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Reviews in Computational Chemistry Volume 18

Reviews in Computational Chemistry Volume 18

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134 Polarizability <strong>in</strong> Computer Simulations<br />

packages, thereby mak<strong>in</strong>g these methods much more accessible to the nonspecialist.<br />

In particular, we expect polarizable models, and especially polarizable<br />

water models, to become more prevalent <strong>in</strong> biomolecular simulations <strong>in</strong>volv<strong>in</strong>g<br />

heterogeneous solvent environments. Inclusion of polarizability <strong>in</strong> the<br />

potentials for prote<strong>in</strong>s and other macromolecular systems is also likely to<br />

become more common, and hence a careful assessment of the importance of<br />

polarizability to these systems is needed. Until the importance of polarizability<br />

has been clearly demonstrated, the added computational cost of model<strong>in</strong>g the<br />

polarization makes it is unlikely that polarizable models will displace more<br />

traditional models for the bulk of rout<strong>in</strong>e simulation, particularly when<br />

applied to large systems.<br />

Future directions <strong>in</strong> the development of polarizable models and simulation<br />

algorithms are sure to <strong>in</strong>clude the comb<strong>in</strong>ation of classical or semiempirical<br />

polarizable models with fully quantum mechanical simulations, and with<br />

empirical reactive potentials. The <strong>in</strong>creas<strong>in</strong>gly frequent application of Car–<br />

Parr<strong>in</strong>ello ab <strong>in</strong>itio simulations methods 156 may also <strong>in</strong>fluence the development<br />

of potential models by provid<strong>in</strong>g additional data for the validation of<br />

models, perhaps most importantly <strong>in</strong> terms of the importance of various <strong>in</strong>teractions<br />

(e.g., polarizability, charge transfer, partially covalent hydrogen<br />

bonds, lone-pair-type <strong>in</strong>teractions). It is also likely that we will see cont<strong>in</strong>ued<br />

work toward better coupl<strong>in</strong>g of charge-transfer models (i.e., EE and semiempirical<br />

models) with purely local models of polarization (polarizable dipole<br />

and shell models).<br />

REFERENCES<br />

1. J. A. McCammon and S. C. Harvey, Dynamics of Prote<strong>in</strong>s and Nucleic Acids, Cambridge<br />

University Press, Cambridge, UK, 1987.<br />

2. M. Rigby, E. B. Smith, W. A. Wakeham, and G. C. Maitland, The Forces Between Molecules,<br />

Oxford Science Publications, Oxford, UK, 1986.<br />

3. T. A. Halgren, J. Am. Chem. Soc., 114, 7827–7843 (1992). Representation of van der Waals<br />

(vdW) Interactions <strong>in</strong> Molecular Mechanics Force Fields: Potential Form, Comb<strong>in</strong>ation<br />

Rules, and vdW Parameters.<br />

4. H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, J. Phys. Chem., 91, 6269–6271 (1987).<br />

The Miss<strong>in</strong>g Term <strong>in</strong> Effective Pair Potentials.<br />

5. K. Watanabe and M. L. Kle<strong>in</strong>, Chem. Phys., 131, 157–167 (1989). Effective Pair Potentials<br />

and the Properties of Water.<br />

6. L. Kuyper, D. Ashton, K. M. Merz Jr., and P. A. Kollman, J. Phys. Chem., 95, 6661–6666<br />

(1991). Free Energy Calculations on the Relative Solvation Free Energies of Benzene,<br />

Anisole, and 1,2,3-Trimethoxybenzene: Theoretical and Experimental Analysis of Aromatic<br />

Methoxy Solvation.<br />

7. W. L. Jorgensen and J. Gao, J. Am. Chem. Soc., 110, 4212–4216 (1988). Cis–Trans Energy<br />

Difference for the Peptide Bond <strong>in</strong> the Gas Phase and <strong>in</strong> Aqueous Solution.<br />

8. D. E. Williams, Biopolymers, 29, 1367–1386 (1990). Alanyl Dipeptide Potential-Derived Net<br />

Atomic Charges and Bond Dipoles, and Their Variation with Molecular Conformation.

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