Cheminformatics
CHEMINFORMATICS: EMERGING TRENDS IN CHEMISTRY
Dr.Keshav Mohan, P G Department of Chemistry, MSM College, Kayamkulam, Kerala.
In recent years computational techniques has emerged as a versatile tool for learning intricacies in chemistry. Cheminformatics or computational chemistry refers to application of tools of information technology for storage, visualization, interpretation , retrieval and acquisition of chemical data. Cheminformatics combines tools and techniques of mathematics, computer science and chemistry to solve problems of bond length, bond energies, heat of reactions, reaction path ways & rates, mechanism and prediction of molecular structures. The term computational chemistry is used when a mathematical description of chemistry is sufficiently developed that it can be run on a computer system.
The major areas of computer application in teaching and research in chemistry are 1.Softwares involving numerical calculations and information processing
2.Computer interfacing in analytical equipments.
To make abreast cheminformatics , one need not become a computer programmer. There are many organizations which supply well documented user friendly computer programmes for academics. Quantum chemistry programme exchange [QCPE], Indiana university provides sophisticated programme developed by researchers for use in graduate courses. CNDUIT is another agency which distributes computer aided educational materials related to chemistry. Chemical Abstract Service [C A S] of American Chemical society has systematically abstracted the world wide chemical literature in terms of both structure and bibliography. The bibliographic information consists of titles, authors, journals, abstracts of papers, patents, structural information and so on. Now CAS offers Chemical structure and information database whereby users can get information at the click of a mouse.
Modeling and simulation of chemical experiments are routinely done to understand interactions between the adjustable parameters and to search for the best value for them. Monte Carlo technique and molecular dynamics can be used on the calculation of the equilibrium properties of many body systems of interacting particles. Computers can be used in simulations to design chemical experiments and then to optimize them with adjustable parameters. This can be economical than conducting prototype experiments. AMBER is a common molecular simulation programme.
Arriving at an appropriate structure for a compound is no longer difficult. Chemdraw Pro is a chemistry programme that combines the most advanced technologies in structure drawing .It understands the IUPAC nomenclature rules. The programme allows one to create high quality structure simply by entering molecular names. It also recognizes many trivial names. It can also assign systematic name to structures. Some other programmes in the generic are chem office pro, chem finder pro etc.
Artificial intelligence has been applied to drug design in recent years. In drug design it is desired to generate suitable molecular structures that can hit and hinder functionality of undesired sites. By combining molecular simulation packages with artificial intelligence it is possible to have numerous invitro trials in an automated fashion in order to arrive at site specific structures.
Some common software in chemistry are listed below.
· ATMOL : an ab initio programmes
· EyeChem : for molecular modeling
· MOPAC : molecular orbital package for molecular structure and reactions
· GRASP : for graphical representation and analysis of structural properties
· MOLDEN : for visualization of molecular structure
· RasMol : for visualization of molecular structure
· CHIME
· STERIC : a programmes for calculating steric effect
· TINKER : a package for molecular mechanics and dynamics
It is also interesting to note some of the relevant websites carrying information related to computational chemistry.
· www.amber.ucsf.edu : for molecular simulation programmes
· www.caos.kun.nl : for visualization of molecular structure
· www.sfu.com : for instructional software for chemistry
· www.ncsa.uiuc.edu : for computational chemistry software packages
· www.auburn.edu : for selected topics in computational chemistry
· www.chem.iupui.edu : for reviews in computational chemistry
A few well written books are also available in the subject.
· G H Grant, W G Richards : Computational Chemistry [ Oxford]
· F Jensen : Introduction to computational chemistry [John Wiley & Sons ]
The application of information technology tools in chemistry is thus revolutionizing learning and research in chemistry in the areas of symbolic calculations, structure – property relationships , molecular modeling , simulations and artificial intelligence leading to site specific drug discovery.