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

Structure, Properties, and Applications of Silica Nanoparticles: Recent Theoretical Modeling Advances, Challenges, and Future Directions

Silica nanoparticles (SNPs), one of the most widely researched materials in modern science, are now commonly exploited in surface coatings, biomedicine, catalysis, and engineering of novel self-assembling materials. Theoretical approaches are invaluable to enhancing fundamental understanding of SNP properties and behavior. Tremendous research attention is dedicated to modeling silica structure, the silica-water interface, and functionalization of silica surfaces for tailored applications. In this review, the range of theoretical methodologies are discussed that have been employed to model bare silica and functionalized silica. The evolution of silica modeling approaches is detailed, including classical, quantum mechanical, and hybrid methods and highlight in particular the last decade of theoretical simulation advances. It is started with discussing investigations of bare silica systems, focusing on the fundamental interactions at the silica-water interface, following with a comprehensively review of the modeling studies that examine the interaction of silica with functional ligands, peptides, ions, surfactants, polymers, and carbonaceous species. The review is concluded with the perspective on existing challenges in the field and promising future directions that will further enhance the utility and importance of the theoretical approaches in guiding the rational design of SNPs for applications in engineering and biomedicine.

The Use of Organoclays as Excipient for Metformin Delivery: Experimental and Computational Study

This work combines experimental and computational modeling studies for the preparation of a composite of metformin and an organoclay, examining the advantages of a Tunisian clay used for drug delivery applications. The clay mineral studied is a montmorillonite-like smectite (Sm-Na), and the organoclay derivative (HDTMA-Sm) was used as a drug carrier for metformin hydrochloride (MET). In order to assess the MET loading into the clays, these materials were characterized by means of cation exchange capacity assessment, specific surface area measurement, and with the techniques of X-ray diffraction (XRD), differential scanning calorimetry, X-ray fluorescence spectroscopy, and Fourier-transformed infrared spectroscopy. Computational molecular modeling studies showed the surface adsorption process, identifying the clay-drug interactions through hydrogen bonds, and assessing electrostatic interactions for the hybrid MET/Sm-Na and hydrophobic interactions and cation exchange for the hybrid MET/HDTMA-Sm. The results show that the clays (Sm-Na and HDTMA-Sm) are capable of adsorbing MET, reaching a maximum load of 12.42 and 21.97 %, respectively. The adsorption isotherms were fitted by the Freundlich model, indicating heterogeneous adsorption of the studied adsorbate-adsorbent system, and they followed pseudo-second-order kinetics. The calculations of ΔGº indicate the spontaneous and reversible nature of the adsorption. The calculation of ΔH° indicates physical adsorption for the purified clay (Sm-Na) and chemical adsorption for the modified clay (HDTMA-Sm). The release of intercalated MET was studied in media simulating gastric and intestinal fluids, revealing that the purified clay (Sm-Na) and the modified organoclay (HDTMA-Sm) can be used as carriers in controlled drug delivery in future clinical applications. The molecular modeling studies confirmed the experimental phenomena, showing that the main adsorption mechanism is the cation exchange process between proton and MET cations into the interlayer space.

Implementing reactivity in molecular dynamics simulations with harmonic force fields

The simulation of chemical reactions and mechanical properties including failure from atoms to the micrometer scale remains a longstanding challenge in chemistry and materials science. Bottlenecks include computational feasibility, reliability, and cost. We introduce a method for reactive molecular dynamics simulations using a clean replacement of non-reactive classical harmonic bond potentials with reactive, energy-conserving Morse potentials, called the Reactive INTERFACE Force Field (IFF-R). IFF-R is compatible with force fields for organic and inorganic compounds such as IFF, CHARMM, PCFF, OPLS-AA, and AMBER. Bond dissociation is enabled by three interpretable Morse parameters per bond type and zero energy upon disconnect. Use cases for bond breaking in molecules, failure of polymers, carbon nanostructures, proteins, composite materials, and metals are shown. The simulation of bond forming reactions is included via template-based methods. IFF-R maintains the accuracy of the corresponding non-reactive force fields and is about 30 times faster than prior reactive simulation methods.

Ion Transport at Polymer-Argyrodite Interfaces

Solid-state electrolytes, particularly polymer/ceramic composite electrolytes, are emerging as promising candidates for lithium-ion batteries due to their high ionic conductivity and mechanical flexibility. The interfaces that arise between the inorganic and organic materials in these composites play a crucial role in ion transport mechanisms. While lithium ions are proposed to diffuse across or parallel to the interface, few studies have directly examined the quantitative impact of these pathways on ion transport and little is known about how they affect the overall conductivity. Here, we present an atomistic study of lithium-ion (Li+) transport across well-defined polymer-argyrodite interfaces. We present a force field for polymer-argyrodite interfacial systems, and we carry out molecular dynamics and enhanced sampling simulations of several composite systems, including poly(ethylene oxide) (PEO)/Li6PS5Cl, hydrogenated nitrile butadiene rubber (HNBR)/Li6PS5Cl, and poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP)/Li6PS5Cl. For the materials considered here, Li-ion exhibits a preference for the ceramic material, as revealed by free energy differences for Li-ion between the inorganic and the organic polymer phase in excess of 13 kBT. The relative free energy profiles of Li-ion for different polymeric materials exhibit similar shapes, but their magnitude depends on the strength of interaction between the polymers and Li-ion: the greater the interaction between the polymer and Li-ions, the smaller the free energy difference between the inorganic and organic materials. The influence of the interface is felt over a range of approximately 1.5 nm, after which the behavior of Li-ion in the polymer is comparable to that in the bulk. Near the interface, Li-ion transport primarily occurs parallel to the interfacial plane, and ion mobility is considerably slower near the interface itself, consistent with the reduced segmental mobility of the polymer in the vicinity of the ceramic material. These findings provide insights into ionic complexation and transport mechanisms in composite systems, and will help improve design of improved solid electrolyte systems.

Structure and Intercalation of Cysteine-Asparagine-Serine Peptide into Montmorillonite as an Anti-Inflammatory Agent Preparation-A DFT Study

Peptides are receiving significant attention in pharmaceutical sciences due to their applications as anti-inflammatory drugs; however, many aspects of their interactions and mechanisms at the molecular level are not well-known. This work explores the molecular structure of two peptides-(i) cysteine (Cys)-asparagine (Asn)-serine (Ser) (CNS) as a molecule in the gas phase and solvated in water in zwitterion form, and (ii) the crystal structure of the dipeptide serine-asparagine (SN), a reliable peptide indication whose experimental cell parameters are well known. A search was performed by means of atomistic calculations based on density functional theory (DFT). These calculations matched the experimental crystal structure of SN, validating the CNS results and useful for assignments of our experimental spectroscopic IR bands. Our calculations also explore the intercalation of CNS into the interlayer space of montmorillonite (MNT). Our quantum mechanical calculations show that the conformations of these peptides change significantly during intercalation into the confined interlayer space of MNT. This intercalation is energetically favorable, indicating that this process can be a useful preparation for therapeutic anti-inflammatory applications and showing high stability and controlled release processes.

