Computational chemistry fundamental problems

Fundamental challenges in computational chemistry include the high computational cost of ab initio calculations in terms of time, memory, and disk space requirements difficulties that arise when standard advanced computational treatments are used to describe processes such as bond breaking determination of the best approach toward functional development in density functional theorgy, understanding the means for quantitative prediction of thermonuclear kinetics and computational chemistry treatment of transition metal systems for reliable prediction of molecular properties. This book addresses these important problems, featuring chapters by leading computational chemists and physicists. 

The credit load for die computational chemistry laboratory course requires that the average student should be able to complete almost all of the work required for the course within die time constraint of one four-hour laboratory period per week. This constraint limits the material covered in the course. Four principal computational methods have been identified as being of primary importance in the practice of chemistry and thus in the education of chemistry students (1) Monte Carlo Methods, (2) Molecular Mechanics Methods, (3) Molecular Dynamics Simulations, and (4) Quantum Chemical Calculations. Clearly, other important topics could be added when time permits. These four methods are developed as separate units, in each case beginning with die fundamental principles including simple programming and visualization, and building to the sophisticated application of the technique to a chemical problem. 

We begin with a brief and mathematieally light-handed treatment of the fundamentals of QM necessary to describe organic molecules. This presentation is meant to acquaint those unfamiliar with the field of computational chemistry with a general understanding of the major methods, concepts, and acronyms. Sufficient depth will be provided so that one can understand why certain methods work well while others may fail when applied to various chemical problems, allowing the casual reader to be able to understand most of any applied computational chemistry paper in the literature. Those seeking more depth and details, particularly more derivations and a fuller mathematical treatment, should consult any of the... 

One of the fundamental problems in chemistry is understanding at the molecular level the effect of the medium on the rate and the equilibrium of chemical reactions which occur in bulk liquids and at surfaces. Recent advances in experimental techniques[l], such as frequency and time-resolved spectroscopy, and in theoretical methods[2,3], such as statistical mechanics of the liquid state and computer simulations, have contributed significantly to our understanding of chemical reactivity in bulk liquids[4] and at solid interfaces. These techniques are also beginning to be applied to the study of equilibrium and dynamics at liquid interfaces[5]. The purpose of this chapter is to review the progress in the application of molecular dynamics computer simulations to understanding chemical reactions at the interface between two immiscible liquids and at the liquid/vapor interface. 

Progress in theory, availability of software and development of computer technology have created highly sophisticated systems for performing complex calculations on various chemical compounds. Computational methods are routinely used nowadays not only by theoretical chemists but also by experimentalists (cf. QCLDB bibliography [1]). There is no doubt that the future of computational methods is bright. However, two fundamental problems face further development of computational chemistry. 

The missing link between the constitution of a molecule and its 3D structure in computational chemistry is a technique capable of automatically generating 3D models starting from the connectivity information of a given molecule. Because of its basic role, 3D structure generation is one of the fundamental problems in computational chemistry. As a consequence, in recent years, a number of automatic 3D model builders and conformer generators have become available [for two recent reviews, see Refs. 3 and 4],... 

David A. Dixon is a Battelle fellow in the Fundamental Science Directorate at the Pacific Northwest National Laboratory (PNNL), where he previously served as associate director for theory, modeling, and simulation at the William R. Wiley Environmental Molecular Sciences Laboratory. His main research interest is the use of numerical simulation to solve complex chemical problems with a primary focus on the quantitative prediction of molecular behavior. He uses numerical simulation methods to obtain quantitative results for molecular systems of interest to experimental chemists and engineers with a specific focus on the design of new materials and production processes. Before moving to PNNL, he was research fellow and research leader in computational chemistry at DuPont Central Research and Development (1983-1995) and a member of the Chemistry Department at the University of Minnesota, Minneapolis (1977-1983). He earned his B.S. in chemistry from the California Institute of Technology and his Ph.D. in physical chemistry from Harvard University, where he served as a junior fellow of the Society of Fellows, Harvard University. He is a fellow of the American Association for the Advancement of Science, and a fellow of the American Physical Society. He is a recipient of the 1989 Leo Hendrik Baekeland Award presented by the American Chemical Society, the Federal Laboratory Consortium Technology Transfer Award (2000), and the 2003 American Chemical Society Award for Creative Work in Fluorine Chemistry. 

John C. Tully is Arthnr T. Kemp Professor of Chemistry, Physics, and Applied Physics in the Department of Chemistry at Yale University. Tully is a leading theorist studying the dynamics of gas surface interactions. He develops theoretical and computational methods to address fundamental problems and then works with experimentalists to integrate theory with observation. Energy exchange and redistribution, adsorption and desorption, and dissociation and recombination are among surface phenomena he has elucidated. He uses mixed quantum-classical dynamics, which allow the extension of conventional molecular dynamics simulation methods to processes involving electronic transitions or quantum atomic motion. He is a member of the National Academy of Sciences. 

Elucidating the stable conformations (conformers) of molecules and the possible transitions among these conformers is one of the most fundamental problems of computational chemistry. Conformational studies were performed long before the availability of computers using mechanical models, and the computer became the most important tool in the analysis of molecular structure only after substantial efforts had been devoted to hardware and software development (see Molecular Models Visualization). In addition to manipulating molecules on the screen (see Molecular Models Visualization), computational approaches can exploit an extremely broad spectrum of conformational analysis methods, ranging from a simple search using a molecular mechanics (MM) potential to Monte Carlo or molecular dynamics (MD) simulations in the presence of explicit solvent. 

C. Having quantitative CE values for all atoms in the periodic table, along with use of LLa, leads to optimism for improved chemical rationalization of charge distributions for molecules and solids. On the other hand, advances in understanding binding energies and geometries are not achieved by any of the discussion in this article and remain as fundamental problems in computational chemistry. 

From this review, the rapid evolution of rigorous free energy calculations and of their applications to a broad range of fundamental and exciting problems is apparent. It has been a thrilling period in the development of computational chemistry. 

---