Literature DB >> 23276161

Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field.

Hendrik Heinz1, Tzu-Jen Lin, Ratan Kishore Mishra, Fateme S Emami.   

Abstract

The complexity of the molecular recognition and assembly of biotic-abiotic interfaces on a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with laboratory instrumentation. We discuss the current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorganic compounds that has been developed and tested over the past decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorganic-organic and inorganic-biomolecular interfaces. The parametrization builds on an in-depth understanding of physical-chemical properties on the atomic scale to assign each parameter, especially atomic charges and van der Waals constants, as well as on the validation of macroscale physical-chemical properties for each compound in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties of up to 2 orders of magnitude using other parametrization protocols and increases the transferability of the parameters by introducing thermodynamic consistency. As a result, a wide range of properties can be computed in quantitative agreement with experiment, including densities, surface energies, solid-water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomolecules, and thermal and mechanical properties. Applications include insight into the assembly of inorganic-organic multiphase materials, the recognition of inorganic facets by biomolecules, growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and nanomechanics. Limitations and opportunities for further development are also described.

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Year:  2013        PMID: 23276161     DOI: 10.1021/la3038846

Source DB:  PubMed          Journal:  Langmuir        ISSN: 0743-7463            Impact factor:   3.882


  62 in total

1.  COMPASS II: extended coverage for polymer and drug-like molecule databases.

Authors:  Huai Sun; Zhao Jin; Chunwei Yang; Reinier L C Akkermans; Struan H Robertson; Neil A Spenley; Simon Miller; Stephen M Todd
Journal:  J Mol Model       Date:  2016-01-27       Impact factor: 1.810

Review 2.  Force fields for simulating the interaction of surfaces with biological molecules.

Authors:  Lewis Martin; Marcela M Bilek; Anthony S Weiss; Serdar Kuyucak
Journal:  Interface Focus       Date:  2016-02-06       Impact factor: 3.906

3.  Force field parametrization of hydrogenoxalate and oxalate anions with scaled charges.

Authors:  Ondřej Kroutil; Milan Předota; Martin Kabeláč
Journal:  J Mol Model       Date:  2017-10-28       Impact factor: 1.810

Review 4.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

5.  Thermodynamic Mechanism and Interfacial Structure of Kaolinite Intercalation and Surface Modification by Alkane Surfactants with Neutral and Ionic Head Groups.

Authors:  Shuai Zhang; Qinfu Liu; Hongfei Cheng; Feng Gao; Cun Liu; Brian J Teppen
Journal:  J Phys Chem C Nanomater Interfaces       Date:  2017-03-31       Impact factor: 4.126

6.  Molecular Dynamics Simulation of Basal Spacing, Energetics, and Structure Evolution of a Kaolinite-Formamide Intercalation Complex and Their Interfacial Interaction.

Authors:  Shuai Zhang; Qinfu Liu; Feng Gao; Brian J Teppen
Journal:  J Phys Chem C Nanomater Interfaces       Date:  2018-01-29       Impact factor: 4.126

7.  Mechanism Associated with Kaolinite Intercalation with Urea: Combination of Infrared Spectroscopy and Molecular Dynamics Simulation Studies.

Authors:  Shuai Zhang; Qinfu Liu; Feng Gao; Xiaoguang Li; Cun Liu; Hui Li; Stephen A Boyd; Cliff T Johnston; Brian J Teppen
Journal:  J Phys Chem C Nanomater Interfaces       Date:  2016-12-14       Impact factor: 4.126

8.  Perspectives on the simulation of protein-surface interactions using empirical force field methods.

Authors:  Robert A Latour
Journal:  Colloids Surf B Biointerfaces       Date:  2014-06-30       Impact factor: 5.268

9.  Using an environmentally-relevant panel of Gram-negative bacteria to assess the toxicity of polyallylamine hydrochloride-wrapped gold nanoparticles.

Authors:  Joseph T Buchman; Ali Rahnamoun; Kaitlin M Landy; Xi Zhang; Ariane M Vartanian; Lisa M Jacob; Catherine J Murphy; Rigoberto Hernandez; Christy L Haynes
Journal:  Environ Sci Nano       Date:  2017-12-20

10.  Mechanism Responsible for Intercalation of Dimethyl Sulfoxide in Kaolinite: Molecular Dynamics Simulations.

Authors:  Shuai Zhang; Qinfu Liu; Hongfei Cheng; Feng Gao; Cun Liu; Brian J Teppen
Journal:  Appl Clay Sci       Date:  2017-11-05       Impact factor: 5.467

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