Type Label Framework for Bonded Force Fields in LAMMPS

New functionality is added to the LAMMPS molecular simulation package, which increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the "type label" framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools, such as VMD and OVITO. An introductory primer on the forms and use of bonded force fields is provided to motivate this new functionality and serve as an entry point for LAMMPS and OpenKIM users unfamiliar with bonded force fields. The type label framework has the potential to streamline modeling workflows that use LAMMPS by increasing the portability of software, files, and scripts for preprocessing, running, and postprocessing a molecular simulation.

Highly specific colloidal ɣ-Fe2O3-DNA hybrids: From bioinspired recognition to large-scale lactoferrin purification

The industry transfer of laboratory-use magnetic separation is still hampered by the lack of suitable nanoparticles, both in terms of their features and large-scale availability. Surface Active Maghemite Nanoparticles (SAMNs) characterized by a unique surface chemistry, low environmental impact, scalable synthesis and functionalization were used to develop a bio-inspired lactoferrin (LF) recognition system. Based on the LF affinity for DNA, a self-assembly process was optimized for obtaining a SAMN@DNA hybrid displaying chemical and colloidal stability and LF specificity. SAMN@DNA was successfully tested for the affinity purification of LF from crude bovine whey. Advantages, such as high selectivity and loading capacity, nanoparticle re-usability, outstanding purity (96 ± 1%), preservation of protein conformation and short operational time, were highlighted. Finally, scalability was demonstrated by an automatic system performing continuous purification of LF from 100 liters day-1 of whey. This study responds to essential prerequisites, such as efficiency, re-usability and industrialization feasibility.

Osteocalcin: Promoter or Inhibitor of Hydroxyapatite Growth?

Osteocalcin is the most abundant noncollagenous bone protein and the functions in bone remineralization as well as in inhibition of bone growth have remained unclear. In this contribution, we explain the dual role of osteocalcin in the nucleation of new calcium phosphate during bone remodeling and in the inhibition of hydroxyapatite crystal growth at the molecular scale. The mechanism was derived using pH-resolved all-atom models for the protein, phosphate species, and hydroxyapatite, along with molecular dynamics simulations and experimental and clinical observations. Osteocalcin binds to (hkl) hydroxyapatite surfaces through multiple residues, identified in this work, and the fingerprint of binding residues varies as a function of the (hkl) crystal facet and pH value. On balance, the affinity of osteocalcin to hydroxyapatite slows down crystal growth. The unique tricalcium γ-carboxylglutamic acid (Gla) domain hereby rarely adsorbs to hydroxyapatite surfaces and faces instead toward the solution. The Gla domain enables prenucleation of calcium phosphate for new bone formation at a slightly acidic pH of 5. The growth of prenucleation clusters of calcium phosphate continues upon increase in pH value from 5 to 7 and is much less favorable, or not observed, on the native osteocalcin structure at and above neutral pH values of 7. The results provide mechanistic insight into the early stages of bone remodeling from the molecular scale, help inform mutations of osteocalcin to modify binding to apatites, support drug design, and guide toward potential cures for osteoporosis and hyperosteogeny.

Molecular Modeling Techniques and In-Silico Drug Discovery

Molecular modeling is the technique to determine the overall structure of an unknown molecule, be it a small one or a macromolecule. The technique encompasses the method of screening ligand libraries for the development of new candidate drug molecules. All these aspects have become an essential topic of research. This field is truly interdisciplinary and finds its applications in almost all fields of life science research. In this chapter, an overview of the protocol associated with molecular modeling techniques will be discussed.

Spermine Oxidase-Substrate Electrostatic Interactions: The Modulation of Enzyme Function by Neighboring Colloidal ɣ-Fe2O3

Protein-nanoparticle hybridization can ideally lead to novel biological entities characterized by emerging properties that can sensibly differ from those of the parent components. Herein, the effect of ionic strength on the biological functions of recombinant His-tagged spermine oxidase (i.e., SMOX) was studied for the first time. Moreover, SMOX was integrated into colloidal surface active maghemite nanoparticles (SAMNs) via direct self-assembly, leading to a biologically active nano-enzyme (i.e., SAMN@SMOX). The hybrid was subjected to an in-depth chemical-physical characterization, highlighting the fact that the protein structure was perfectly preserved. The catalytic activity of the nanostructured hybrid (SAMN@SMOX) was assessed by extracting the kinetics parameters using spermine as a substrate and compared to the soluble enzyme as a function of ionic strength. The results revealed that the catalytic function was dominated by electrostatic interactions and that they were drastically modified upon hybridization with colloidal ɣ-Fe2O3. The fact that the affinity of SMOX toward spermine was significantly higher for the nanohybrid at low salinity is noteworthy. The present study supports the vision of using protein-nanoparticle conjugation as a means to modulate biological functions.

Accurate Force Fields for Atomistic Simulations of Oxides, Hydroxides, and Organic Hybrid Materials up to the Micrometer Scale

The simulation of metals, oxides, and hydroxides can accelerate the design of therapeutics, alloys, catalysts, cement-based materials, ceramics, bioinspired composites, and glasses. Here we introduce the INTERFACE force field (IFF) and surface models for α-Al2O3, α-Cr2O3, α-Fe2O3, NiO, CaO, MgO, β-Ca(OH)2, β-Mg(OH)2, and β-Ni(OH)2. The force field parameters are nonbonded, including atomic charges for Coulomb interactions, Lennard-Jones (LJ) potentials for van der Waals interactions with 12-6 and 9-6 options, and harmonic bond stretching for hydroxide ions. The models outperform DFT calculations and earlier atomistic models (Pedone, ReaxFF, UFF, CLAYFF) up to 2 orders of magnitude in reliability, compatibility, and interpretability due to a quantitative representation of chemical bonding consistent with other compounds across the periodic table and curated experimental data for validation. The IFF models exhibit average deviations of 0.2% in lattice parameters, <10% in surface energies (to the extent known), and 6% in bulk moduli relative to experiments. The parameters and models can be used with existing parameters for solvents, inorganic compounds, organic compounds, biomolecules, and polymers in IFF, CHARMM, CVFF, AMBER, OPLS-AA, PCFF, and COMPASS, to simulate bulk oxides, hydroxides, electrolyte interfaces, and multiphase, biological, and organic hybrid materials at length scales from atoms to micrometers. The nonbonded character of the models also enables the analysis of mixed oxides, glasses, and certain chemical reactions, and well-performing nonbonded models for silica phases, SiO2, are introduced. Automated model building is available in the CHARMM-GUI Nanomaterial Modeler. We illustrate applications of the models to predict the structure of mixed oxides, and energy barriers of ion migration, as well as binding energies of water and organic molecules in outstanding agreement with experimental data and calculations at the CCSD(T) level. Examples of model building for hydrated, pH-sensitive oxide surfaces to simulate solid-electrolyte interfaces are discussed.

