by "unified groups" of several atoms, or by simple descriptions (spheres, ellipsoids, etc) of entire molecules and one can treat collections of perhaps up to a million molecules.
  2. Molecular Coordinates. Molecular modellers were amongst the first to take full advantage of on-line databases and information sources, and were the first chemists to adapt to the modern Internet. 3D atom coordinates are an essential feature of many modelling methods.
  3. Molecular Visualisation. Once 3D coordinates are available, they can be visualised, an important aid to interpretation of molecular modelling:
  4. Molecular Structure Analysis. Once a visual model is available, simple "heuristics" (rules) can be applied. These include:
  5. Molecular Structure and Property Prediction
  6. Molecular Reactivity and Potential energy surfaces

The next two aspects of modelling are largely beyond the scope of the current lecture course:

Typical Molecular Modelling Software Tools

The "tools of the trade" have gradually evolved from physical models (Dreiding, CPK, etc) and calculators, including the use of programmable computers (starting around 1956 with the introduction of the first scientific programming language called Fortran), computers as visualisation aids (around 1970-), computers running commercially written analysis "packages" such as e.g. Sybyl (around 1984-) and most recently integration using Internet based tools and Workbenches (1994-) based on languages such as HTML, JavaScript, Java and C++. A Forum for discussing such tools, and other general queries is the Computational Chemistry List (CCL).

A typical selection of molecular modelling teaching tools available within the department is listed below.

  1. Mercury: A (free) Crystallographic unit cell viewer and editor.
  2. Jmol: A (free) Web-browser applet that can display molecules, and some of their properties such as surfaces, spectra, vibrations, etc.
  3. Ghemical: an OpenSource molecular editing and molecular mechanics program. Superceded by Avogadro.
  4. ChemDraw/ChemBio3D: Molecule editor and 3D geometry molecular mechanics/quantum mechanics optimisation and display tool (STEREO ENABLED)
  5. Gaussview+Gaussian 09: Ab initio quantum mechanics editors and programs.
  6. DS Viewer Pro (STEREO ENABLED)
  7. VMD visualisation of molecular dynamics (STEREO ENABLED)

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(c) H. S. Rzepa 1998-2012. No reproduction rights granted to this material without permission.