Advancing DBD Plasma Chemistry: Insights into Reactive Nitrogen Species such as NO2, N2O5, and N2O Optimization and Species Reactivity through Experiments and MD Simulations

This study aims to fine-tune the plasma composition with a particular emphasis on reactive nitrogen species (RNS) including nitrogen dioxide (NO2), dinitrogen pentoxide (N2O5), and nitrous oxide (N2O), produced by a self-constructed cylindrical dielectric barrier discharge (CDBD). We demonstrated the effective manipulation of the plasma chemical profile by optimizing electrical properties, including the applied voltage and frequency, and by adjusting the nitrogen and oxygen ratios in the gas mixture. Additionally, quantification of these active species was achieved using Fourier transform infrared spectroscopy. The study further extends to exploring the aerosol polymerization of acrylamide (AM) into polyacrylamide (PAM), serving as a model reaction to evaluate the reactivity of different plasma-generated species, highlighting the significant role of NO2 in achieving high polymerization yields. Complementing our experimental data, molecular dynamics (MD) simulations, based on the ReaxFF reactive force field potential, explored the interactions between reactive oxygen species, specifically hydroxyl radicals (OH) and hydrogen peroxide (H2O2), with water molecules. Understanding these interactions, combined with the optimization of plasma chemistry, is crucial for enhancing the effectiveness of DBD plasma in environmental applications like air purification and water treatment.

Nanocellulose-Bovine Serum Albumin Interactions in an Aqueous Medium: Investigations Using In Situ Nanocolloidal Probe Microscopy and Reactive Molecular Dynamics Simulations

As a versatile nanomaterial derived from renewable sources, nanocellulose has attracted considerable attention for its potential applications in various sectors, especially those focused on water treatment and remediation. Here, we have combined atomic force microscopy (AFM) and reactive molecular dynamics (RMD) simulations to characterize the interactions between cellulose nanofibers modified with carboxylate or phosphate groups and the protein foulant model bovine serum albumin (BSA) at pH 3.92, which is close to the isoelectric point of BSA. Colloidal probes were prepared by modification of the AFM probes with the nanofibers, and the nanofiber coating on the AFM tip was for the first time confirmed through fluorescence labeling and confocal optical sectioning. We have found that the wet-state normalized adhesion force is approximately 17.87 ± 8.58 pN/nm for the carboxylated cellulose nanofibers (TOCNF) and about 11.70 ± 2.97 pN/nm for the phosphorylated ones (PCNF) at the studied pH. Moreover, the adsorbed protein partially unfolded at the cellulose interface due to the secondary structure's loss of intramolecular hydrogen bonds. We demonstrate that nanocellulose colloidal probes can be used as a sensitive tool to reveal interactions with BSA at nano and molecular scales and under in situ conditions. RMD simulations helped to gain a molecular- and atomistic-level understanding of the differences between these findings. In the case of PCNF, partially solvated metal ions, preferentially bound to the phosphates, reduced the direct protein-cellulose connections. This understanding can lead to significant advancements in the development of cellulose-based antifouling surfaces and provide crucial insights for expanding the pH range of use and suggesting appropriate recalibrations.

Development of a ReaxFF reactive force field for ternary phosphate-based bioactive glasses

Phosphate-based glasses (PBGs) in the CaO-Na2O-P2O5 system have diverse applications as biomaterials due to their unique dissolution properties. A reactive force field (ReaxFF) has been developed to simulate these materials at the atomic level. The ReaxFF parameters of PBGs, including the interaction between phosphorus and calcium atoms, have been developed using a published code based on genetic algorithms. The training data, including the atomic charges, atomic forces, bond and angle parameters, and different differential energies, are chosen and measured from static quantum-mechanical calculations and ab initio molecular dynamics of PBGs. We did different short- and medium-range structural analyses on the bulk simulated PBGs with different compositions to validate the developed potential. Radial and angular distribution functions and coordination numbers of network formers and modifiers, as well as the network connectivity of the glass, are in agreement with experimental and previous simulations using both shell-model classical force fields and ab initio simulated data; for example, the coordination number of phosphorus is 4.0. This successful development of ReaxFF parameters being able to describe the bulk PBGs enables us to work on the dissolution behavior of the glasses, including the interaction of water molecules with PBGs, in future works.

Reactive Force Field Development for Propane Dehydrogenation on Platinum Surfaces

Propane dehydrogenation (PDH) is an on-purpose catalytic technology to produce propylene from propane that operates at high temperatures, 773-973 K. Several key industry players have been active in developing new catalysts and processes with improved carbon footprint and economics, where Pt-based catalysts have played a central role. The optimization of these catalytic systems through computational and atomistic simulations requires large-scale models that account for their reactivity and dynamic properties. To address this challenge, we developed a new reactive ReaxFF force field (2023-Pt/C/H) that enables large-scale simulations of PDH reactions catalyzed on Pt surfaces. The optimization of force-field parameters relies on a large training set of density functional theory (DFT) calculations of Pt-catalyzed PDH mechanism, including geometries, adsorption and relative energies of reaction intermediates, and key C-H and C-C bond-breaking/forming reaction steps on the Pt(111) surface. The internal validation supports the accuracy of the developed 2023-Pt/C/H force-field parameters, resulting in mean absolute errors (MAE) against DFT data of 14 and 12 kJ mol-1 for relative energies of intermediates and energy barriers, respectively. We demonstrated the applicability of the 2023-Pt/C/H force field with reactive molecular dynamics simulations of propane on different Pt surface topologies and temperatures. The simulations successfully model the formation of propene in the gas phase as well as competitive, unproductive reactions such as deep dehydrogenation and C-C bond cleavage that produce H, C1 and C2 adsorbed species responsible of catalytic deactivation of Pt surface. Results show the following reactivity order: Pt(111) < Pt(100) < Pt(211), and that for the stepped Pt(211) surface, propane activation occurs on low-coordinated Pt atoms at the steps. The measured selectivity as a function of surface topology follows the same trend as activity, the Pt(211) facet being the most selective. The 2023-Pt/C/H reactive force field can also describe the increase of reactivity with the temperature. From these simulations, we were able to estimate the Arrhenius activation energy, 73 kJ mol-1, whose value is close to those reported experimentally for PDH catalyzed by large, supported Pt nanoparticles . The newly developed 2023-Pt/C/H reactive force field can be used in subsequent investigations of different Pt topologies and of collective effects such as temperature, propane pressure, or H surface coverage.