Molecular Insights into Antioxidant Efficiency of Melanin: A Sustainable Antioxidant for Natural Rubber Formulations

N-(1,3-Dimethyl butyl)-N'-phenyl-p-phenylenediamine (6-PPD) is a worldwide antioxidant commonly added to delay the thermo-oxidative degradation of tire rubbers. Unfortunately, 6PPD and its transformation product 6PPD-quinone are toxic to aquatic organisms (e.g., coho salmon). Herein, we explore the free radical scavenging activity and protective mechanism of melanin (MLN) on natural rubber's (NR's) oxidative resistance using molecular dynamics (MD) and quantum mechanical (QM) calculations. The relationship between the molecular structure and the chemical nature of the antioxidant molecules via transition state calculations is explored to unravel the reaction mechanisms of antioxidants interacting with peroxy radicals (ROO·) of NR with the estimation of reaction barriers. Following this, the radical scavenging activity of antioxidants was quantified via a hydrogen atom transfer mechanism and bond dissociation energy calculations. Parallel MD simulations were considered to study the interfacial interactions of antioxidant molecules with polymer chains and fillers with a quantifiable structure-property correlation. Given these results, the nanocomposite (NR-MLN-SiO2) with natural antioxidant melanin manifested outstanding antioxidant properties by preferentially bagging the ROO· radicals, thus improving NR's thermal-oxidative aging relative to 6-PPD. The MD results revealed that the intermolecular interactions at the NR/antioxidant interface benefited the antioxidant MLN to bind tightly to the NR in NR-MLN-SiO2 composite, thus exhibiting improved dispersion, O2 barrier properties, and thermo-oxidative stability, which could extend the service life of NR products (e.g., tires). In addition, as a sustainable antioxidant, MLN could replace toxic antioxidants like 6-PPD. More importantly, the QM/MD simulations provided a fundamental understanding of the mechanistic pathways of antioxidant molecules in NR composites, which are conducive to designing high-performance and sustainable green elastomers.

Investigating Solvent-Induced Aggregation in Edge-Functionalized Layered Silicates via All-Atom Molecular Dynamics Simulations

Molecular dynamics simulations can provide the means to visualize and understand the role of intermolecular interactions in the mechanisms involved in molecular aggregation. Along these lines, simulations can allow the study of how surface chemical modifications can influence nanomaterial assembly at the molecular level. Layered silicate clays have been of significant interest for some time, particularly with regard to their use in organic/inorganic nanocomposites. However, despite numerous reports on the covalent linkage of organic moieties via silanol condensation, the theoretical understanding of these systems has heretofore been limited to noncovalent interactions, specifically ionic interactions at the charged basal surfaces. Herein, a model for edge-functionalized layered aluminosilicate clay, based on the siloxane linkage, is presented. In addition to reproducing experimentally observed degrees of molecular aggregation of clay-linked perylene diimide derivatives with different terminal functional groups as a function of solvent composition, a molecular-level understanding of the role of van der Waals interactions and hydrogen bonding of the different end-groups on the aggregation state in different water/N,N-dimethylformamide mixtures is obtained. The reported model provides a means to simulate organic moieties covalently bound to the layered silicate edge, which will enable future simulations of nanocomposites and organic/inorganic hybrids based on this system.

Improved reweighting protocols for variationally enhanced sampling simulations with multiple walkers

In molecular dynamics simulations utilizing enhanced-sampling techniques, reweighting is a central component for recovering the targeted ensemble averages of the "unbiased" system by calculating and applying a bias-correction function c(t). We present enhanced reweighting protocols for variationally enhanced sampling (VES) simulations by exploiting a recent reweighting method, originally introduced in the metadynamics framework [Giberti et al. J. Chem. Theory Comput., 2020, 16, 100-107], which was modified and extended to multiple-walker simulations: these may be implemented either as "independent" walkers (associated with one unique correction function per walker) or "cooperative" ones that all share one correction function, which is the hitherto only explored option. When each case is combined with the two possibilities of determining c(t) by time integration up to either t or over the entire simulation period , altogether four reweighting options result. Their relative merits were assessed by well-tempered VES simulations of two model problems: locating the free-energy difference between two metastable molecular conformations of the N-acetyl-L-alanine methylamide dipeptide, and the recovery of an a priori known distribution when one water molecule in the liquid phase is perturbed by a periodic free-energy function. The most rapid convergence occurred for large cooperative walkers, regardless of the upper integration limit, but integrating up to t proved advantageous for small walker ensembles. That novel reweighting method compared favorably to the standard VES reweighting, as well as to current state-of-the-art reweighting options introduced for metadynamics simulations that estimate c(t) by integration over the collective variables. For further gains in computational speed and accuracy, we also introduce analytical solutions for c(t), as well as offering further insight into its features by approximative analytical expressions in the "high-temperature" regime.

Insight into the Binding Mechanisms of Quartz-Selective Peptides: Toward Greener Flotation Processes

Mining practices, chiefly froth flotation, are being critically reassessed to replace their use of biohazardous chemical reagents in favor of biofriendly alternatives as a path toward green processes. In this regard, this study aimed at evaluating the interactions of peptides, as potential floatation collectors, with quartz using phage display and molecular dynamics (MD) simulations. Quartz-selective peptide sequences were initially identified by phage display at pH = 9 and further modeled by a robust simulation scheme combining classical MD, replica exchange MD, and steered MD calculations. Our residue-specific analyses of the peptides revealed that positively charged arginine and lysine residues were favorably attracted by the quartz surface at basic pH. The negatively charged residues at pH 9 (i.e., aspartic acid and glutamic acid) further showed affinity toward the quartz surface through electrostatic interactions with the positively charged surface-bound Na⁺ ions. The best-binding heptapeptide combinations, however, contained both positively and negatively charged residues in their composition. The flexibility of peptide chains was also shown to directly affect the adsorption behavior of the peptide. While attractive intrapeptide interactions were dominated by a weak peptide-quartz binding, the repulsive self-interactions in the peptides improved the binding propensity to the quartz surface. Our results showed that MD simulations are fully capable of revealing mechanistic details of peptide adsorption to inorganic surfaces and are an invaluable tool to accelerate the rational design of peptide sequences for mineral processing applications.

Hierarchically structured bioinspired nanocomposites

Next-generation structural materials are expected to be lightweight, high-strength and tough composites with embedded functionalities to sense, adapt, self-repair, morph and restore. This Review highlights recent developments and concepts in bioinspired nanocomposites, emphasizing tailoring of the architecture, interphases and confinement to achieve dynamic and synergetic responses. We highlight cornerstone examples from natural materials with unique mechanical property combinations based on relatively simple building blocks produced in aqueous environments under ambient conditions. A particular focus is on structural hierarchies across multiple length scales to achieve multifunctionality and robustness. We further discuss recent advances, trends and emerging opportunities for combining biological and synthetic components, state-of-the-art characterization and modelling approaches to assess the physical principles underlying nature-inspired design and mechanical responses at multiple length scales. These multidisciplinary approaches promote the synergetic enhancement of individual materials properties and an improved predictive and prescriptive design of the next era of structural materials at multilength scales for a wide range of applications.

