Interactive molecular dynamics in virtual reality for modelling materials and catalysts.

Interactive molecular dynamics simulation in virtual reality (iMD-VR) is emerging as a promising technique in molecular science. Here, we demonstrate its use in a range of fifteen applications in materials science and heterogeneous catalysis. In this work, the iMD-VR package Narupa is used with the MD package, DL_POLY [1]. We show how iMD-VR can be used to: (i) investigate the mechanism of lithium fast ion conduction by directing the formation of defects showing that vacancy transport is favoured over interstitialcy mechanisms, and (ii) guide a molecule through a zeolite pore to explore diffusion within zeolites, examining in detail the motion of methyl n-hexanoate in H-ZSM-5 zeolite and identifying bottlenecks restricting diffusion. iMD-VR allows users to manipulate these systems intuitively, to drive changes in them and observe the resulting changes in structure and dynamics. We make these simulations available, as a resource for both teaching and research. All simulation files, with videos, can be found online (https://doi.org/10.5281/zenodo.8252314) and are provided as open-source material.

Data on the intermolecular interactions of 1,1,1,2-tetrafluoroethane liquids from molecular dynamics simulations.

Detailed atomistic interactions of 1,1,1,2-tetrafluoroethane (HFA-134a) liquid were presented in a data format, namely, DL_ANALYSER Notation for Atomic Interactions (DANAI), that annotates precisely the nature of interactions that is discoverable and searchable without having to resolve to diagrammatic illustrations. The datasets were obtained from raw atomic trajectory files of HFA-134a pure liquid models produced by using DL_POLY molecular dynamics software package. The trajectory datafiles contain expressions of atomic species in a natural chemical sense, and hence, provide localized key interactions, 'at a glance', of the liquid model on otherwise a typically disordered system consists of complex network of intermolecular interactions. The data provide insights to detailed structural behavior of molecules in liquid phase, and can be used as cheminformatics comparative investigations, linking to other molecular system models that contain similar interaction types and chemical species. This can form the foundation of investigations into the role of HFA-134a plays within different applications. For example, it can be used to compare structural and atomic interaction differences with alternative refrigerants, or as liquid propellants in pharmaceutical devices when solvating formulation ingredients.

Cellulose Iß microfibril interaction with pristine graphene in water: Effects of amphiphilicity by molecular simulation.

Graphene-cellulose interactions have considerable potential in the development of new materials. In previous computational work (Biomacromolecules2016, 16, 1771), we predicted that the model 100 hydrophobic surface of cellulose interacted favourably with pristine graphene in aqueous solution molecular dynamics simulations; conversely, a model of the hydrophilic 010 surface of cellulose exhibited progressive rearrangement to present a more hydrophobic face with the graphene, with weakened hydrogen bonds between cellulose chains and partial permeation of water. Here, we extend this work by simulating the interaction in aqueous solution of the amphiphilic 110 surface of a cellulose Iß microfibril model, comprising 36 chains of 40 glucosyl residues, with an infinite sheet of pristine graphene. This face of the microfibril is of intermediate hydrophilicity and progressively associates with graphene over replicate simulations. As cellulose chains adhere to the graphene surface, forming interactions via its CH and OH groups, we observe a degree of local and global untwisting of the microfibril. Complementary rippling of the graphene surface is also observed, as it adapts to interaction with the microfibril. This adsorption process is accompanied by increased exclusion of water between cellulose and graphene although some water localises between chains at the immediate interface. The predicted propensity of a cellulose microfibril to adsorb spontaneously on the graphene surface, with mutual structural accommodation, highlights the amphiphilic nature of cellulose and the types of interactions that can be harnessed to design new graphene-carbohydrate biopolymer materials.

Combining quasielastic neutron scattering and molecular dynamics to study methane motions in ZSM-5.

Quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulations are applied in combination to investigate the dynamics of methane in H-ZSM-5 zeolite catalysts used for methanol-to-hydrocarbons reactions. Methane is employed as an inert model for the methanol reaction feedstock, and studies are made of the fresh catalyst and used catalysts with varying levels of coke buildup to investigate the effect of coking on reactant mobility. Measurements are made in the temperature range from 5 to 373 K. Methane mobility under these conditions is found to be extremely high in fresh ZSM-5, with the majority of movements occurring too fast to be resolved by the QENS instrument used. A small fraction of molecules undergoing jump diffusion on QENS time scales is identified and found to correspond with short-range jump diffusion within single zeolite pores as identified in MD simulations. Agreement between QENS and MD mobility measurements is found to be within 50%, validating the simulation approach employed. Methane diffusion is found to be minimally affected by moderate levels of coke buildup, while highly coked samples result in the confinement of methane to single pores within the zeolite with minimal long-range diffusion.

The structural pathway from its solvated molecular state to the solution crystallisation of the α- and ß-polymorphic forms of para amino benzoic acid.

Para amino benzoic acid (PABA) has two well-characterised α- and ß-polymorphic forms and, whilst both crystallise in the monoclinic space group P21/n, they have quite different crystal chemistry and crystallisability behaviour. Previous work has shown that the molecular conformation deformation energy in the crystalline state is higher for the ß-form than for the α-form and that the lattice energy for the former converges more slowly than for the latter overall. This suggests that not only is there a higher barrier to crystallisation for the ß-form but also that low solution supersaturations might be needed for it to preferentially nucleate. Additionally, solute cluster propensity and solute solvation energetic analysis highlight the importance of an aqueous solvation environment in inhibiting the α-form's strong OH⋯O carboxylic acid hydrogen bond (H-bond) dimer. Despite this, the detailed molecular-scale pathway from solvated molecules to 3D crystallographic structure still remains unclear, most notably regarding how the nucleation process is activated and how, as a result, this mediates the preferential formation of either of the two polymorphic forms. Molecular dynamics (MD) simulations coupled with FTIR studies and intermolecular synthon analysis address this issue through characterisation of the propensity of the incipient bulk synthons that are important in the crystallisation of the two polymorphic forms within the solution state. MD molecular trajectory analysis within crystallisation solutions reveals a greater propensity for OH⋯O synthons (both single H-bonds and homodimers) typical of the α-form and NH⋯O synthons found in both the α- and ß-forms when compared to aqueous solution but much lower propensities for the ß-form's "fingerprinting" OH⋯N and π-π stacking synthons. In contrast, data from the aqueous solution environment reveals a much greater propensity for the ß-form's π-π interaction synthons. IR dilution studies in acetonitrile in the carbonyl region reveal the presence of two CO vibrational stretching bands, whose relative intensities vary as a function of solution dilution. These were assigned to the solvated PABA monomer and a COOH dimer of PABA. Similar data in ethanol shows a main CO stretching band with a shoulder peak suggesting a similar monomer vs. dimer speciation may exist in this solvent. The IR data is consistent with the organic solvent MD data, albeit the corresponding analysis for the aqueous solution was precluded due to the latter's strong OH vibrational mode which restricted validation in aqueous solutions.

Evolving requirements for materials modelling software and underlying method developments: an inventory and future outlook.

This European Materials Modelling Council (EMMC) study provides an outline of the survey intent and ambitions, followed by an analysis of the results and a follow up discussion, focused on the future perspectives of the EMMC. The survey covers materials modelling and characterisation communities in both academia and industry. It provides a profile of the surveyed players in these communities and a scaled measure on their usage of computational methodologies. The survey outcomes include: (i) summary views of the recent as well as perceived future trends of materials modelling and its associated fields, with respect to two focus areas surveyed, Model Development and Software, (ii) the main adoption factors and associated bottlenecks for computational methods and software, (iii) the most targeted materials properties and digital twins approaches, and (iv) the wider communities expectations of how EMMC can help facilitate, fulfil and drive further the European Materials Modelling Roadmap to the benefit of the European Commission's (ECs') research and innovation.

Triglycine (GGG) Adopts a Polyproline II (pPII) Conformation in Its Hydrated Crystal Form: Revealing the Role of Water in Peptide Crystallization.

Polyproline II (pPII) is a left-handed 31-helix conformation, which has been observed to be the most abundant secondary structure in unfolded peptides and proteins compared to α-helix and ß-sheet. Although pPII has been reported as the most stable conformation for several unfolded short chain peptides in aqueous solution, it is rarely observed in their solid state. Here, we show for the first time a glycine homopeptide (gly-gly-gly) adopting the pPII conformation in its crystalline dihydrate structure. The single crystal X-ray structure with molecular dynamic simulation suggests that a network of water and the charged carboxylate group is critical in stabilizing the pPII conformation in solid state, offering an insight into the structures of unfolded regions of proteins and the role of water in peptide crystallization.

