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

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.

Silver‐Assisted Synthesis of Gold Nanorods: the Relation between Silver Additive and Iodide Impurities

“…This is consistent with the minimal fraction of Ag 0 eventually retained at the Au NR particles . Interestingly, molecular dynamics simulations also highlight the impact of the diverse geometric coordination of CTAB molecules at different Au faces in determining the accessibility of ions from the bulk solution to the gold surface …”

Understanding and Designing the Gold–Bio Interface: Insights from Simulations

“…The alternative approach introduces a number of tailored parameters aimed at differentiating the interactions between particular biomolecular species and different crystallographic facets and shapes of gold, while keeping the geometry of gold substrate/center rigidly intact. For detailed description of both methods and validation data please refer to the discussions found in and , and references therein. Herein we give a general account of both approaches, as well as others, used in developing custom FFs able to represent the interactions occurring between gold (surfaces/clusters) and biomolecules (water/ligand/protein/DNA).…”

“…Furthermore, the recently published thiolated nanocluster FF of Guberman‐Pfeffer et al also features similar magnitude ε values for gold atoms. For further details and benchmarking we refer the reader to the most recent extensive review …”

“…For further details and benchmarking we refer the reader to the most recent extensive review. [ 120 ] Besides the METAL FF, several other sets of LJ parameters have been used to model bio-gold systems while relying on cross-terms to govern gold's interactions with organic and biomolecular components. [ 106,132 ] These include the hydrophilic parameters of Vila Verde, [ 133 ] parameters borrowed and modifi ed from the generic Dreiding [ 134 ] and universal [ 135 ] force fi elds, parameters adapted from experimental data, [ 136 ] and those taken from self-assembled organic monolayers on gold substrates.…”

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

“…The atomistic molecular dynamics (MD) simulation has evolved into a powerful tool suitable for addressing the atomic scale interfacial structures in clay related materials and environment sciences. 17–23 However, the simulations in order to accurately characterize the energetic properties of the dynamic intercalation process of clays by surfactants require the system size and simulation time scale beyond the traditional MD techniques. Recent advances in accelerated molecular dynamics such as the adaptive biasing force (ABF) method substantially speed up the MD simulations by enhancing the conformational space sampling and are capable of accurately describing the free energy surface of processes of large systems at long time scale.…”