Colloidal Synthesis of Metal Nanocrystals: From Asymmetrical Growth to Symmetry Breaking

Nanocrystals offer a unique platform for tailoring the physicochemical properties of solid materials to enhance their performances in various applications. While most work on controlling their shapes revolves around symmetrical growth, the introduction of asymmetrical growth and thus symmetry breaking has also emerged as a powerful route to enrich metal nanocrystals with new shapes and complex morphologies as well as unprecedented properties and functionalities. The success of this route critically relies on our ability to lift the confinement on symmetry by the underlying unit cell of the crystal structure and/or the initial seed in a systematic manner. This Review aims to provide an account of recent progress in understanding and controlling asymmetrical growth and symmetry breaking in a colloidal synthesis of noble-metal nanocrystals. With a touch on both the nucleation and growth steps, we discuss a number of methods capable of generating seeds with diverse symmetry while achieving asymmetrical growth for mono-, bi-, and multimetallic systems. We then showcase a variety of symmetry-broken nanocrystals that have been reported, together with insights into their growth mechanisms. We also highlight their properties and applications and conclude with perspectives on future directions in developing this class of nanomaterials. It is hoped that the concepts and existing challenges outlined in this Review will drive further research into understanding and controlling the symmetry breaking process.

Nuclear Magnetic Resonance and Metadynamics Simulations Reveal the Atomistic Binding of l-Serine and O-Phospho-l-Serine at Disordered Calcium Phosphate Surfaces of Biocements

Interactions between biomolecules and structurally disordered calcium phosphate (CaP) surfaces are crucial for the regulation of bone mineralization by noncollagenous proteins, the organization of complexes of casein and amorphous calcium phosphate (ACP) in milk, as well as for structure-function relationships of hybrid organic/inorganic interfaces in biomaterials. By a combination of advanced solid-state NMR experiments and metadynamics simulations, we examine the detailed binding of O-phospho-l-serine (Pser) and l-serine (Ser) with ACP in bone-adhesive CaP cements, whose capacity of gluing fractured bone together stems from the close integration of the organic molecules with ACP over a subnanometer scale. The proximity of each carboxy, aliphatic, and amino group of Pser/Ser to the Ca²⁺ and phosphate species of ACP observed from the metadynamics-derived models agreed well with results from heteronuclear solid-state NMR experiments that are sensitive to the ¹³C-³¹P and ¹⁵N-³¹P distances. The inorganic/organic contacts in Pser-doped cements are also contrasted with experimental and modeled data on the Pser binding at nanocrystalline HA particles grown from a Pser-bearing aqueous solution. The molecular adsorption is driven mainly by electrostatic interactions between the negatively charged carboxy/phosphate groups and Ca²⁺ cations of ACP, along with H bonds to either protonated or nonprotonated inorganic phosphate groups. The Pser and Ser molecules anchor at their phosphate/amino and carboxy/amino moieties, respectively, leading to an extended molecular conformation across the surface, as opposed to an "upright standing" molecule that would result from the binding of one sole functional group.

Molecular origin of structural defects in the zinc phthalocyanine film

Controlling the growth of thin phthalocyanine films is a long-term challenge for the science of applied nanomaterials. So, this contribution deals with films of unsubstituted zinc phthalocyanine (ZnPc) and seeks to acquire structural information that is unavailable via physical experiments, thus, finding out how the film morphology can be seriously improved. A model of the vapor-deposited film has been created using the molecular dynamics method. Specifically, the ZnPc molecules are dosed into the simulation box under normal conditions, reproducing key features of the real film, such as the trimolecular wetting layer and the island-like three-dimensional (3D) phase that is structured like the α-polymorph; then all film fragments are characterized via their radial distribution functions and mean-squared displacements. The simulation model indicates that the 3D phase starts to develop smoothly through multimolecular cofacial stacking but finally becomes fragmental because the wetting layer is too meager to be a good platform for regular film growth. Accordingly, the film morphology may be improved if the wetting layer is thickened via restraining the vertical development of the 3D phase. Following this idea, uniform ZnPc films impaired by neither grain boundaries nor coarser defects were deposited from solutions and visualized at the nanometer scale.

Adsorption and Diffusion of Oxygen on Pure and Partially Oxidized Metal Surfaces in Ultrahigh Resolution

The interaction of gas molecules with metal and oxide surfaces plays a critical role in corrosion, catalysis, sensing, and heterogeneous materials. However, insights into the dynamics of O₂ from picoseconds to microseconds have remained unavailable to date. We obtained 3D potential energy surfaces for adsorption of O₂ on 11 common pristine and partially oxidized (hkl) surfaces of Ni and Al in picometer resolution and high accuracy of 0.1 kcal/mol, identified binding sites, and surface mobility from 25 to 300 °C. We explain relative oxidation rates and parameters for oxide growth. We employed over 150 000 molecular mechanics and molecular dynamics simulations with the interface force field (IFF) using structural data from X-ray diffraction (XRD) and low-energy electron diffraction (LEED). The methods reach 10 to 50 times higher accuracy than possible before and are suited to analyze gas interactions with metals up to the micrometer scale including defects and irregular nanostructures.

Machine Learning: An Advanced Platform for Materials Development and State Prediction in Lithium-Ion Batteries

Lithium-ion batteries (LIBs) are vital energy-storage devices in modern society. However, the performance and cost are still not satisfactory in terms of energy density, power density, cycle life, safety, etc. To further improve the performance of batteries, traditional "trial-and-error" processes require a vast number of tedious experiments. Computational chemistry and artificial intelligence (AI) can significantly accelerate the research and development of novel battery systems. Herein, a heterogeneous category of AI technology for predicting and discovering battery materials and estimating the state of the battery system is reviewed. Successful examples, the challenges of deploying AI in real-world scenarios, and an integrated framework are analyzed and outlined. The state-of-the-art research about the applications of ML in the property prediction and battery discovery, including electrolyte and electrode materials, are further summarized. Meanwhile, the prediction of battery states is also provided. Finally, various existing challenges and the framework to tackle the challenges on the further development of machine learning for rechargeable LIBs are proposed.

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

The main goal of this mini-review is to provide an updated state-of-the-art of the hybrid organic-inorganic materials focusing mainly on interface phenomena involving ionic and electronic transport properties. First, we review the most relevant preparation techniques and the structural features of hybrid organic-inorganic materials prepared by solution-phase reaction of inorganic/organic precursor into organic/inorganic hosts and vapor-phase infiltration of the inorganic precursor into organic hosts and molecular layer deposition of organic precursor onto the inorganic surface. Particular emphasis is given to the advances in joint experimental and theoretical studies discussing diverse types of computational simulations for hybrid-organic materials and interfaces. We make a specific revision on the separately ionic, and electronic transport properties of these hybrid organic-inorganic materials focusing mostly on interface phenomena. Finally, we deepen into mixed ionic-electronic transport properties and provide our concluding remarks and give some perspectives about this growing field of research.

