Polarizability force

Keywords Polarizable force field, Molecular orbital and valence bond theory, Nuclear quantum... 

Keywords Polarizable force fields, Intermolecular interactions, Energy decomposition, Density... 

DEVELOPMENT OF NEXT GENERATION POLARIZABLE FORCE FIELDS FROM SIBFA TO GEM... 

Piquemal J-P, Chelli R, Procacci P, Gresh N (2007) Key role of the polarization anisotropy of water in modeling classical polarizable force fields. J Phys Chem A 111 8170... 

Piquemal J-P (2004) Evaluation of molecular interactions in bioinorganic systems from ab initio computations to polarizable force fields. PhD Thesis, UPMC number 2004PA066267, Universite Pierre et Marie Curie, Paris, France... 

Keywords Empirical force field, Electronic polarization, Polarizability, Force field, Inducible dipoles,... 

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... 

While nonbonded atom pairs will typically not come within 1A of each other, it is possible for covalently bound pairs, either directly bounds, as in 1-2 pairs, or at the vertices of an angle, as in 1-3 pairs. Accordingly it may be considered desirable to omit the 1-2 and 1-3 dipole-dipole interactions as is commonly performed on additive force fields for the Coulombic and van der Waals terms. However, it has been shown that inclusion of the 1-2 and 1-3 dipole-dipole interactions is required to achieve anistropic molecular polarizabilites when using isotropic atomic polariz-abilites [50], For example, in a Drude model of benzene in which isotropic polarization was included on the carbons only inclusion of the 1-2 and 1-3 dipole-dipole interactions along with the appropriate damping of those interactions allowed for reproduction of the anisotropic molecular polarizability of the molecule [64], Thus, it may be considered desirable to include these short range interactions in a polarizable force field. 

MOLECULAR DYNAMICS WITH POLARIZABLE FORCE FIELDS... 

An important advance in making explicit polarizable force fields computationally feasible for MD simulation was the development of the extended Lagrangian methods. This extended dynamics approach was first proposed by Sprik and Klein [91], in the sipirit of the work of Car and Parrinello for ab initio MD dynamics [168], A similar extended system was proposed by van Belle et al. for inducible point dipoles [90, 169], In this approach each dipole is treated as a dynamical variable in the MD simulation and given a mass, Mm, and velocity, p.. The dipoles thus have a kinetic energy, JT (A)2/2, and are propagated using the equations of motion just like the atomic coordinates [90, 91, 170, 171]. The equation of motion for the dipoles is... 

POLARIZABLE FORCE FIELDS IN CHARMM 9.5.1. Classical Drude Oscillatory... 

Halgren TA, Damm W (2001) Polarizable force fields. Curr Opin Struct Biol 11(2) 236-242... 

Warshel A, Kato M, Pisliakov AV (2007) Polarizable force fields history, test cases, and prospects. J Chem Theory Comput 3(6) 2034-2045... 

Swart M, van Duijnen PT (2006) DRF90 a polarizable force field. Mol Simul 32(6) 471-484... 

Grossfield A, Ren PY, Ponder JW (2003) Ion solvation thermodynamics from simulation with a polarizable force field. J Am Chem Soc 125(50) 15671—15682... 

Anisimov VM, Lamoureux G, Vorobyov IV, Huang N, Roux B, MacKerell AD (2005) Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator. J Chem Theory Comput 1 (1) 153—168... 

Lamoureux G, Roux B (2006) Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field. J Phys Chem B 110(7) 3308-3322... 

Harder E, Anisimov VM, Whitfield TW, MacKerell AD, Roux B (2008) Understanding the dielectric properties of liquid amides from a polarizable force field. J Phys Chem B 112(11 ) 3509—3521... 

Banks JL, Kaminski GA, Zhou RH, Mainz DT, Berne BJ, Friesner RA (1999) Parametrizing a polarizable force field from ab initio data. I. The fluemating point charge model. J Chem Phys 110(2) 741—754... 

Kaminski GA, Stern HA, Berne BJ, Friesner RA, Cao YXX, Murphy RB, Zhou RH, Halgren TA (2002) Development of a polarizable force field for proteins via ab initio quantum chemistry first generation model and gas phase tests. J Comput Chem 23(16) 1515—1531... 

Studies of ferredoxin [152] and a photosynthetic reaction center [151] have analyzed further the protein s dielectric response to electron transfer, and the protein s role in reducing the reorganization free energy so as to accelerate electron transfer [152], Different force fields were compared, including a polarizable and a non-polarizable force field [151]. One very recent study considered the effect of point mutations on the redox potential of the protein azurin [56]. Structural relaxation along the simulated reaction pathway was analyzed in detail. Similar to the Cyt c study above, several slow relaxation channels were found, which limited the ability to obtain very precise free energy estimates. Only semiquantitative values were... 

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