Computational chemistry forces

There are several excellent publications in the literature which compare force fields, their apphcation areas, and their pros and cons [1-5]. Available force field parameters are published in a comprehensive and very extensive form, e.g., within the R views in Computational Chemistry series [6, 7j. 

I. Pettersson, T. Liljefors, Molecular mechanics calculated conformational energies of organic molecules a comparison of force fields, in Reviews in Computational Chemistry, Vbl. 9,... 

M. Jalaie, K. B. Lipkowitz, Published force field parameters for molecular mechanics, molecular dynamics, and Monte Carlo simulations, in Reviews in Computational Chemistry, Vol. 14, K.B. Lipkowitz, D. B. Boyd (Eds.), Wiley-VCH, New York, 2000, pp. 441-486. 

W L. Jorgensen, OPLS force fields, in 77ie Encydopedia of Computational Chemistry, Vol. 3, P. v. R. Schleyer,... 

Many of llic i(Jc isati(J insucs sii non rutin g ihc use of molecular mechanics (or force field technology) in computational chemistry are common to all force fields and in this section we describe many of Lli esc basic ideas. 

Dinur U and A T Hagler 1991. New Approaches to Empirical Force Fields. In K B Lipkowitz and D B Boyd (Editors). Reviews in Computational Chemistry Volmne 2. New York, VCH Publishers, pp. 99-164. 

Halgren T A 1996a. Merck Molecular Force Field I. Basis, Form, Scope, Parameterisation and Performance of MMFF94. Journal of Computational Chemistry 17 490-519. 

Halgren T A 1996b. Merck Molecular Force Field II MMEF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions. Journal of Computational Chemistry 17 520-552. 

Tripos a molecular mechanics force field, also the name of a company that sells computational chemistry software TST (transition state theory) method for computing rate constants UHF (unrestricted Hartree-Fock)... 

Caution If you are new to computational chemistry, do not use United Atoms for AMBER calculations. This HyperChem option is available for researchers who want to alter atom types and parameters for this force field. 

Note All of the force fields provided in HyperChem are built on new implementations of force fields developed by various computational chemistry research groups. However, HyperChem improves on the original force fields and uses new code. 

In computational chemistry it can be very useful to have a generic model that you can apply to any situation. Even if less accurate, such a computational tool is very useful for comparing results between molecules and certainly lowers the level of pain in using a model from one that almost always fails. The MM+ force field is meant to apply to general organic chemistry more than the other force fields of HyperChem, which really focus on proteins and nucleic acids. HyperChem includes a default scheme such that when MM+ fails to find a force constant (more generally, force field parameter), HyperChem substitutes a default value. This occurs universally with the periodic table so all conceivable molecules will allow computations. Whether or not the results of such a calculation are realistic can only be determined by close examination of the default parameters and the particular molecular situation. ... 

AD MacKerell Jr. Protein force fields. In PvR Schleyer, NL Allmger, T Clark, I Gasteiger, PA Kollman, HP Schaefer III, PR Schreiner, eds. The Encyclopedia of Computational Chemistry, Vol 3. Chichester, UK, Wiley 1998, pp 2191-2200. 

A few comments on the layout of the book. Definitions or common phrases are marked in italic, these can be found in the index. Underline is used for emphasizing important points. Operators, vectors and matrices are denoted in bold, scalars in normal text. Although I have tried to keep the notation as consistent as possible, different branches in computational chemistry often use different symbols for the same quantity. In order to comply with common usage, I have elected sometimes to switch notation between chapters. The second derivative of the energy, for example, is called the force constant k in force field theory, the corresponding matrix is denoted F when discussing vibrations, and called the Hessian H for optimization purposes. 

As the twentieth century came to a close, the job market for computational chemists had recovered from the 1992-1994 debacle. In fact, demand for computational chemists leaped to new highs each year in the second half of the 1990s [135]. Most of the new jobs were in industry, and most of these industrial jobs were at pharmaceutical or biopharmaceutical companies. As we noted at the beginning of this chapter, in 1960 there were essentially no computational chemists in industry. But 40 years later, perhaps well over half of all computational chemists were working in pharmaceutical laboratories. The outlook for computational chemistry is therefore very much linked to the health of the pharmaceutical industry itself. Forces that adversely affect pharmaceutical companies will have a negative effect on the scientists who work there as well as at auxiliary companies such as software vendors that develop programs and databases for use in drug discovery and development. 

When addressing problems in computational chemistry, the choice of computational scheme depends on the applicability of the method (i.e. the types of atoms and/or molecules, and the type of property, that can be treated satisfactorily) and the size of the system to be investigated. In biochemical applications the method of choice - if we are interested in the dynamics and effects of temperature on an entire protein with, say, 10,000 atoms - will be to run a classical molecular dynamics (MD) simulation. The key problem then becomes that of choosing a relevant force field in which the different atomic interactions are described. If, on the other hand, we are interested in electronic and/or spectroscopic properties or explicit bond breaking and bond formation in an enzymatic active site, we must resort to a quantum chemical methodology in which electrons are treated explicitly. These phenomena are usually highly localized, and thus only involve a small number of chemical groups compared with the complete macromolecule. 

Chemists seeking to use computational chemistry to support experimental efforts now have three generd theoretical tools available to them force field or molecular mechanics models, ab initio molecular orbital (MO) models and semiempirical MO models (1). Each of these tools have strengths and weaknesses which must be evaluated to determine which is most appropriate for a given applications. 

Wang, J., Wolf R.M., Caldwell, J.W, Kollman, P.A. and Case, D.A. (2004) Development and testing of a general amber force field. Journal of Computational Chemistry, 25, 1157-1174. 

For a spectroscopic observation to be understood, a theoretical model must exist on which the interpretation of a spectrum is based. Ideally one would like to be able to record a spectrum and then to compare it with a spectrum computed theoretically. As is shown in the next section, the model based on the harmonic oscillator approximation was developed for interpreting IR spectra. However, in order to use this model, a complete force-constant matrix is needed, involving the calculation of numerous second derivatives of the electronic energy which is a function of nuclear coordinates. This model was used extensively by spectroscopists in interpreting vibrational spectra. However, because of the inability (lack of a viable computational method) to obtain the force constants in an accurate way, the model was not initially used to directly compute IR spectra. This situation was to change because of significant advances in computational chemistry. 

The term computational chemistry can refer in its broadest sense to a wide range of methods that have been developed to give insight into the fundamental behavior of chemical species. Such methods include, but are not necessarily limited to, those related to quantum mechanics (1), molecular mechanics (or force-field calculations) (2), perturbation theory (3), graph theory (4), or statistical thermodynamics (5). For the purposes of this chapter, comments will be restricted to force-field and quantum-based calculations, since these are the techniques that have been used in work on lignin. Furthermore, these methods have been reviewed in a very readable book by Clark (6). 

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