Multiscale Modeling of Bio-Nano Interactions of Zero-Valent Silver Nanoparticles

Understanding the specifics of interaction between the protein and nanomaterial is crucial for designing efficient, safe, and selective nanoplatforms, such as biosensor or nanocarrier systems. Routing experimental screening for the most suitable complementary pair of biomolecule and nanomaterial used in such nanoplatforms might be a resource-intensive task. While a range of computational tools are available for prescreening libraries of proteins for their interactions with small molecular ligands, choices for high-throughput screening of protein libraries for binding affinities to new and existing nanomaterials are very limited. In the current work, we present the results of the systematic computational study of interaction of various biomolecules with pristine zero-valent noble metal nanoparticles, namely, AgNPs, by using the UnitedAtom multiscale approach. A set of blood plasma and dietary proteins for which the interaction with AgNPs was described experimentally were examined computationally to evaluate the performance of the UnitedAtom method. A set of interfacial descriptors (log P^NM, adsorption affinities, and adsorption affinity ranking), which can characterize the relative hydrophobicity/hydrophilicity/lipophilicity of the nanosized silver and its ability to form bio(eco)corona, was evaluated for future use in nano-QSAR/QSPR studies.

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

Molecular modeling and simulation are invaluable tools for nanoscience that predict mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide molecular-level insight into underlying mechanisms. However, building nanomaterial-containing systems remains challenging due to the lack of reliable and integrated cyberinfrastructures. Here we present Nanomaterial Modeler in CHARMM-GUI, a web-based cyberinfrastructure that provides an automated process to generate various nanomaterial models, associated topologies, and configuration files to perform state-of-the-art molecular dynamics simulations using most simulation packages. The nanomaterial models are based on the interface force field, one of the most reliable force fields (FFs). The transferability of nanomaterial models among the simulation programs was assessed by single-point energy calculations, which yielded 0.01% relative absolute energy differences for various surface models and equilibrium nanoparticle shapes. Three widely used Lennard-Jones (LJ) cutoff methods are employed to evaluate the compatibility of nanomaterial models with respect to conventional biomolecular FFs: simple truncation at r = 12 Å (12 cutoff), force-based switching over 10 to 12 Å (10-12 fsw), and LJ particle mesh Ewald with no cutoff (LJPME). The FF parameters with these LJ cutoff methods are extensively validated by reproducing structural, interfacial, and mechanical properties. We find that the computed density and surface energies are in good agreement with reported experimental results, although the simulation results increase in the following order: 10-12 fsw <12 cutoff < LJPME. Nanomaterials in which LJ interactions are a major component show relatively higher deviations (up to 4% in density and 8% in surface energy differences) compared with the experiment. Nanomaterial Modeler's capability is also demonstrated by generating complex systems of nanomaterial-biomolecule and nanomaterial-polymer interfaces with a combination of existing CHARMM-GUI modules. We hope that Nanomaterial Modeler can be used to carry out innovative nanomaterial modeling and simulations to acquire insight into the structure, dynamics, and underlying mechanisms of complex nanomaterial-containing systems.

Biomineralization from the Perspective of Ion Aggregation: Calcium Phosphate Nucleation in the Physiological Environment

Biomineralization is an important process of bone tissue generation. Calcium (Ca) and phosphate (P) ions aggregate and nucleate under the regulation of biomolecules at the initial mineralization stage. Due to the complexity of the physiological environment, the movement behavior and mineralization mechanism of calcium and phosphate ions, as well as the effect of biomolecules on them, are not clear. In this study, computer simulations and experimental verification were applied to investigate the characteristics of the initial biomineralization from the view of ion aggregation and nucleation. The results prove that P ions play a more important role in mineralization than Ca ions. The guanidyl group and surrounding carboxyl terminal groups are a potential excellent nucleation domain on proteins. The interval distribution of acidic/basic residues on protein is more conductive to the formation of large Ca and P ions clusters. The involvement of protein could increase the probability of hydroxyapatite phase precipitation, especially in the presence of a helical conformation. The detailed information on Ca and P ions behavior provided by the computer simulations is helpful for further understanding the mechanism of biomineralization, which will promote the development of bone repair materials to the biomimetic mineralized materials.

Highly Heterogeneous Polarization and Solvation of Gold Nanoparticles in Aqueous Electrolytes

The performance of gold nanoparticles (NPs) in applications depends critically on the structure of the NP-solvent interface, at which the electrostatic surface polarization is one of the key characteristics that affects hydration, ionic adsorption, and electrochemical reactions. Here, we demonstrate significant effects of explicit metal polarizability on the solvation and electrostatic properties of bare gold NPs in aqueous electrolyte solutions of sodium salts of various anions (Cl^-, BF₄^-, PF₆^-, nitrophenolate, and 3- and 4-valent hexacyanoferrate), using classical molecular dynamics simulations with a polarizable core-shell model for the gold atoms. We find considerable spatial heterogeneity of the polarization and electrostatic potentials on the NP surface, mediated by a highly facet-dependent structuring of the interfacial water molecules. Moreover, ion-specific, facet-dependent ion adsorption leads to considerable alterations of the interfacial polarization. Compared to nonpolarizable NPs, surface polarization modifies water local dipole densities only slightly but has substantial effects on the electrostatic surface potentials and leads to significant lateral redistributions of ions on the NP surface. Besides, interfacial polarization effects cancel out in the far field for monovalent ions but not for polyvalent ions, as anticipated from continuum "image-charge" concepts. Far-field effective Debye-Hückel surface potentials change accordingly in a valence-specific fashion. Hence, the explicit charge response of metal NPs is crucial for the accurate description and interpretation of interfacial electrostatics (e.g., for charge transfer and interfacial polarization in catalysis and electrochemistry).

Accurate and Compatible Force Fields for Molecular Oxygen, Nitrogen, and Hydrogen to Simulate Gases, Electrolytes, and Heterogeneous Interfaces

Gas molecules and interfaces with liquids and solids play a critical role in living organisms, sorption, catalysis, and the environment. Monitoring adsorption and heterogeneous interfaces remains difficult in experiments, and earlier models for molecular simulations lead to errors over 100% in fundamental molecular properties. We introduce conceptually new force field parameters for molecular oxygen, nitrogen, and hydrogen that reduce deviations to <5%. We employ a combination of a harmonic bond stretching potential and Lennard-Jones parameters with 12-6 and 9-6 options, leading to computed bond lengths, Raman peaks, liquid densities, vaporization enthalpies, and free energies of hydration in impressive agreement with experiments. Reliable free energies of hydration were obtained upon validation of density and vaporization energy without significant further parameter adjustments. We illustrate applications to O₂ adsorption on Pt electrocatalysts and N₂ adsorption in zeolites, showing <5% deviation in adsorption energies measured in experiments without additional fitting parameters. We discuss the chemical interpretation of all parameters and explain the reasons for discrepancies in earlier models. Compatibility with the Interface Force Field (IFF), CHARMM, AMBER, OPLS-AA, GROMOS, DREIDING, CVFF, PCFF, COMPASS, and QM/MM methods enables reliable simulations of gases and liquid/solid interfaces with biopolymers, minerals, and metals. The parametrization protocol can be applied to similar molecules.