Conformational States of the CXCR4 Inhibitor Peptide EPI-X4-A Theoretical Analysis

EPI-X4, an endogenous peptide inhibitor, has exhibited potential as a blocker of CXCR4-a G protein-coupled receptor. This unique inhibitor demonstrates the ability to impede HIV-1 infection and halt CXCR4-dependent processes such as tumor cell migration and invagination. Despite its promising effects, a comprehensive understanding of the interaction between EPI-X4 and CXCR4 under natural conditions remains elusive due to experimental limitations. To bridge this knowledge gap, a simulation approach was undertaken. Approximately 150,000 secondary structures of EPI-X4 were subjected to simulations to identify thermodynamically stable candidates. This simulation process harnessed a self-developed reactive force field operating within the ReaxFF framework. The application of the Two-Phase Thermodynamic methodology to ReaxFF facilitated the derivation of crucial thermodynamic attributes of the EPI-X4 conformers. To deepen insights, an ab initio density functional theory calculation method was employed to assess the electrostatic potentials of the most relevant (i.e., stable) EPI-X4 structures. This analytical endeavor aimed to enhance comprehension of the inhibitor's structural characteristics. As a result of these investigations, predictions were made regarding how EPI-X4 interacts with CXCR4. Two pivotal requirements emerged. Firstly, the spatial conformation of EPI-X4 must align effectively with the CXCR4 receptor protein. Secondly, the functional groups present on the surface of the inhibitor's structure must complement the corresponding features of CXCR4 to induce attraction between the two entities. These predictive outcomes were based on a meticulous analysis of the conformers, conducted in a gaseous environment. Ultimately, this rigorous exploration yielded a suitable EPI-X4 structure that fulfills the spatial and functional prerequisites for interacting with CXCR4, thus potentially shedding light on new avenues for therapeutic development.

Advantages of Multidimensional Biasing in Accelerated Dynamics: Application to the Calculation of the Acid pKa for Acetic Acid

The use of accelerated sampling methods such as metadynamics has shown a significant advantage in calculations that involve infrequent events, which would otherwise require sampling a prohibitive number of configurations to determine the difference in free energies between two or more chemically distinct states such as in the calculation of acid dissociation constants Ka. In this case, the most common method is to bias the system via a single collective variable (CV) representing the coordination number of the proton donor group, which yields results in reasonable agreement with experiments. Here we study the deprotonation of acetic acid using the reactive force field ReaxFF and observe a significant dependence of Ka on the simulation box size when biasing only the coordination number CV, which is due to incomplete sampling of the deprotonated state for small simulation systems and inefficient sampling for larger ones. Incorporating a second CV representing the distance between the H3O+ cation and the acetate anion results in substantially more efficient sampling, both accelerating the dynamics and virtually eliminating the computational box size dependence.

Mechanisms of chemical-reaction-induced tensile deformation of an Fe/Ni/Cr alloy revealed by reactive atomistic simulations

High entropy alloys (HEAs) have demonstrated excellent potential in various applications owing to the unique properties. One of the most critical issues of HEAs is the stress corrosion cracking (SCC) which limits its reliability in practical applications. However, the SCC mechanisms have not been fully understood yet because of the difficulty of experimental measuring of atomic-scale deformation mechanisms and surface reactions. In this work, we conduct atomistic uniaxial tensile simulations using an FCC-type Fe₄₀Ni₄₀Cr₂₀ alloy as a typical simplification of normal HEAs, in order to reveal how a corrosive environment such as high-temperature/pressure water affects the tensile behaviors and deformation mechanisms. In a vacuum, we observe the generation of layered HCP phases in an FCC matrix during tensile simulation induced by the formation of Shockley partial dislocations from surface and grain boundaries. While, in the corrosive environment of high-temperature/pressure water, the alloy surface is oxidized by chemical reactions with water and this oxide surface layer can suppress the formation of Shockley partial dislocation as well as the resulting FCC-to-HCP phase transition; instead, a BCC phase is preferred to generate in the FCC matrix for releasing the tensile stress and stored elastic energy, leading to a reduced ductility as the BCC phase is typically more brittle than the FCC and HCP. Overall, the deformation mechanism of the FeNiCr alloy is changed by the presence of a high-temperature/pressure water environment-from FCC-to-HCP phase transition in vacuum to FCC-to-BCC phase transition in water. This theoretical fundamental study may contribute to the further improvement of HEAs with high resistance to SCC in experiments.

Hydrophobic Nanoconfinement Enhances CO2 Conversion to H2CO3

Understanding the formation of H₂CO₃ in water from CO₂ is important in environmental and industrial processes. Although numerous investigations have studied this reaction, the conversion of CO₂ to H₂CO₃ in nanopores, and how it differs from that in bulk water, has not been understood. We use ReaxFF metadynamics molecular simulations to demonstrate striking differences in the free energy of CO₂ conversion to H₂CO₃ in bulk and nanoconfined aqueous environments. We find that nanoconfinement not only reduces the energy barrier but also reverses the reaction from endothermic in bulk water to exothermic in nanoconfined water. Also, charged intermediates are observed more often under nanoconfinement than in bulk water. Stronger solvation and more favorable proton transfer with increasing nanoconfinement enhance the thermodynamics and kinetics of the reaction. Our results provide a detailed mechanistic understanding of an important step in the carbonation process, which depends intricately on confinement, surface chemistry, and CO₂ concentration.

