Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA‐LF

Piquemal, Jean‐Philip; Williams-Hubbard, Benjamin; Fey, Natalie; Deeth, Robert J.; Gresh, Nohad; Giessner‐Prettre, Claude

doi:10.1002/jcc.10415

Cited by 11 publications

(13 citation statements)

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“…Wheatley & Mitchell (1994) proposed replacing the point multipole with Gaussian multipoles to correctly model the penetration effect at short range. Piquemal et al (2003) used s -type Gaussian functions distributed at multi-sites to represent the charge density. In the recent development of Quantum Mechanics Polarizable Force Field (QMPFF) (Donchev, 2006; Donchev et al , 2005), a model was developed that consists of a nuclear charge and a negative electron cloud of exponential form located off the nuclear center.…”

Section: Modeling Biomolecular Charge Distributionsmentioning

confidence: 99%

Biomolecular electrostatics and solvation: a computational perspective

Ren

Chun

Thomas

et al. 2012

Quart. Rev. Biophys.

166

168

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An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide a background to understand the different types of solvation models.

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Section: Modeling Biomolecular Charge Distributionsmentioning

confidence: 99%

Biomolecular electrostatics and solvation: a computational perspective

Ren

Chun

Thomas

et al. 2012

Quart. Rev. Biophys.

166

168

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“…There are plethoras of POL models for water, and three main approaches have emerged to calculating POL in empirical force fields: the fluctuating charge method 17,20,21 ; the Drude-oscillator approach 15,23,33,34 ; and the well-studied induced dipole method. 16,24,25,31,32,[35][36][37][38][39] The fluctuating charge and Drude oscillator approaches are unique from the induced dipole model in that they are essentially attempts to extend previous fixed, atom-centered charge models to accommodate POL. By contrast, the induced dipole model incorporates multipole moments beyond the point charge in a formalism where the natural link between the higher order permanent multipoles and the polarizabilities is clear from the fact they are terms of a Taylor expansion of the energy in the electric field E.…”

Section: Polarizable Modelsmentioning

confidence: 99%

Advanced models for water simulations

Demerdash

Wang

Head‐Gordon

2017

WIREs Comput Mol Sci

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Molecular simulations of water using classical, molecular mechanic potential energy functions have enjoyed a 50-year history of development, and much has been learned regarding their parameterization and the essential physics that must be captured in order to reproduce water properties across the phase diagram and across system sizes, from the dimer to the condensed phase. While pairwise-additive force fields using fixed, point charge-based electrostatics have dominated this history owing to computational cost, their limitations in transferability are being recognized, owing particularly to the lack of many-body effects, as well as an inherent difficulty in capturing quantum mechanical effects that become important at short intermolecular separation. This has spurred an impressive development of novel functional forms and parameterization schemes to account for such effects, especially the leading many-body effect of polarization. This review discusses recent efforts in the development of advanced models of water, particularly with regard to important details of their parameterization from quantum mechanical or experimental data, the development of novel functional forms including machine learning-based models, and algorithms that reduce the computational cost of polarization dramatically, permitting them to potentially become competitive with pairwise-additive models as the standby of condensed-phase simulation. These technical developments are appraised based on their ability to impact numerical calculations on water, particularly the condensed phase, and it is hoped that this article provides a clear connection between the essential physics captured by the model and their fitness across a range of environments.

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“…223 The original, pre-DommiMOE implementation of LFMM has been abandoned due to the lack of robust support for the organic force field, 216 and other implementations either depend on DommiMOE, 227 or have not yet been released. 31,[228][229][230][231] Therefore, to increase the accessibility to the LFMM method and support its systematic use in fast fitness, the LFMM method was integrated into the popular and easily accessible cooperatively between the metal centers and might lead to hysteresis, which is a tailored property for technological applications. [241][242][243] Therefore, many Fe(II)-N 6…”

Section: Ligand Field Molecular Mechanics (Lfmm)mentioning

confidence: 99%

Automated Design of Realistic Organometallic Molecules from Fragments

Foscato

Occhipinti

Venkatraman

et al. 2014

J. Chem. Inf. Model.

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A method for the automated generation of realistic, synthetically accessible transition metal and organometallic complexes is described. Computational tools were designed to generate molecular fragments, preferably harvested from libraries of existing, stable compounds, to be used as building blocks for the construction of new molecules. These fragments are enriched with information about the number and type of possible connections to other fragments and are stored in library files. When connecting fragments in the subsequent building process, compatibility matrices, which define the connection rules between fragments, are used to delineate organometallic fragment spaces from which molecules can be generated in an automated fashion. The approach is flexible and allows ample structural variation at the same time as the combination of known fragments is easily restrained to avoid generation of exotic and unrealistic substructures and molecules. The method was tested in the generation of ruthenium complexes, with a given coordination environment, which can serve as candidates in catalyst development. The results demonstrate that molecules generated with the described method do not contain exotic arrangements of atoms and are by far more realistic than those obtained by the application of valence rules alone.

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Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA‐LF

Cited by 11 publications

References 0 publications

Biomolecular electrostatics and solvation: a computational perspective

Biomolecular electrostatics and solvation: a computational perspective

Advanced models for water simulations

Automated Design of Realistic Organometallic Molecules from Fragments

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