Force-field approach

Bernard A, A M CapeUi, A Comotti, C Gannari, J M Goodman and I Paterson 1990. Transltion-St Modeling of the Aldol Reaction of Boron Enolates A Force Field Approach. Journal of Orga Chemistry 55 3576-3581. 

Chymotrypsin, 170,171, 172, 173 Classical partition functions, 42,44,77 Classical trajectories, 78, 81 Cobalt, as cofactor for carboxypeptidase A, 204-205. See also Enzyme cofactors Condensed-phase reactions, 42-46, 215 Configuration interaction treatment, 14,30 Conformational analysis, 111-117,209 Conjugated gradient methods, 115-116. See also Energy minimization methods Consistent force field approach, 113 Coulomb integrals, 16, 27 Coulomb interactions, in macromolecules, 109, 123-126... 

Folding energy and catalysis, 227 Force field approach, consistent 113 Free energy, 43,47 of activation, 87-90, 92-93, 93, 138 of charging processes, 82 convergence of calculations of, 81 in proteins, SCAAS model for, 126 of reaction, 90... 

Thus, in contrast to preceding MM approaches explicit treatment of electronic polarisability is integral to a semi-empirical QM approach and promises excellent prospects for quantitative theoretical modelling of carbohydrates across a range of condensed phase environments. The results of the PM3CARB-1 model do however indicate in line with classical force field approaches [65, 73] that perhaps greater... 

As a consequence, the electronic properties of these ligands are replaced by the electronic properties of hydrogen atoms, while their steric influence is taken into account by the empirical force field approach. 

Kollman, P.A. Case, D.A. Dmg-target binding forces advances in force field approaches, 169-185 Mason, J.S. Pickett, S.D. Combinatorial library design. Molecular similarity and diversity applications, 187-242 Muegge, I. 

The rest of this chapter examines the various components of the molecular energy and the force-field approaches taken for their computation. The discussion is, for the most part, general. At the end of the chapter, a comprehensive listing of reported/available force fields is provided with some description of their form and intended applicability. 

In the majority of continuum solvation models incorporating a surface-tension approach to estimating the non-electrostatic solvation components, the index k in Eq. (11.22) runs over a list of atom types, and die user assigns the appropriate type to each atom of the solute. This is particularly straightforward for MM models, like the Generalized Bom/Surface Area (GB/SA) model (Still el al. 1990 see also Best, Merz, and Reynolds 1997), since atom types are already intrinsic to the force field approach. This same formalism has been combined with the CHARMM and Cornell et al. force fields (see Table 2.1) to define GB models for proteins and nucleic acids (Dominy and Brooks 1999 Jayaram, Sprous, and Beveridge 1998). Considering this approach applied within the QM arena, the MST-ST models of Orozco and Luque have been the most extensively developed (see, for instance, Curutchet, Orozco, and Luque 2001). 

For discussions, sec Beckwith Tetrahedron 1981, 37, 3073-3100 Verhocven Revl. Trav. Chim. Pays-Bas 1980, 99, 143. For molecular mechanics force-field approaches to this problem, see Beckwith Schiesser Tetrahedron 1985, 41, 3925 Spellmeyer Houk J. Org. Chem. 1987, 52, 959. 

There are a large number of different force field approaches published. The following section deals only with those programs most frequently used in the calculation of oligosaccharides. The other programs deviate from the described ones usually only by either the parametrization or the use and/or the weighting of the individual functions which contribute to the force field. 

The force field approach assumes that it is possible to describe the geometry of a molecule by a set of mechanical equivalents. Changes in bond length are, for example, represented by- a modified Hook s law V(r) = 0.5 x 1 x (r — r0)2 for a spring or bending of a bond angle is modelled by a bending potential VB = kB x (0 — 0O)2, where kB, ks, r0, and 0O are parameters that are dependent on the incorporated atom... 

Kostov MK, Cheng H, Cooper AC, Pez GP (2002) Influence of carbon curvature on molecular adsorptions in carbon-based materials a force field approach. Phys. Rev. Lett. 89 146105—1— 146105 1... 

It is also possible to combine the supermolecule and continuum approaches by using specific solvent molecules to capture the short-range effects (i.e., those involving specific noncovalent interactions between solute and solvent) and a reaction field to treat longer range effects.33-35 Alternatively, structures along the gas phase reaction coordinate can be immersed in a box of hundreds (or more) of explicit solvent molecules that are treated using force field approaches.36,37 Each type of method - the SCRF, solvent box, and supermolecule approaches - tests the importance of particular features of the solvent on the reactivity of the solute dielectric constant, multiple specific classical electrostatic interactions, and specific local directional noncovalent interactions, respectively. 

The periodic approach is not the only one available for atomistic simulations of these materials and we should first mention that much progress has been made in the application of molecular quantum chemical methods using cluster representations of the local structure of oxide materials [1, 2], More recently, this has given way to mixed quantum mechanics/molecular mechanics (QM/MM) calculations. In QM/MM simulations the important region, the active site for catalysis, is represented at a quantum chemical level while the influence of its environment, the extended solid, is represented using the computationally less-demanding atomistic force field approach. This allows complex structures such as metal particles supported on oxides to be tackled [3]. 

The large body of literature on calculations of structures of proteins, polypeptides, polysacharides and polynucleotides is not reviewed. These calculations, in so far as they apply to the force-field approach, are necessarily based on highly simplified fields (hard- or soft sphere approach) and furthermore, due to limits in computer memory capacity and speed, full relaxation of the atomic coordinates of such large molecules (> 75 atoms) is as yet unattainable. 

Drug-Target Binding Forces Advances in Force Field Approaches... 

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