Molecular Modeling Insights into the Structure and Behavior of Integrins: A Review

Integrins are heterodimeric glycoproteins crucial to the physiology and pathology of many biological functions. As adhesion molecules, they mediate immune cell trafficking, migration, and immunological synapse formation during inflammation and cancer. The recognition of the vital roles of integrins in various diseases revealed their therapeutic potential. Despite the great effort in the last thirty years, up to now, only seven integrin-based drugs have entered the market. Recent progress in deciphering integrin functions, signaling, and interactions with ligands, along with advancement in rational drug design strategies, provide an opportunity to exploit their therapeutic potential and discover novel agents. This review will discuss the molecular modeling methods used in determining integrins' dynamic properties and in providing information toward understanding their properties and function at the atomic level. Then, we will survey the relevant contributions and the current understanding of integrin structure, activation, the binding of essential ligands, and the role of molecular modeling methods in the rational design of antagonists. We will emphasize the role played by molecular modeling methods in progress in these areas and the designing of integrin antagonists.

A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part I: Force Field Development

This work presents a novel parametrization for the ReaxFF formalism as a means to investigate reaction processes of chlorinated organic compounds. Force field parameters cover the chemical elements C, H, O, Cl and were obtained using a novel optimization approach involving relaxed potential energy surface scans as training targets. The resulting ReaxFF parametrization shows good transferability, as demonstrated on two independent ab initio validation sets. While this first part of our two-paper series focuses on force field parametrization, we apply our parameters to the simulation of chlorinated dibenzofuran formation and decomposition processes in Part II.

ReaxFF-based nonadiabatic dynamics method for azobenzene derivatives

ReaxFF reactive force fields have been parameterized for the ground and first excited states of azobenzene and its derivatives. In addition, an extended set of ab initio reference data ensures wide applicability, including to azosystems in complex environments. Based on the optimized force fields, nonadiabatic surface hopping simulations produce photoisomerization quantum yields and decay times of azobenzene, both in the gas phase and in n-hexane solution, in reasonable agreement with higher level theory and experiment. The transferability to other azo-compounds is illustrated for different arylazopyrazoles as well as ethylene-bridged azobenzene. Moreover, it has been shown that the model can be easily extended to adsorbates on metal surfaces. The simulation of the ring-opening of cyclobutene triggered by the photoisomerization of azobenzene in a macrocycle highlights the advantages of a reactive force field model.

Reactive Molecular Dynamics Simulation of the Structural Damages of the B-DNA Induced by the Oxidation/Nitration of Guanine

Reactive molecular dynamics simulations (RMD) have been carried out to investigate structural alterations of the dodecamer double-strand B-DNA due to the oxidation/nitration modifications introduced to its guanine bases, including 8-oxoguanine, 8-nitroguanine, and 5-guanidino-4-nitroimidazole, considering two distribution patterns. These modifications may arise in the case of cancer treatment using oxidative/nitrosative reactive nitrogen species as anticancer agents. Results show that these mutations affect structural characteristics of the B-DNA dodecamer in the order 8-nitroguanine > 5-guanidino-4-nitroimidazole ≫ 8-oxoguanine. For instance, the base-pair per turn for these modified B-DNA are changed respectively to 9.79, 10.88 and 10.58 from 10.51 in the native defect-free B-DNA, which is compatible with the experimental value of 10.10. In addition, these mutations allow more water molecules to diffuse into the dodecamer structure and consequently increase the possibility of the penetration of reactive and nonreactive species toward constituting nucleic base-pairs. The largest variation of the B-DNA structure is observed for the mutated B-DNA with 8-nitroguanine modifications applied to its separated CG base-pairs along the dodecamer chain. The structural changes introduced by these nitro-/oxo-modified guanine bases can be considered as a critical step in the damage of the DNA structure and alterations of its function.

Exploring the mechanisms of drug-delivery by decorated ZnO nanoparticles through predictive ReaxFF molecular dynamics simulations

Herein, we study the assembling of a drug delivery nanocarrier through reactive molecular dynamics simulations based on an appropriately tuned force field. First, we focus on the combination of the various components (all selected in agreement with experiments), namely nanoparticle (ZnO), functional chains (oleic acid), drug (carfilzomib), and solvent molecules (ethanol), and then on the ability of the assembled nanotool to release its cargo in a physiological environment (water). The simulation results reveal that reactivity is crucial for characterizing the stability of the functionalized ZnONP, its dynamics, and its interactions with lipid chains and drug molecules. The chains are stably chemisorbed on the ZnONP through monodentate or bidentate binding of the carboxyls to the Zn atoms (the hydrogens are released to the surface oxygens). Chains' self-interactions reinforce the lipid cover's stability and distribution on the ZnONP interface. The added drug migrates from the solution to the nano assembly and is captured by the lipids. The molecules are entrapped among the oleic acid chains and adsorbed on the uncoated regions of the nanoparticle surface, partially physisorbed or chemisorbed. The analysis of the simulations confirms that the supramolecular assembly is compact and stable in ethanol. However, upon injection into the water, the size of the aggregate gradually increases, and the lipids start to swell with the aqueous medium. The system evolves towards an unpacked structure where the chains are elongated, separated, and prone to release the cargo depending on local water activity and depth of cargo insertion. All the results agree with the literature confirming the reliability of our predictive computational procedure for disclosing the structure and dynamics of complex materials relevant to the medicinal chemistry field.