Binding mechanism and binding free energy of amino acids and citrate to hydroxyapatite surfaces as a function of crystallographic facet, pH, and electrolytes

Hydroxyapatite (HAP) is the major mineral phase in bone and teeth. The interaction of individual amino acids and citrate ions with different crystallographic HAP surfaces has remained uncertain for decades, creating a knowledge gap to rationally design interactions with peptides, proteins, and drugs. In this contribution, we quantify the binding mechanisms and binding free energies of the 20 end-capped natural amino acids and citrate ions on the basal (001) and prismatic (010)/(020) planes of hydroxyapatite at pH values of 7 and 5 for the first time at the molecular scale. We utilized over 1500 steered molecular dynamics simulations with highly accurate potentials that reproduce surface and hydration energies of (hkl) hydroxyapatite surfaces at different pH values. Charged residues demonstrate a much higher affinity to HAP than charge-neutral species due to the formation of superficial ion pairs and ease of penetration into layers of water molecules on the mineral surface. Binding free energies range from 0 to -60 kJ/mol and were determined with ∼ 10% uncertainty. The highest affinity was found for citrate, followed by Asp(-) and Glu(-), and followed after a gap by Arg(+), Lys(+), as well as by His(+) at pH 5. The (hkl)-specific area density of calcium ions, the protonation state of phosphate ions, and subsurface directional order of the ions in HAP lead to surface-specific binding patterns. Amino acids without ionic side groups exhibit weak binding, between -3 and 0 kJ/mol, due to difficulties to penetrate the first layer of water molecules on the apatite surfaces. We explain recognition processes that remained elusive in experiments, in prior simulations, discuss agreement with available data, and reconcile conflicting interpretations. The findings can serve as useful input for the design of peptides, proteins, and drug molecules for the modification of bone and teeth-related materials, as well as control of apatite mineralization.

Toward the Specificity of Bare Nanomaterial Surfaces for Protein Corona Formation

Aiming at creating smart nanomaterials for biomedical applications, nanotechnology aspires to develop a new generation of nanomaterials with the ability to recognize different biological components in a complex environment. It is common opinion that nanomaterials must be coated with organic or inorganic layers as a mandatory prerequisite for applications in biological systems. Thus, it is the nanomaterial surface coating that predominantly controls the nanomaterial fate in the biological environment. In the last decades, interdisciplinary studies involving not only life sciences, but all branches of scientific research, provided hints for obtaining uncoated inorganic materials able to interact with biological systems with high complexity and selectivity. Herein, the fragmentary literature on the interactions between bare abiotic materials and biological components is reviewed. Moreover, the most relevant examples of selective binding and the conceptualization of the general principles behind recognition mechanisms were provided. Nanoparticle features, such as crystalline facets, density and distribution of surface chemical groups, and surface roughness and topography were encompassed for deepening the comprehension of the general concept of recognition patterns.

The nanotube express: Delivering a stapled peptide to the cell surface

HYPOTHESIS

Carbon nanotubes (CNTs) represent a novel platform for cellular delivery of therapeutic peptides. Chemically-functionalized CNTs may enhance peptide uptake by improving their membrane targeting properties.

EXPERIMENTS

Using coarse-grained (CG) molecular dynamics (MD) simulations, we investigate membrane interactions of a peptide conjugated to pristine and chemically-modified CNTs. As proof of principle, we focus on their interactions with PM2, an amphipathic stapled peptide that inhibits the E3 ubiquitin ligase HDM2 from negatively regulating the p53 tumor suppressor. CNT interaction with both simple planar lipid bilayers as well as spherical lipid vesicles was studied, the latter as a surrogate for curved cellular membranes.

FINDINGS

Membrane permeation was rapid and spontaneous for both pristine and oxidized CNTs when unconjugated. This was slowed upon addition of a noncovalently attached peptide surface "sheath", which may be an effective way to slow CNT entry and avert membrane rupture. The CNT conjugates were observed to "desheath" their peptide layer at the bilayer interface upon insertion, leaving their cargo behind in the outer leaflet. This suggests that a synergy may exist to optimize CNT safety whilst enhancing the delivery efficiency of "hitchhiking" therapeutic molecules.

Lessons from a Challenging System: Accurate Adsorption Free Energies at the Amino Acid/ZnO Interface

We undertake steps to overcome four challenges that have hindered the understanding of ZnO/biomolecule interfaces at the atomic scale: parametrization of a classical force field, ZnO surface termination and amino acid protonation state in methanol, and convergence of enhanced sampling molecular dynamics simulations. We predict adsorption free energies for histidine, serine, cysteine, and tryptophan in remarkable agreement with experimental measurements obtained via a novel indicator-displacement assay. Adsorption is driven by direct surface/amino-acid interactions mediated by terminal hydroxyl groups and stabilized by strongly structured methanol solvation shells.

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

The oxygen reduction reaction (ORR) on platinum catalysts is essential in fuel cells. Quantitative predictions of the relative ORR activity in experiments, in the range of 1 to 50 times, have remained challenging because of incomplete mechanistic understanding and lack of computational tools to account for the associated small differences in activation energies (<2.3 kilocalories per mole). Using highly accurate molecular dynamics (MD) simulation with the Interface force field (0.1 kilocalories per mole), we elucidated the mechanism of adsorption of molecular oxygen on regular and irregular platinum surfaces and nanostructures, followed by local density functional theory (DFT) calculations. The relative ORR activity is determined by oxygen access to platinum surfaces, which greatly depends on specific water adlayers, while electron transfer occurs at a similar slow rate. The MD methods facilitate quantitative predictions of relative ORR activities of any platinum nanostructures, are applicable to other catalysts, and enable effective MD/DFT approaches.

Involvement of prenucleation clusters in calcium phosphate mineralization of collagen

Involvement of thermodynamically-stable prenucleation clusters (PNCs) in the biomineralization of collagen has been speculated since their existence was reported in mineralization systems. It has been hypothesized that intrafibrillar mineralization proceeds via nucleation of inhibitor-stabilized intermediates produced by liquid-liquid separation (aka. polymer-induced liquid precursors; PILPs). Here, the contribution of PNCs and PILPs to calcium phosphate intrafibrillar mineralization of collagen was examined in a model with a semipermeable membrane that excludes nucleation inhibitor-stabilized PILPs from reaching the collagen fibrils, using cryogenic electron microscopy of reconstituted fibrils and conventional transmission electron microscopy of collagen sponges. Molecular dynamics simulation with the Interface force field (IFF) was used to confirm the existence of PILPs with amorphous calcium phosphate and elucidate details of the dynamics. Furthermore, intrafibrillar mineralization of single collagen fibrils was experimentally observed with unstabilized PNCs when anionic/cationic polyelectrolytes were used to establish Donnan equilibrium across the semipermeable membrane. Molecular dynamics simulation verified PNC formation within the collagen intrafibrillar gap zones at the atomic scale and explained the role of external PILPs. The PILPs decrease the interfibrillar water content and increase the interfibrillar ionic concentration. Nevertheless, intrafibrillar mineralization of collagen sponges with PNCs alone was inefficacious, being constrained by competition from extrafibrillar mineral precipitation. STATEMENT OF SIGNIFICANCE: Compared with conventional PILP-based intrafibrillar mineralization, mineralization of collagen fibrils using unstabilized PNCs is constrained by competition from extrafibrillar mineral deposition. The narrow window of opportunity for PNCs to produce intrafibrillar mineralization provides a plausible explanation for the feasibility of nucleation inhibitor-free intrafibrillar apatite assembly during reconstitution of type I collagen.

