Organic–inorganic interface simulation for new material discoveries

Abstract

International audienceOrganic–inorganic interactions are of high importance in several biological pro- cesses and in modern nanobiotechnological applications. Despite its signifi- cance in interface sciences, the basic mechanism of biomolecules’ specific binding to a surface is still not well understood. Current experimental methods have not reached the level either to follow the dynamics of interactions at the picosecond scale or to observe the surface morphology at the nanoscale level. The increasing interest in bio-interfaces particularly for engineering applica- tions demands proteins or peptides to be designed to recognize the inorganic surface with high specificity. Molecular simulation has been well adopted in the past couple of decades to decipher the protein–surface interactions at differ- ent levels of time and length scales. Several molecular simulation methods such as quantum mechanics, atomistic, and coarse grain simulations were employed in this domain of research, but the continuous improvements in interfacial force field (FF) development, availability of experimental data and new sampling methods make the atomistic simulation more attractive due to the offered accu- rate representation of protein adsorption behavior at the atomic level. However, the exactitude of such simulations entirely depends on the applied FF para- meters, conformational sampling, and the solvation effects. In this overview, we briefly summarize the applicability of different simulation methods and of interface FFs. We also present the recent advances in the simulation of protein– surface interactions, and the challenges posed by the current simulation meth- ods to reproduce the exact phenomenon. Future directions in this research field are also discussed

Energy Landscape Mapping and Replica Exchange Molecular Dynamics of an Adsorbed Peptide

“…Computational studies have led to an improved understanding of peptide–surface interactions in recent years. − Modeling interactions that occur over time scales longer than the microsecond range remain a challenge, however, since all-atom simulation methods such as molecular dynamics (MD) are not currently capable of probing these scales sufficiently . This limitation poses a particular barrier to assessing the conformations of many material-binding peptides, which possess complex, flexible natures that cannot be reliably sampled in so short a time .…”

Effect of Biomolecules on the Nanostructure and Nanomechanical Property of Calcium-Silicate-Hydrate

“…The observed influence of lysozyme on the interlayer distance of C-S-H at C/S of 1.5 could be related to the specificity of this biomolecule favoring such effect on C-S-H. The specificity of biomolecules in their interaction with inorganic surfaces has been observed and studied in prior investigations 58 , 59 . Further investigations based on computational approaches can provide valuable insights into the effect of protein conformation on the atomic structure of C-S-H.

Figure 4 Schematic of how proteins undergo conformational changes with increasing pH.

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Hybrid Organic-Inorganic Materials and Interfaces With Mixed Ionic-Electronic Transport Properties: Advances in Experimental and Theoretical Approaches

“…Computational simulation is quite relevant to predict or explain structural features of h OI materials and interfaces. For instance, classical Montecarlo (MC) and molecular dynamics (MD) are one of the best (non-atomistic and atomistic, respectively) approaches to model up to several nanometer large crystalline or amorphous organic and inorganic materials allowing obtaining rich information about molecular and nuclear position-related properties ( Zeng et al, 2003 ; Heinz and Ramezani-Dakhel, 2016 ; Ramakrishnan et al, 2017 ; Eckert et al, 2020 ). To compute electronic-related properties, we must perform first-principles calculations such as Density Functional Theory (DFT) and ab-initio MD (AIMD) to access static and dynamic information, respectively ( Zeng et al, 2003 ; Heinz and Ramezani-Dakhel, 2016 ; Ramakrishnan et al, 2017 ; Eckert et al, 2020 ).…”

“…For instance, classical Montecarlo (MC) and molecular dynamics (MD) are one of the best (non-atomistic and atomistic, respectively) approaches to model up to several nanometer large crystalline or amorphous organic and inorganic materials allowing obtaining rich information about molecular and nuclear position-related properties ( Zeng et al, 2003 ; Heinz and Ramezani-Dakhel, 2016 ; Ramakrishnan et al, 2017 ; Eckert et al, 2020 ). To compute electronic-related properties, we must perform first-principles calculations such as Density Functional Theory (DFT) and ab-initio MD (AIMD) to access static and dynamic information, respectively ( Zeng et al, 2003 ; Heinz and Ramezani-Dakhel, 2016 ; Ramakrishnan et al, 2017 ; Eckert et al, 2020 ). When performing first-principles calculations, due to the complexity of the h OI interface, one of the organic or inorganic phases is usually oversimplified to systems comprising organic monomer/inorganic surface ( Alexandre et al, 2010 ; Semoto et al, 2011 ; Hofmann et al, 2013 ; Motta et al, 2015 ; Wang et al, 2017a ; Pourrahimi et al, 2017 ; Liao et al, 2019 ) or organic oligomers/inorganic small clusters ( Mombrú et al, 2017a ; Ullah et al, 2017 ; Wang et al, 2020a ).…”