Molecular Dynamics Simulation of a Single Carbon Chain through an Asymmetric Double-Layer Graphene Nanopore for Prolonging the Translocation Time

In recent years, sensing technology based on nanopores has become one of the trustworthy options for characterization and even identification of a single biomolecule. In nanopore based DNA sequencing technology, the DNA strand in the electrolyte solution passes through the nanopore under an applied bias electric field. Commonly, the ionic current signals carrying the sequence information are difficult to detect effectively due to the fast translocation speed of the DNA strand, so that slowing down the translocation speed is expected to make the signals easier to distinguish and improve the sequencing accuracy. Modifying the nanopore structure is one of the effective methods. Through all-atom molecular dynamics simulations, we designed an asymmetric double-layer graphene nanopore structure to regulate the translocation speed of a single carbon chain. The structure consists of two nanopores with different sizes located on two layers. The simulation results indicate that the asymmetric nanopore structure will affect the chain's translocation speed and the ionic current value. When the single carbon chain passes from the smaller pore to the larger pore, the translocation time is significantly prolonged, which is about three times as long as the chain passing from the larger pore to the smaller pore. These results provide a new idea for designing more accurate and effective single-molecule solid-state nanopore sensors.

Chemo-enzymatic functionalized sustainable cellulosic membranes: Impact of regional selectivity on ions capture and antifouling behavior

Most of the polymeric membranes synthesized for decentralization of polluted water use fossil-based components. Thus, there is an urgent need to create robust and tunable nano/micro materials for confidently designing efficient and selective polymeric water filters with guaranteed sustainability. We have chosen a robust high-grade microfibrillated cellulose (MFC) as the functional material and selectively tuned it via enzymatic catalysis, which led to the attachment of phosphate group at the C6 position, followed by esterification (fatty acid attachment at C2 and C3 carbon), which led to the increase in its antifouling properties. We have demonstrated the robustness of the functionalization by measuring the separation of various metal ions, and the antifouling properties by adding foulants, such as Bovine Serum Albumin (BSA) and cancerous cells to the test solutions. These prototype affinity MFC membranes represent the most promising type of next-generation high-performance filtration devices for a more sustainable society.

Development and application of ReaxFF methodology for understanding the chemical dynamics of metal carbonates in aqueous solutions

A new ReaxFF reactive force field has been developed for metal carbonate systems including Na⁺, Ca²⁺, and Mg²⁺ cations and the CO₃^2- anion. This force field is fully transferable with previous ReaxFF water and water/electrolyte descriptions. The Me-O-C (Me = metal) three-body valence angle parameters and Me-C non-reactive parameters of the force field have been optimized against quantum mechanical calculations including equations of state, heats of formation, heats of reaction, angle distortions and vibrational frequencies. The new metal carbonate force field has been validated using molecular dynamics simulations to study the solvation and reactivity of metal and carbonate ions in water at 300 K and 700 K. The coordination radius and self-diffusion coefficient show good consistency with existing experimental and simulation results. The angular distribution analysis explains the structural preference of carbonate ions to form carbonates and bicarbonates, where Na⁺ predominantly forms carbonates due to weaker angular strain, while Ca²⁺ and Mg²⁺ prefer to form bicarbonate monodentate in nature. Residence time distribution analyses on different systems reveal the role of ions in accelerating and decelerating the dynamics of water and carbonate ions under different thermodynamic conditions. The formation and dissolution of bicarbonates and carbonates in solution were explored on the basis of the protonation capability in different systems. The nucleation phenomenon of metal carbonates at ambient and supercritical conditions is explained from the perspective of cluster formation over time: Ca²⁺ ions can form prenucleation clusters at ambient temperature but show saturation with increasing temperature, whereas Na⁺ and Mg²⁺ ions show a rapid increase in cluster size and amount upon increasing time and temperature.

Protein C-GeM: A Coarse-Grained Electron Model for Fast and Accurate Protein Electrostatics Prediction

The electrostatic potential (ESP) is a powerful property for understanding and predicting electrostatic charge distributions that drive interactions between molecules. In this study, we compare various charge partitioning schemes including fitted charges, density-based quantum mechanical (QM) partitioning schemes, charge equilibration methods, and our recently introduced coarse-grained electron model, C-GeM, to describe the ESP for protein systems. When benchmarked against high quality density functional theory calculations of the ESP for tripeptides and the crambin protein, we find that the C-GeM model is of comparable accuracy to ab initio charge partitioning methods, but with orders of magnitude improvement in computational efficiency since it does not require either the electron density or the electrostatic potential as input.

Thermophysical properties of water using reactive force fields

The widescale importance and rich phenomenology of water continue to motivate the development of computational models. ReaxFF force fields incorporate many characteristics desirable for modeling aqueous systems: molecular flexibility, polarization, and chemical reactivity (bond formation and breaking). However, their ability to model the general properties of water has not been evaluated in detail. We present comprehensive benchmarks of the thermophysical properties of water for two ReaxFF models, the water-2017 and CHON-2017_weak force fields. These include structural, electrostatic, vibrational, thermodynamic, coexistence, and transport properties at ambient conditions (300 K and 0.997 g cm^-3) and along the standard pressure (1 bar) isobar. Overall, CHON-2017_weak predicts more accurate thermophysical properties than the water-2017 force field. Based on our results, we recommend potential avenues for improvement: the dipole moment to quadrupole moment ratio, the self-diffusion coefficient, especially for water-2017, and the gas phase vibrational frequencies with the aim to improve the vibrational properties of liquid water.

Recent Advances for Improving the Accuracy, Transferability, and Efficiency of Reactive Force Fields

Reactive force fields provide an affordable model for simulating chemical reactions at a fraction of the cost of quantum mechanical approaches. However, classically accounting for chemical reactivity often comes at the expense of accuracy and transferability, while computational cost is still large relative to nonreactive force fields. In this Perspective, we summarize recent efforts for improving the performance of reactive force fields in these three areas with a focus on the ReaxFF theoretical model. To improve accuracy, we describe recent reformulations of charge equilibration schemes to overcome unphysical long-range charge transfer, new ReaxFF models that account for explicit electrons, and corrections for energy conservation issues of the ReaxFF model. To enhance transferability we also highlight new advances to include explicit treatment of electrons in the ReaxFF and hybrid nonreactive/reactive simulations that make it possible to model charge transfer, redox chemistry, and large systems such as reverse micelles within the framework of a reactive force field. To address the computational cost, we review recent work in extended Lagrangian schemes and matrix preconditioners for accelerating the charge equilibration method component of ReaxFF and improvements in its software performance in LAMMPS.

