Force-field studies, empirical

J. C. Smith and M. Karplus, Empirical force field study of geometries and confrontational transitions of some organic molecules, J. Am. Chem. Soc. 114 801 (1982). 

Metal-n-allyl complexes are important in a number of stereoselective catalytic reactions and are therefore attractive for computational chemists (see also Chapter 13, Section 13.2). An empirical force field study based on the MM2 parameterization scheme aimed at predicting stereoselective nickel(0)-catalyzed cycloadditions was recently conducted 56. As in a similar study 57, where a force field for the structure optimization of palladium-allyl systems was developed, dummy atoms were needed to define the structural model. Based on the assumptions required to model a catalytic process, the results obtained have to be interpreted with caution. 

Emsley and coworkers125 have made an X-ray crystallographic and empirical force-field study of a simple non-hydrogen-bonded 2-acetylenamine (50). The molecule has the EZ configuration in the crystal, but the calculations (MM2 and MMP2) predict the ZZ form to be more stable by 0.7 kcal mol - Ab initio calculations on 3-aminoacrolein also favor the ZZ form, but here the intramolecular hydrogen bond plays a decisive role. 

In this chapter we refer to recent reports describing the successful development and application of NMR-based techniques to study lipids in various contexts, to develop new methods to study recombinant proteins and peptides in artificial lipid membranes and last, but not least, to validate other methods such as all-atomistic force field and empirical models on the basis of NMR parameters. 

Example Jensen and Gorden calculated the potential energy surface of glycine using ab initio and semi-empirical methods.This study is of special interest to developers of molecular mechanics force fields. They frequently check their molecular mechanics methods by comparing their results with ab initio and semi-empir-ical calculations for small amino acids. 

Empirical energy functions can fulfill the demands required by computational studies of biochemical and biophysical systems. The mathematical equations in empirical energy functions include relatively simple terms to describe the physical interactions that dictate the structure and dynamic properties of biological molecules. In addition, empirical force fields use atomistic models, in which atoms are the smallest particles in the system rather than the electrons and nuclei used in quantum mechanics. These two simplifications allow for the computational speed required to perform the required number of energy calculations on biomolecules in their environments to be attained, and, more important, via the use of properly optimized parameters in the mathematical models the required chemical accuracy can be achieved. The use of empirical energy functions was initially applied to small organic molecules, where it was referred to as molecular mechanics [4], and more recently to biological systems [2,3]. 

Knowledge of the approaches and target data used in the optimization of an empirical force field aids in the selection of the appropriate force field for a given study and acts... 

Central to the quality of any computational smdy is the mathematical model used to relate the structure of a system to its energy. General details of the empirical force fields used in the study of biologically relevant molecules are covered in Chapter 2, and only particular information relevant to nucleic acids is discussed in this chapter. 

Previous theoretical studies of isolated and doped PA have mostly dealt with geometrical structures and charge and spin wavess. A few have dealt with the vibrational spectrumS2i = using force fields derived from fits to experimental infrared and Raman spectra of smaller polyenes or from scaled force constants obtained from semi-empirical SCF calculations on these systems. Very little the-... 

Despite advent of theoretical methods and techniques and faster computers, no single theoretical method seems to be capable of reliable computational studies of reactivities of biocatalysts. Ab initio quantum mechanical (QM) methods may be accurate but are still too expensive to apply to large systems like biocatalysts. Semi-empirical quantum methods are not as accurate but are faster, but may not be fast enough for long time simulation of large molecular systems. Molecular mechanics (MM) force field methods are not usually capable of dealing with bond-breaking and formation... 

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