Polarizable Force Fields for Biomolecular Modeling

Yue Shi/ Pengyu Ren/ Michael Schnieders, and Jean-Philip PiquemaP 

The University of Iowa, Iowa City, I A 52242, USA Laboratoire de Chimie Theorique (UMR 7616), UPMC, Sorbonne Universites, Paris, Cedex 05 75252, France 

Reviews in Computational Chemistry, Volume 28, First Edition. Edited by Abby L. Parrill and Kenny B. Lipkowitz. 

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The total electric field, E, is composed of the external electric field from the permanent charges E° and the contribution from other induced dipoles. This is the basis of most polarizable force fields currently being developed for biomolecular simulations. In the present chapter an overview of the formalisms most commonly used for MM force fields will be presented. It should be emphasized that this chapter is not meant to provide a broad overview of the field but rather focuses on the formalisms of the induced dipole, classical Drude oscillator and fluctuating charge models and their development in the context of providing a practical polarization model for molecular simulations of biological macromolecules [12-21], While references to works in which the different methods have been developed and applied are included throughout the text, the major discussion of the implementation of these models focuses... 

Ren and coworkers report a new polarizable development and parameterization of their atomic multipole-based optimized energetics for biomolecular simulation, AMOEBA2013 force field for proteins. It uses atomic multipole-based electrostatics and has explicit treatment of dipole polarization. Based on a mutual induction model with Thole damping it describes both intra- and intermolecular polarization. 

An important subset of many-body potentials shown to be important for simulating interfacial systems are those referred to as polarizable force fields.Various aspects of polarizable force fields, especially for use in biomolecular modeling, is explained by Ren et al. in Chapter 3 of this volume. If one treats the fixed charges in Eq. [3] as parameters to be fitted to obtain the best agreement of the condensed phase simulations with experiments, in many cases one finds that the optimal values are considerably different from those obtained from a fit to a molecular (gas phase) dipole moment or from quantum calculations on isolated molecules. This is because in a condensed medium, the local electric field E, (at the location of a particle i) is determined by all the fixed charges and by all the induced dipoles in the system ... 

Comparison offeree fields vs. high-quality ab initio data is especially interesting for tt-interactions because one might wonder whether the delocalized nature and polarizability of the tt electrons might make them more difficult to model accurately using standard force fields. Additionally, 7t interactions can be quite important in biomolecular systems (Salonen, Ellermann, and Diederich, 2011). Around 60% of aromatic side-chains in proteins are involved in tt-7T interactions (Burley and Petsko, 1985), and simulations indicate that base stacking interactions are critical for the stability of DNA and RNA (Cerny et al., 2008). 

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