Embedding Quantum Statistical Excitations in a Classical Force Field

Quantum-mechanically driven charge polarization and charge transfer are ubiquitous in biomolecular systems, controlling reaction rates, allosteric interactions, ligand-protein binding, membrane transport, and dynamically driven structural transformations. Molecular dynamics (MD) simulations of these processes require quantum mechanical (QM) information in order to accurately describe their reactive dynamics. However, current techniques-empirical force fields, subsystem approaches, ab initio MD, and machine learning-vary in their ability to achieve a consistent chemical description across multiple atom types, and at scale. Here we present a physics-based, atomistic force field, the ensemble DFT charge-transfer embedded-atom method, in which QM forces are described at a uniform level of theory across all atoms, avoiding the need for explicit solution of the Schrödinger equation or large, precomputed training data sets. Coupling between the electronic and atomistic length scales is effected through an ensemble density functional theory formulation of the embedded-atom method originally developed for elemental materials. Charge transfer is expressed in terms of ensembles of ionic state basis densities of individual atoms, and charge polarization, in terms of atomic excited-state basis densities. This provides a highly compact yet general representation of the force field, encompassing both local and system-wide effects. Charge rearrangement is realized through the evolution of ensemble weights, adjusted at each dynamical time step via chemical potential equalization.

Atomistic Insights into H2O2 Direct Synthesis of Ni-Pt Nanoparticle Catalysts under Water Solvents by Reactive Molecular Dynamics Simulations

In computational catalysis, density-functional theory (DFT) calculations are usually utilized, although they suffer from high computational costs. Thus, it would be challenging to explicitly predict the catalytic properties of nanoparticles (NPs) at the nanoscale under solvents. Using molecular dynamics (MD) simulations with a reactive force field (ReaxFF), we investigated the catalytic performance of Ni-Pt NPs for the direct synthesis of hydrogen peroxide (H₂O₂), in which water solvents were explicitly considered along with the effects of the sizes (1.5, 2.0, 3.0, and 3.5 nm) and compositions (Ni₉₀Pt₁₀, Ni₈₀Pt₂₀, and Ni₅₀Pt₅₀) of the NPs. Among the Ni-Pt NPs, 3.0 nm NPs show the highest activity and selectivity for the direct synthesis of H₂O₂, revealing that the catalytic performance is not well correlated with the surface areas of NPs. The superior catalytic performance results from the high H₂ dissociation and low O₂ dissociation properties, which are correlated with the numbers of NiNiPt-fcc and NiNi-bridge sites on the surface of Ni-Pt NPs, respectively. The ReaxFF-MD simulations propose the optimum composition (Ni₈₀Pt₂₀) of 3.0 nm Ni-Pt NPs, which is also explained by the numbers of NiNiPt-fcc and NiNi-bridge sites. Furthermore, from the ReaxFF-MD simulations, the direct synthesis of H₂O₂ for the Ni-Pt NPs can be achieved not only with the Langmuir-Hinshelwood mechanism, which has been conventionally considered, but also with the water-induced mechanism, which is unlikely to occur on pure Pd and Pd-based alloy catalysts; these results are supported by DFT calculations. These results reveal that the ReaxFF-MD method provides significant information for predicting the catalytic properties of NPs, which could be difficult to provide with DFT calculations; thus, it can be a useful framework for the design of nanocatalysts through complementation with a DFT method.

Development of ReaxFF Reactive Force Field for Aqueous Iron-Sulfur Clusters with Applications to Stability and Reactivity in Water

Iron-sulfur clusters serve unique roles in biochemistry, geochemistry, and renewable energy technologies. However, a full theoretical understanding of their structures and properties is still lacking. To facilitate large-scale reactive molecular dynamics simulations of iron-sulfur clusters in aqueous environments, a ReaxFF reactive force field is developed, based on an extensive set of quantum chemical calculations. This force field compares favorably with the reference calculations on gas-phase species and significantly improves on a previous ReaxFF parametrization. We employ the new potential to study the stability and reactivity of iron-sulfur clusters in explicit water with constant-temperature reactive molecular dynamics. The aqueous species exhibit a dynamic, temperature-dependent behavior, in good agreement with previous much more costly ab initio simulations.

Computational Assessment of the Three-Dimensional Configuration of Dissolved Organic Matter Chromophores and Influence on Absorption Spectra

The three-dimensional configuration of dissolved organic matter (DOM) is an important factor in determining the role of DOM in natural and engineered systems, yet there is still considerable uncertainty regarding the formation and potential stability of molecular aggregates within DOM. In this paper, we describe a computational assessment of the three-dimensional configuration of DOM. Specifically, we were interested in evaluating the hypothesis that DOM forms thermodynamically stable molecular aggregates that as a result were potentially shielded from water solvent molecules. Molecular dynamics simulations of DOM model compounds carefully selected based on ultrahigh-resolution mass spectrometry data revealed that, while DOM does indeed form molecular aggregates, the large majority of molecules (especially, O-atom bearing molecules) are solvent accessible. Additionally, these computations revealed that molecular aggregates are weak and dissociate when placed in organic solvents (tetrahydrofuran, methyl tert-butyl ether). Time-dependent density functional theory calculations demonstrated long-wavelength absorbance for both model DOM chromophores and their molecular aggregates. This study has important implications for determining the origin of DOM optical properties and for enhancing our collective understanding of DOM three-dimensional structures.

