Overview on computational chemistry

Abstract

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:\rGaussian xx, Gaussian 94 currently\rGAMESS\rMOPAC\rSpartan\rSybyl\rComputational 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:\relectronic structure determinations\rgeometry optimizations\rfrequency calculations\rtransition structures\rprotein calculations, i.e. docking\relectron and charge distributions\rpotential energy surfaces (PES)\rrate constants for chemical reactions (kinetics)\rthermodynamic calculations- heat of reactions, energy of activation\rCurrently, 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.\rWe 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:\r\rab 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).\rSemi-empirical techniques use approximations from empirical (experimental) data to provide the input into the mathematical models.\rMolecular mechanics uses classical physics to explain and interpret the behavior of atoms and molecules\rThe table below attempts to capture the specifics of each of these three methods:\r\rMethod Type\tAdvantages\tDisadvantages\tBest for\rMolecular Mechanics\t\ruses classical physics\rrelies on force-field with embedded empirical parameters\rComputationally least intensive - fast and useful with limited computer resources\rcan be used for molecules as large as enzymes\rparticular force field applicable only for a limited class of molecules\rdoes not calculate electronic properties\rrequires experimental data (or data from ab initio) for parameters\rlarge systems (thousands of atoms)\rsystems or processes with no breaking or forming of bonds\rSemi-Empirical\t\ruses quantum physics\ruses experimentally derived empirical parameters\ruses approximation extensively\rless demanding computationally than ab initio methods\rcapable of calculating transition states and excited states\rrequires experimental data (or data from ab initio) for parameters\rless rigorous than ab initio) methods\rmedium-sized systems (hundreds of atoms)\rsystems involving electronic transitions\rAb Initio\t\ruses quantum physics\rmathematically rigorous, no empirical parameters\ruses approximation extensively\ruseful for a broad range of systems\rdoes not depend on experimental data\rcapable of calculating transition states and excited states\rcomputationally expensive\rsmall systems (tens of atoms)\rsystems involving electronic transitions\rmolecules or systems without available experimental data ("new" chemistry)\rsystems requiring rigorous accuracy\r\rTo summarize, computational chemistry is:\r\ra 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:\rcalculation of electron and charge distributions\rmolecular geometry in ground and excited states\rpotential energy surfaces\rrate constants for elementary reactions\rdetails of the dynamics of molecular collisions\rparticularly useful for:\rdetermination of properties that are inaccessible experimentally\rinterpretation of experimental data\r