Literature DB >> 26750724

Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities.

Hendrik Heinz1, Hadi Ramezani-Dakhel.   

Abstract

Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.

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Year:  2016        PMID: 26750724     DOI: 10.1039/c5cs00890e

Source DB:  PubMed          Journal:  Chem Soc Rev        ISSN: 0306-0012            Impact factor:   54.564


  23 in total

Review 1.  Metal Ion Modeling Using Classical Mechanics.

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

2.  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

3.  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

4.  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

5.  Mitigation of peri-implantitis by rational design of bifunctional peptides with antimicrobial properties.

Authors:  E Cate Wisdom; Yan Zhou; Casey Chen; Candan Tamerler; Malcolm L Snead
Journal:  ACS Biomater Sci Eng       Date:  2019-09-24

6.  Lysozyme orientation and conformation on MoS2 surface: Insights from molecular simulations.

Authors:  Hongjie Fan; Daohui Zhao; Yingtu Li; Jian Zhou
Journal:  Biointerphases       Date:  2017-06-02       Impact factor: 2.456

7.  Interfacial Structure and Interaction of Kaolinite Intercalated with N-methylformamide Insight from Molecular Dynamics Modeling.

Authors:  Shuai Zhang; Qinfu Liu; Feng Gao; Rujia Ma; Zeguang Wu; Brian J Teppen
Journal:  Appl Clay Sci       Date:  2018-04-04       Impact factor: 5.467

8.  Direct correlation of oxygen adsorption on platinum-electrolyte interfaces with the activity in the oxygen reduction reaction.

Authors:  Shiyi Wang; Enbo Zhu; Yu Huang; Hendrik Heinz
Journal:  Sci Adv       Date:  2021-06-09       Impact factor: 14.136

9.  CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems.

Authors:  Yeol Kyo Choi; Nathan R Kern; Seonghan Kim; Krishan Kanhaiya; Yaser Afshar; Sun Hee Jeon; Sunhwan Jo; Bernard R Brooks; Jumin Lee; Ellad B Tadmor; Hendrik Heinz; Wonpil Im
Journal:  J Chem Theory Comput       Date:  2021-12-06       Impact factor: 6.006

10.  Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition.

Authors:  Juan Liu; Jin Zeng; Cheng Zhu; Jianwei Miao; Yu Huang; Hendrik Heinz
Journal:  Chem Sci       Date:  2020-07-21       Impact factor: 9.825

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