Reactive molecular dynamics simulation for isotope-exchange reactions in H/D systems: ReaxFFHD development

To investigate the chemical isotope-exchange reactions within a system composed of a mixture of hydrogen and deuterium (H/D) in the plasma media, the ReaxFF_HD potential was parameterized against an appropriate quantum mechanics (QM)-based training set. These QM data involve structures and energies related to bond dissociation, angle distortion, and an exchange reaction of the tri-atomic molecular ions, H₃ ⁺, D₃ ⁺, H₂D⁺, and D₂H⁺, produced in the hydrogen plasma. Using the ReaxFF_HD potential, a range of reactive molecular dynamics simulations were performed on different mixtures of H/D systems. Analysis of the reactions involved in the production of these tri-atomic molecular ions was carried out over 1 ns simulations. The results show that the ReaxFF_HD potential can properly model isotope-exchange reactions of tri-atomic molecular ions and that it also has a perfect transferability to reactions taking place in these systems. In our simulations, we observed some intermediate molecules (H₂, D₂, and HD) that undergo secondary reactions to form the tri-atomic molecular ions as the most likely products in the hydrogen plasma. Moreover, there remains a preference for D in the produced molecular ions, which is related to the lower zero-point energy of the D-enriched species, showing the isotope effects at the heart of the ReaxFF_HD potential.

A Multiscale Model to Predict Neuronal Cell Deformation with Varying Extracellular Matrix Stiffness and Topography

INTRODUCTION

Neuronal cells are sensitive to mechanical properties of extracellular matrix (ECM) such as stiffness and topography. Cells contract and exert a force on ECM to detect the microenvironment, which activates the signaling pathway to influence the cell functions such as differentiation, migration, and proliferation. There are numerous transmembrane proteins that transmit signals; however, integrin and neural cellular adhesion molecules (NCAM) play an important role in sensing the ECM mechanical properties. Mechanotransduction of cell-ECM is the key to understand the influence of ECM stiffness and topography; therefore, in this study, we develop a multiscale computational model to investigate these properties.

METHODS

This model couples the molecular behavior of integrin and NCAM to microscale interactions of neuronal cell and the ECM. We analyze the atomistic/molecular behavior of integrin and NCAM due to mechanical stimuli using steered molecular dynamics. The microscale properties of the neuronal cell and the ECM are simulated using non-linear finite element analysis by applying cell contractility.

RESULTS

We predict that by increasing the ECM stiffness, a neuronal cell exerts greater stress on the ECM. However, this stress reaches a saturation value for a threshold stiffness of ECM, and the saturation value is affected by the ECM thickness, topography, and clustering of integrin and NCAMs. Further, the ECM topography leads to asymmetric stress and deformation in the neuronal cell. Predicted stress distribution in neuronal cell and ECM are consistent with experimental results from the literature.

CONCLUSION

The multiscale computational model will guide in selecting the optimal ECM stiffness and topography range for in vitro studies.

Transforming the Accuracy and Numerical Stability of ReaxFF Reactive Force Fields

Molecular dynamics (MD) simulations provide an important link between theories and experiments. While ab initio methods can be prohibitively costly, the ReaxFF force field has facilitated in silico studies of chemical reactivity in complex, condensed-phase systems. However, the relatively poor energy conservation in ReaxFF MD has either limited the applicability to short time scales, in cases where energy propagation is important, or has required a continuous coupling of the system to a heat bath. In this study, we reveal the root cause of the unsatisfactory energy conservation, and offer a straightforward solution. The new scheme results in orders of magnitude improvement in energy conservation, numerical stability, and accuracy of ReaxFF force fields, compared to the previous state-of-the-art, at no additional cost. We anticipate that these improvements will open new avenues of research for more accurate reactive simulations in complex systems on long time scales.

Enhancing Thermal Boundary Conductance of Graphite-Metal Interface by Triazine-Based Molecular Bonding

Thermal boundary conductance between graphite and metal plays an important role in developing thermally conductive composites and contacts for thermal management. On the basis of the premise that the thermal boundary conductance (TBC) correlates with interfacial bonding strength, we conducted triazine-based molecular-bonding process to improve interfacial adhesion forces between a-axis of highly oriented pyrolytic graphite and aluminum. The surface coverage of molecular bonding at the interface is estimated by the X-ray photoelectron spectroscopy and thermal boundary conductance is measured by the time-domain thermoreflectance method. It is found that the TBC is directly proportional to the surface coverage of covalently bonded triazine linkers, with the proportionality constant for their increment rates being about unity. The experimental finding is supported by the corresponding simulation using the atomic Green's function method, which exhibits the same linear dependence on the surface coverage.

Experimental and theoretical elucidation of catalytic pathways in TiO2-initiated prebiotic polymerization

The tendency of glycine to form polymer chains on a rutile(110) surface under wet/dry conditions (dry-wet cycles at high temperature) is studied through a conjunction of surface sensitive experimental techniques and sequential periodic multilevel calculations that mimics the experimental procedures with models of decreasing complexity and increasing accuracy. X-ray photoemission spectroscopy (XPS) and thermal desorption spectroscopy (TDS) experimentally confirmed that the dry-wet cycles lead to Gly polymerization on the oxide support. This was supported by all the theoretical characterizations. First, classical reactive molecular dynamics (MD) simulations based on the ReaxFF approach were used to reproduce the adsorption of the experimental glycine solution droplets sprayed onto an oxide support and to identify the most probable arrangement of the molecules that triggered the polymerization mechanisms. Then, quantum chemistry density functional tight binding (DF-TB) MDs and static density functional theory (DFT) calculations were carried out to further explore favorable configurations and to evaluate the energy barriers of the most promising reaction pathways for the peptide bond-formation reactions. The results confirmed the fundamental role played by the substrate to thermodynamically and kinetically favor the process and disclosed its main function as an immobilizing agent: the molecules accommodated in the surface channels close to each other were the ones starting the key events of the dimerization process and the most favorable mechanism was the one where a water molecule acted as a proton exchange mediator in the condensation process.