Glyphosate adsorption onto kaolinite and kaolinite-humic acid composites: Experimental and molecular dynamics studies

Glyphosate (PMG) has been the most widely used herbicide in the world, and its environmental mobility and fate are mainly controlled by interactions with mineral surfaces. In soil systems, kaolinite is typically associated with humic acids (HAs) in the form of mineral-HA complexes, and hence it is crucial to characterize the molecular-scale interactions that occur between PMG and kaolinite and kaolinite-HA complexes. Batch experiments, Fourier transform infrared spectrum (FTIR) and X-ray photoelectron spectroscopy (XPS), isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulations were performed to decipher the molecular interactions between PMG and kaolinite and kaolinite-HA composites. Our results reveal that kaolinite-HA composites adsorb higher concentrations of PMG than does kaolinite alone, likely due to more adsorption sites existed on kaolinite-HA than on kaolinite. FTIR and XPS analysis reveal that the carboxyl, phosphonyl and amino groups of PMG interacted with kaolinite and kaolinite-humic acid via Hydrogen bonds. The ITC results and interaction energy calculations indicate that the adsorption of PMG onto the kaolinite-HA is more energetically favorable relative to that onto kaolinite. MD simulations suggest that the PMG molecule adsorbs parallel to the surface of kaolinite and the composites through hydrogen bonding. Humic acid increases the adsorption of PMG through the creation of H-bond networks between PMG, the kaolinite surface, and humic acid. The results from this study improve our molecular-level understanding of the interactions between PMG and two important components of soil systems, and hence yield valuable information for characterizing the fate and behavior of PMG in soil environments.

A new mechanism for reduced cell adhesion: Adsorption dynamics of collagen on a nanoporous gold surface

Nanostructured materials such as nanoparticles and nanoporous materials strongly affect cell behaviors such as cell viability. Because cellular uptake of nanoporous materials does not occur, mechanisms for the effects of nanoporous materials on cells are different from those of nanoparticles. The effects of nanoporous materials on cells are thought to result from large conformational changes in the extracellular matrix (ECM) induced by the nanoporous materials, although the mechanotransduction and the critical focal adhesion cluster size also have an effect on the cell response. However, we show that the adhesion of mesenchymal stem cells to a gold surface is reduced for nanoporous gold (NPG), despite the conformational changes in collagen induced by NPG being below the detection limits of the experimental analyses. The adsorption dynamics of collagen on NPG are investigated by molecular dynamics simulations to determine the origin of the reduced cell adhesion to NPG. The adsorption energy of collagen on NPG is lower than that on flat gold (FG) despite there being little difference between the global conformation of collagen segments adsorbed on NPG compared with FG. This finding is related to the surface strain of NPG and the limited movement of collagen amino acids owing to interchain hydrogen bonds. The results obtained in this study provide new insight into the interactions between nanostructured materials and the ECM.

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

Molybdenum disulfide (MoS2) is a layered material with outstanding electrical and optical properties. Numerous studies evaluate the performance in sensors, catalysts, batteries, and composites that can benefit from guidance by simulations in all-atom resolution. However, molecular simulations remain difficult due to lack of reliable models. We introduce an interpretable force field for MoS2 with record performance that reproduces structural, interfacial, and mechanical properties in 0.1% to 5% agreement with experiments. The model overcomes structural instability, deviations in interfacial and mechanical properties by several 100%, and empirical fitting protocols in earlier models. It is compatible with several force fields for molecular dynamics simulation, including the interface force field (IFF), CVFF, DREIDING, PCFF, COMPASS, CHARMM, AMBER, and OPLS-AA. The parameters capture polar covalent bonding, X-ray structure, cleavage energy, infrared spectra, bending stability, bulk modulus, Young's modulus, and contact angles with polar and nonpolar solvents. We utilized the models to uncover the binding mechanism of peptides to the MoS2 basal plane. The binding strength of several 7mer and 8mer peptides scales linearly with surface contact and replacement of surface-bound water molecules, and is tunable in a wide range from -86 to -6 kcal mol-1. The binding selectivity is multifactorial, including major contributions by van-der-Waals coordination and charge matching of certain side groups, orientation of hydrophilic side chains towards water, and conformation flexibility. We explain the relative attraction and role of the 20 amino acids using computational and experimental data. The force field can be used to screen and interpret the assembly of MoS2-based nanomaterials and electrolyte interfaces up to a billion atoms with high accuracy, including multiscale simulations from the quantum scale to the microscale.

Nanoscale in silico classification of ligand functionalised surfaces for protein adsorption resistance

Non-specific protein adsorption represents a significant challenge for the design of efficient and safe nanoparticles for biomedical applications since it may prevent functional ligands to target the desired specific receptors which can limit the efficacy of novel drug delivery systems and biosensors. The biofilm formation initiated by protein adsorption on surfaces limits the lifetime and safety of medical implants and tissue regenerative scaffolds. The development of biofouling resistant surfaces is therefore a major goal for the widespread uptake of nanomedicine. Here, we provide a relatively simple computational screening method based on the rational physically grounded criteria that may suffice in selection of surface grafted ligands for protein rejection, and test whether these criteria can be extrapolated from a specific protein to generic protein-resistant surfaces. Using all-atom molecular dynamics simulations we characterise four types of ligand functionalised surfaces at aqueous interfaces in terms of the surface hydrophobicity and ligand dynamics. We demonstrate how our hypothesised interfacial design based on the select physical characteristics of the ligated surfaces can enable the rejection of a protein from the surface. The ligand screening procedure and the detailed atomistic characterisation of the protein rejection process presented suggest that minimizing the adsorption of surface active proteins requires specific surface topographies and ligand chemistries that are able to maximise the entropic penalty associated with the restriction of the ligand dynamics and trapping interfacial water by adsorbed proteins.

Energy Landscapes of a Pair of Adsorbed Peptides

The wide relevance of peptide adsorption in natural and synthetic contexts means it has attracted much attention. Molecular dynamics (MD) simulation has been widely used in these endeavors. Much of this has focused on single peptides due to the computational effort required to capture the rare events that characterize their adsorption. This focus is, however, of limited practical relevance as in reality, most systems of interest operate in the nondilute regime where peptides will interact with other adsorbed peptides. As an alternative to MD simulation, we have used energy landscape mapping (ELM) to investigate two met-enkephalin molecules adsorbed at a gas/graphite interface. Major conformations of the adsorbed peptides and the connecting transition states are elucidated along with the associated energy barriers and rates of exchange. The last of these makes clear that MD simulations are currently of limited use in probing the co-adsorption of two peptides, let alone more. The constant volume heat capacity as a function of temperature is also presented. Overall, this study represents a significant step toward characterizing peptide adsorption beyond the dilute limit.

