A Force Field for Molecular Simulation of Tetrabutylphosphonium Amino Acid Ionic Liquids

2007 ◽  
Vol 111 (25) ◽  
pp. 7078-7084 ◽  
Author(s):  
Guohui Zhou ◽  
Xiaomin Liu ◽  
Suojiang Zhang ◽  
Guangren Yu ◽  
Hongyan He
Keyword(s):  
Ionic Liquids ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Simulation

Molecular simulation of imidazolium amino acid-based ionic liquids

2010 ◽  
Vol 36 (14) ◽  
pp. 1123-1130 ◽  
Author(s):  
Xiaomin Liu ◽  
Guohui Zhou ◽  
Suojiang Zhang ◽  
Guangwen Wu
Keyword(s):  
Ionic Liquids ◽  
Amino Acid ◽  
Molecular Simulation

scholarly journals The scaled-charge additive force field for amino acid based ionic liquids

2014 ◽  
Vol 616-617 ◽  
pp. 205-211 ◽  
Author(s):  
Eudes Eterno Fileti ◽  
Vitaly V. Chaban
Keyword(s):  
Ionic Liquids ◽  
Amino Acid ◽  
Force Field

New Force Field for Molecular Simulation of Guanidinium-Based Ionic Liquids

2006 ◽  
Vol 110 (24) ◽  
pp. 12062-12071 ◽  
Author(s):  
Xiaomin Liu ◽  
Suojiang Zhang ◽  
Guohui Zhou ◽  
Guangwen Wu ◽  
Xiaoliang Yuan ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Force Field ◽  
Molecular Simulation

A Refined Force Field for Molecular Simulation of Imidazolium-Based Ionic Liquids

2004 ◽  
Vol 108 (34) ◽  
pp. 12978-12989 ◽  
Author(s):  
Zhiping Liu ◽  
Shiping Huang ◽  
Wenchuan Wang
Keyword(s):  
Ionic Liquids ◽  
Force Field ◽  
Molecular Simulation

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

A Transferable, Polarisable Force Field for Ionic Liquids

2019 ◽  
Author(s):  
Kateryna Goloviznina ◽  
José N. Canongia Lopes ◽  
Margarida Costa Gomes ◽  
Agilio Padua
Keyword(s):  
Ionic Liquids ◽  
Force Field ◽  
Force Fields ◽  
Dipole Moments ◽  
Van Der Waals Interactions ◽  
First Principles Calculations ◽  
Ion Diffusion ◽  
Fixed Integer ◽  
Molecular Compounds ◽  
Induced Dipoles

A general, transferable polarisable force field for molecular simulation of ionic liquids and their mixtures with molecular compounds is developed. This polarisable model is derived from the widely used CL\&P fixed-charge force field that describes most families of ionic liquids, in a form compatible with OPLS-AA, one of the major force fields for organic compounds. Models for ionic liquids with fixed, integer ionic charges lead to pathologically slow dynamics, a problem that is corrected when polarisation effects are included explicitly. In the model proposed here, Drude induced dipoles are used with parameters determined from atomic polarisabilities. The CL\&P force field is modified upon inclusion of the Drude dipoles, to avoid double-counting of polarisation effects. This modification is based on first-principles calculations of the dispersion and induction contributions to the van der Waals interactions, using symmetry-adapted perturbation theory (SAPT) for a set of dimers composed of positive, negative and neutral fragments representative of a wide variety of ionic liquids. The fragment approach provides transferability, allowing the representation of a multitude of cation and anion families, including different functional groups, without need to re-parametrise. Because SAPT calculations are expensive an alternative predictive scheme was devised, requiring only molecular properties with a clear physical meaning, namely dipole moments and atomic polarisabilities. The new polarisable force field, CL\&Pol, describes a broad set set of ionic liquids and their mixtures with molecular compounds, and is validated by comparisons with experimental data on density, ion diffusion coefficients and viscosity. The approaches proposed here can also be applied to the conversion of other fixed-charged force fields into polarisable versions.<br>

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