A complete depolymerization of scrap tire with supercritical water participation: A molecular dynamic simulation study

The growth of scrap tire (ST) has become an urgent environmental problem. In this work, the depolymerization process of ST in supercritical water (SCW) was studied with the ReaxFF molecular dynamic simulation. The depolymerization process and reaction pathway of ST in SCW were revealed. The simulation results indicated that the SCW molecules could promote the depolymerization of rubber into smaller molecules by releasing the OH radicals. After providing the OH radicals, the SCW molecules banded with the free H and turned into H₃O radicals which were the main resources to produce H₂. In the ST-SCW reaction system, more than 95% organic components in ST depolymerized into the valuable fuel (oil and fuel gas). The main compound in oil product was light oil with low viscosity. The gas products included the H₂, CO and C1-C4 gas. It was found that reaction temperature could dominate the component of final products from ST. In order to produce more oil, the optimal temperature to recycle ST with SCW participation was 647-659 K. This study demonstrates the feasibility of SCW in recovering the chemical products from ST, and provides a theoretical support for its further development.

Development of the ReaxFF Methodology for Electrolyte-Water Systems

A new ReaxFF reactive force field has been developed for water-electrolyte systems including cations Li⁺, Na⁺, K⁺, and Cs⁺ and anions F^-, Cl^-, and I^-. The reactive force field parameters have been trained against quantum mechanical (QM) calculations related to water binding energies, hydration energies and energies of proton transfer. The new force field has been validated by applying it to molecular dynamics (MD) simulations of the ionization of different electrolytes in water and comparison of the results with experimental observations and thermodynamics. Radial distribution functions (RDF) determined for most of the atom pairs (cation or anion with oxygen and hydrogen of water) show a good agreement with the RDF values obtained from DFT calculations. On the basis of the applied force field, the ReaxFF simulations have described the diffusion constants for water and electrolyte ions in alkali metal hydroxide and chloride salt solutions as a function of composition and electrolyte concentration. The obtained results open opportunities to advance ReaxFF methodology to a wide range of applications involving electrolyte ions and solutions.

ReaxFF Molecular Dynamics Study on the Influence of Temperature on Adsorption, Desorption, and Decomposition at the Acetic Acid/Water/ZnO(101̅0) Interface Enabling Cold Sintering

The reaction dynamics of a liquid-solid interface with the example of an acetic acid/water solution interacting with a ZnO(101̅0) surface was investigated using ReaxFF reactive force field-based molecular dynamics. The interactions were studied over a broad temperature range to assess the kinetics and reaction pathways. Two different acetic acid dissociation mechanisms are observed in the simulations: (1) deprotonation to surface cation, which produces a terminal hydroxyl and (2) deprotonation to a bridging hydroxyl, which results in water production. An increase in temperature promotes the dissociation of acetic acids and its adsorption to surface at first, but as the temperature increase continues, the surface coverage by acetates decreases due to evaporation from the surface or decomposition. The acetate decomposition starts with a nucleophilic attack of oxygen to methyl carbon and results in the production of carbon dioxide, which is consistent with experimental findings in the literature. The coverage of the surface by water molecules decreases as the system is heated up, which is also observed in other molecular dynamics studies. At elevated temperatures, acetate molecules are more stable than water molecules or bridging hydroxyls on the surface. These simulations validate the ReaxFF method for the water/organic mixture and metal oxide surface interactions and provide insights into structure and reactivity of aqueous solvents on metal oxide surfaces at elevated temperatures. Adsorption trends that are observed in this study are consistent with phenomenological Langmuir models. The reaction of acetic acid decomposition to smaller molecules such as CO₂ and CH₂O agrees with experimental observations. Understanding the details of these dynamic surface reactions are critical to understand important new cold sintering processes that utilize transient liquid and solid reactions, and the latter could be used to predict solvent selection for cold sintering.

Docking of Covalent Ligands: Challenges and Approaches

Covalent ligands have recently regained considerable attention in drug discovery. The rational design of such ligands, however, is still faced with particular challenges, mostly related to the fact that covalent bond formation is a quantum mechanical phenomenon which cannot adequately be handled by the force fields or empirical approaches typically used for noncovalent protein-ligand interactions. Although the necessity for quantum chemical approaches is clear, they cannot yet routinely be applied on large data sets of ligands or for a broader exploration of binding modes in docking calculations. On the other hand, technical solutions for performing docking calculations with covalent ligands are available, but their scope is normally quite limited. Scoring functions typically neglect the contribution from covalent bond formation completely. In this situation, the question arises how to approach covalent ligands and which methods to choose for their docking and design.

ReaxFF molecular dynamics simulation of intermolecular structure formation in acetic acid-water mixtures at elevated temperatures and pressures

The intermolecular structure formation in liquid and supercritical acetic acid-water mixtures was investigated using ReaxFF-based molecular dynamics simulations. The microscopic structures of acetic acid-water mixtures with different acetic acid mole fractions (1.0 ≥ x_HAc ≥ 0.2) at ambient and critical conditions were examined. The potential energy surface associated with the dissociation of acetic acid molecules was calculated using a metadynamics procedure to optimize the dissociation energy of ReaxFF potential. At ambient conditions, depending on the acetic acid concentration, either acetic acid clusters or water clusters are dominant in the liquid mixture. When acetic acid is dominant (0.4 ≤ x_HAc), cyclic dimers and chain structures between acetic acid molecules are present in the mixture. Both structures disappear at increased water content of the mixture. It was found by simulations that the acetic acid molecules released from these dimer and chain structures tend to stay in a dipole-dipole interaction. These structural changes are in agreement with the experimental results. When switched to critical conditions, the long-range interactions (e.g., second or fourth neighbor) disappear and the water-water and acetic acid-acetic acid structural formations become disordered. The simulated radial distribution function for water-water interactions is in agreement with experimental and computational studies. The first neighbor interactions between acetic acid and water molecules are preserved at relatively lower temperatures of the critical region. As higher temperatures are reached in the critical region, these interactions were observed to weaken. These simulations indicate that ReaxFF molecular dynamics simulations are an appropriate tool for studying supercritical water/organic acid mixtures.