Effects of Nanoparticle Electrostatics and Protein-Protein Interactions on Corona Formation: Conformation and Hydrodynamics

All-atom molecular dynamics simulations of plasma proteins (human serum albumin, fibrinogen, immunoglobulin gamma-1 chain-C, complement C3, and apolipoprotein A-I) adsorbed onto 10 nm sized cationic, anionic, and neutral polystyrene (PS) particles in water are performed. In simulations of a single protein with a PS particle, proteins eventually bind to all PS particles, regardless of particle charge, in agreement with experiments showing the binding between anionic proteins and particles, which is further confirmed by calculating the binding free energies from umbrella sampling simulations. Simulations of mixtures of multiple proteins and a PS particle show the formation of the protein layer on the surface via the adsorption competition between proteins, which influences the binding affinity and structure of adsorbed proteins. In particular, diffusivities are much higher for proteins bound to the particle surface or to the boundary of the protein layer than for those bound to both the particle surface and other proteins, indicating the dependence of protein mobility on their positions in the layer. These findings help to explain in detail experimental observations regarding the replacement of plasma proteins at the early stage of corona formation and the difference in the binding strength of proteins in inner and outer protein-layers.

Comparative Study on Factors Governing Binding Mechanisms in Polylactic Acid-Hydroxyapatite and Polyethylene-Hydroxyapatite Systems via Molecular Dynamics Simulations

Binding mechanisms in polylactic acid-hydroxyapatite (PLA-HAp) and polyethylene-hydroxyapatite (PE-HAp) systems are comparatively elucidated on HAp (110) surfaces in unprecedented detail using molecular dynamics simulations conducted with the systematically varying number of monomers (N) between 10 and 400 at 310 K (NVT). Although PE seems to gradually cover the HAp surface more effectively compared to PLA, evident from the corresponding radius of gyration and occupied area values, the interface density and total binding energy in PLA-HAp systems is higher compared to those of PE-HAp systems. It is shown that a linear relationship between the binding energy and the surface area occupied by the monomer exists, consistent with our finding that binding energy converges to a limiting value with respect to monomer size on a constant surface area. The major constituent of the total binding energy is, rather surprisingly, shown to be the energy change in the bulk structure in HAp upon interaction; the next most important contributor is found to be the energy corresponding to surface-polymer interactions. The interplay between mainly these two contributors, acting in different fashions in two systems investigated here, seems to control the total binding energies. Increasing monomer size N initially results in enhanced densification of the interface in the HAp-PLA system up until N ≈ 200 with the positioning of mainly ═O units of PLA onto the HAp surface, consistent with the increasing Ca-O coordination numbers. Further increases in PLA size (N > 200) result in decreasing intensities of the peaks in the concentration profile consistent with the decreasing surface-polymer interaction energies while increased stabilization of the energy of the bulk is pronounced in this region. On the other hand, increasing N leads to a constantly increasing concentration at the interface in PE-HAp systems; -H atoms of the PE chain are positioned closer to the HAp surface than are -C atoms. These changes are coupled with increasing surface-polymer interaction energies in PE-HAp complexes, while slight destabilization in the energy of the bulk is observed for N > 100. A detailed examination of binding mechanisms in these technologically important systems as presented here is essential in material discovery; this valuable information, that will not be available from experiments can be attained through molecular simulations. The current study, to the best of our knowledge, comprises one of the first steps in achieving this goal for PLA/PE-HAp systems.

Thermal Selection of Aqueous Molecular Conformations for Tailored Energetics of Peptide Assemblies at Solid Interfaces

Key to the development of functional bioinorganic soft interfaces is the predictive control over the micron-scale assembly structure and energetics of biomolecules at solid interfaces. While assembly of labile biomolecules, such as short peptides, at interfaces is a great deal affected by the shape of the molecule, biomolecular conformations are prompted by external solution conditions, involving temperature, pH, and salt concentration. In this light, one can expect that the environmental conformational selection of aqueous biomolecules could potentially allow for fine-tuning of the equilibrium assembly structure at interfaces, as well as, the binding strength and molecular mobility within these assemblies. Here, we demonstrate the energetic and structural tailoring of two-dimensional surface assemblies of graphite-binding dodecapeptides, through the thermal selection of aqueous peptide conformations. Our findings based on a scanning probe energetic analysis, supplemented by molecular dynamics modeling, show that peptide-graphite and peptide-peptide intermolecular interactions strongly depend on the thermally selected molecular conformation and that the extent of the conformational change is directly related to the observed assembled structure. Enabled by these results was the design of a peptide with predictable binding and assembled structure, thus, suggesting environmental preconditioning of peptides as a means for controlling self-assembling active bioinorganic interfaces for bioelectronic implementations such as biomolecular fuel cells and biosensors.

Giant thermal expansion of a two-dimensional supramolecular network triggered by alkyl chain motion

Thermal expansion, the response in shape, area or volume of a solid with heat, is usually large in molecular materials compared to their inorganic counterparts. Resulting from the intrinsic molecule flexibility, conformational changes or variable intermolecular interactions, the exact interplay between these mechanisms is however poorly understood down to the molecular level. Here, we investigate the structural variations of a two-dimensional supramolecular network on Au(111) consisting of shape persistent polyphenylene molecules equipped with peripheral dodecyl chains. By comparing high-resolution scanning probe microscopy and molecular dynamics simulations obtained at 5 and 300 K, we determine the thermal expansion coefficient of the assembly of 980 ± 110 × 10^-6 K^-1, twice larger than other molecular systems hitherto reported in the literature, and two orders of magnitude larger than conventional materials. This giant positive expansion originates from the increased mobility of the dodecyl chains with temperature that determine the intermolecular interactions and the network spacing.

Chiral Restructuring of Peptide Enantiomers on Gold Nanomaterials

The use of biomolecules has been invaluable at generating and controlling optical chirality in nanomaterials; however, the structure and properties of the chiral biotemplate are not well understood due to the complexity of peptide-nanoparticle interactions. In this study, we show that the complex interactions between d-peptides and gold nanomaterials led to a chiral restructuring of peptides as demonstrated by circular dichroism and proteolytic cleavage of d-peptides via gold-mediated inversion of peptide chirality. The gold nanoparticles synthesized using d-peptide produce a highly ordered atomic surface and restructured peptide bonds for enzyme cleavage. Differences in gold nanoparticle catalyzed reduction of 4-nitrophenol were observed on the basis of the chiral peptide used in nanoparticle synthesis. Notably, the proteolytic cleavage of d-peptides on gold provides an opportunity for designing nanoparticle based therapeutics to treat peptide venoms, access new chemistries, or modulate the catalytic activity of nanomaterials.