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Quantum Simulation of Alkanes and Proteins

© Adam Hughes

The most basic type of chemistry simulation to perform is a quantum calculation (it's basic, but not necessarily, simple!) where electronic properties are treated in some explicit way. The most basic types of molecules that can be studied to begin to understand biological properties are proteins and alkanes (alkanes consist of carbon and hydrogen atoms bonded in various configurations). Therefore, to begin looking at biological simulation, it behooves us to take a look at some studies involving quantum calculations on alkanes and proteins.

There has been a lot of work done over the years to understand the structures and interactions of many alkanes in their various forms (solid, liquid, gas). Much of the computational work has been focused on developing reliable parameters for quantities such as carbon-hydrogen bond energies in a variety of molecules and conformations. One place where much recent effort has been expended in this direction is MSI, or Molecular Simulations, Inc., based in San Diego, CA. A good example of this is MSI's Class II Force Field, or CFF. This forcefield, designed to be used in molecular dynamics-type simulations, was developed by computing properties for thousands of molecules and configurations to produce millions of energies and related quantities. To learn more about CFF, visit http://www.msi.com/life/products/insight... .

One area of great interest in the study of proteins is the determination of optical and vibrational spectral properties of the chemical species. Researchers at Ludwig-Maximilians University in Munchen (Munich), Germany, have been investigating this problem in recent years. Their efforts have yielded a hybrid method of examining protein species contained in some liquid matrix. The protein, or solute, is treated with ab initio methods; while the surrounding liquid, the solvent, is treated using a classical molecular mechanics approach. These advances in technique, as well as other efforts to speed calculation, have allowed the scientists to study several molecules in solution as well as a species of retinal chromophore in bacteriorhodopsin. To read more about these efforts, check out http://www.imo.physik.uni-muenchen.de/ta... .

On a larger scale still are the studies of researchers at Vilnius University and Oklahoma State University, who have used quantum mechanical techniques to study large molecules such as fullerenes and photoactive molecules. Their efforts include energy calculations to determine the most stable in a series of fullerenes. More information can be found at http://fondazione-elba.org/54.htm .

Of course these examples are just a tiny sampling of some of the work that has been done or is still being conducted in the area of quantum simulation for biologically interesting molecules. An interesting place to learn more about quantum mechanical processes in biological systems is the Quantum Biology homepage, housed at the

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