Aqueous ionic liquids influence the disulfide bond isoform equilibrium in conotoxin AuIB: a consequence of the Hofmeister effect?

The appearance of several disulfide bond isoforms in multiple cysteine containing venom peptides poses a significant challenge in their synthesis and purification under laboratory conditions. Recent experiments suggest that careful tuning of solvent and temperature conditions can propel the disulfide bond isoform equilibrium in favor of the most potent, native form. Certain aqueous ionic liquids (ILs) have proven significantly useful as solvents for this purpose, while exceptions have also been noted. To elucidate the molecular level origin behind such a preference, we report a detailed explicit solvent replica exchange molecular dynamics study of a conotoxin, AuIB, in pure water and four different aqueous IL solutions (~45-60% v/v). The ILs studied here are comprised of cations like 1-ethyl-3-methyl-imidazolium (Im₂₁⁺) or 1-butyl-3-methyl-imidazolium (Im₄₁⁺) coupled with either acetate (OAc^-) or chloride (Cl^-) as the counter anion. Our simulations unfold interesting features of the conformational spaces sampled by the peptide and its solvation in pure water and aqueous IL solutions. Detailed investigation into populations of the globular disulfide bond isoform of AuIB in aqueous IL solutions reveal distinct trends which might be related to the Hofmeister effect of the cation and anion of the IL and of specific interactions of the aqueous IL solutions with the peptide. In accordance with experimental observations, the aqueous [Im₂₁][OAc] solution is found to promote the highest globular isoform population in AuIB.

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth

Despite decades of research, how life began on Earth remains one of the most challenging scientific conundrums facing modern science. It is agreed that the first step was synthesis of organic compounds essential to obtain amino acids and their polymers. Several possible scenarios that could accomplish this step, using simple inorganic molecules, have been suggested and studied over the years. The present study examines, using atomistic reactive molecular dynamics simulations, the long-standing suggestion that natural cavitation in primordial oceans was a dominant mechanism of organic molecule synthesis. The simulations allow, for the first time, direct observation of the rich and complex sonochemistry occurring inside a collapsing bubble filled with water and dissolved gases of the early atmosphere. The simulation results suggest that dissolved CH₄ is the most efficient carbon source to produce amino acids, while CO and CO₂ lead to amino acid synthesis with lower yields. The efficiency of amino acid synthesis also depends on the nitrogen source used (i.e., N₂, NH₃) and on the presence of HCN. Moreover, cavitation may have contributed to the increase in concentration of NH₃ in primordial oceans and to the production and liberation of molecular O₂ into the early atmosphere. Overall, the picture that emerges from the simulations indicates that collapsing bubbles may have served as natural bioreactors in primordial oceans, producing the basic chemical ingredients required for the beginning of life.

Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters

Computational prediction of noncovalent binding free energies with methods based on molecular mechanical force fields has become increasingly routine in drug discovery projects, where they promise to speed the discovery of small molecule ligands to bind targeted proteins with high affinity. Because the reliability of free energy methods still has significant room for improvement, new force fields, or modifications of existing ones, are regularly introduced with the aim of improving the accuracy of molecular simulations. However, comparatively little work has been done to systematically assess how well force fields perform, particularly in relation to the calculation of binding affinities. Hardware advances have made these calculations feasible, but comprehensive force field assessments for protein–ligand sized systems still remain costly. Here, we turn to cyclodextrin host–guest systems, which feature many hallmarks of protein–ligand binding interactions but are generally much more tractable due to their small size. We present absolute binding free energy and enthalpy calculations, using the attach-pull-release (APR) approach, on a set of 43 cyclodextrin-guest pairs for which experimental ITC data are available. The test set comprises both α- and β-cyclodextrin hosts binding a series of small organic guests, each with one of three functional groups: ammonium, alcohol, or carboxylate. Four water models are considered (TIP3P, TIP4Pew, SPC/E, and OPC), along with two partial charge assignment procedures (RESP and AM1-BCC) and two cyclodextrin host force fields. The results suggest a complex set of considerations when choosing a force field for biomolecular simulations. For example, some force field combinations clearly outperform others at the binding enthalpy calculations but not for the binding free energy. Additionally, a force field combination which we expected to be the worst performer gave the most accurate binding free energies – but the least accurate binding enthalpies. The results have implications for the development of improved force fields, and we propose this test set, and potential future elaborations of it, as a powerful validation suite to evaluate new force fields and help guide future force field development.

Modified Random Sequential Adsorption Model for Understanding Kinetics of Proteins Adsorption at a Liquid-Solid Interface

In this Article, we experimentally measure the adsorption kinetics of human serum albumin (HSA) on a hydrophobic hexadecanethiolated gold surface. We use micromachined quartz crystal resonators with fundamental frequency of 83 MHz to accomplish these measurements in real time. In this work, we focus on two key results: (i) asymptotic behavior of the sensor responses upon HSA adsorption and (ii) the jamming limit of adsorbed layer formed by both single-injection and multi-injection experiments with the same value of final concentration. We develop a new interface-depletion modified random sequential adsorption (RSA) model to elucidate the adsorption kinetics and the transport properties of the protein molecules. Analysis of the experimentally measured data shows that the results can be explained on the basis of the exponentially depleting interfacial layer RSA model. To better understand the origin of the formation of the interfacial depletion region where the supply of protein molecules is dramatically reduced, we performed a series of molecular dynamics (MD) simulations using the ReaxFF method. These simulations predict that the resulting adsorption of the protein molecules on the thiolated surface results in a specific orientation at the interface and the diffusion constant of the protein molecules in this layer is significantly reduced. This interplay between the surface adsorption rate and the reduced diffusion coefficient leads to the depletion of the protein molecules in the interfacial layer where the concentration of the protein molecules is much less than the bulk concentration and explains the observed slowdown of the HSA adsorption characteristics on a hydrophobic surface.