Reactive Molecular Dynamics at Constant Pressure via Nonreactive Force Fields: Extending the Empirical Valence Bond Method to the Isothermal-Isobaric Ensemble.

The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of nonreactive force fields. In this formalism, most of the implemented coupling terms are built using functional forms that depend on spatial coordinates, while parameters are fitted against reference data to model the change of chemistry between the participating nonreactive states. In this work, we demonstrate that the use of such coupling terms precludes the computation of the stress tensor for condensed phase systems and prevents the possibility to carry out EVB molecular dynamics in the isothermal-isobaric (NPT) ensemble. Alternatively, we make use of coupling terms that depend on the energy gaps, defined as the energy differences between the participating nonreactive force fields, and derive a general expression for the EVB stress tensor suitable for computation. Implementation of this new methodology is tested for a model of a single reactive malonaldehyde solvated in nonreactive water. Mass densities and probability distributions for the values of the energy gaps computed in the NPT ensemble reveal a negligible role of the reactive potential in the limit of low concentrated solutions, thus corroborating for the first time the validity of approximations based on the canonical NVT ensemble, customarily adopted for EVB simulations. The presented formalism also aims to contribute to future implementations and extensions of the EVB method to research the limit of highly concentrated solutions.

Four simple recommendations to encourage best practices in research software.

Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.

DL_ANALYSER Notation for Atomic Interactions (DANAI): A Natural Annotation System for Molecular Interactions, Using Ethanoic Acid Liquid as a Test Case.

The DL_ANALYSER Notation for Atomic Interactions, DANAI, is the notation syntax to describe interactions between molecules. This notation can annotate precisely the detailed atomistic interactions without having to resolve to diagrammatic illustrations, and yet can be interpreted easily by both human users and computational means. By making use of the DL_F Notation, a universal atom typing scheme for molecular simulations, DANAI contains the expression of atomic species in a natural chemical sense. It is implemented within DL_ANALYSER, a general analysis software program for DL_POLY molecular dynamics simulation software. By making references to the molecular dynamics simulations of pure ethanoic acid liquid, it is shown that DL_ANALYSER can identify and distinguish a variety of hydrogen bond and hydrophobic contact networks through the use of the DANAI expression. It was found that the carboxylic groups preferentially orientated in a "head-to-tail" conformation to form hydrogen bonds between the carbonyl oxygen and hydroxyl hydrogen, resulting in a series of linear structures that intertwined with pockets of methyl clusters.

Advanced Potential Energy Surfaces for Molecular Simulation.

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

Salmonella enteritidis primary bacteremia in previously healthy patient from Taiwan: case report.

BACKGROUND: Diseases caused by invasive nontyphoidal Salmonella strains present with various extraintestinal manifestations, including bacteremia. Factors affecting the incidence include Salmonella serotype, geographic location, and host factors. CASE: We present an unusual case of Salmonella enteritidis primary bacteremia in a patient without any risk factors and originating from a region with the lowest burden of invasive nontyphoidal Salmonella infections. We observed an incomplete clinical response to the treatment with a third-generation cephalosporin, despite the in vitro susceptibility of the strain. DISCUSSION: The diagnosis of Salmonella bacteremia was far from expected in our previously healthy patient from Taiwan, without any preceding diarrhea and the lack of marked response to therapy with ceftriaxone. Making the diagnosis was a challenge, requiring wide range of laboratory, imaging, and consultative work to rule out alternative diagnoses and complications. CONCLUSION: Invasive Salmonella infections are uncommon in our clinical practice at the present. Air transportation, intensive migration processes, and changes in climate are able to change the burden of infectious diseases dramatically in the near future. That fact along with the raising antibacterial resistance among invasive nontyphoidal Salmonella strains make imperative the profound understanding of the epidemiology and pathophysiology of those infections.

Order parameter and connectivity topology analysis of crystalline ceramics for nuclear waste immobilization.

We apply bond order and topological methods to the problem of analysing the results of radiation damage cascade simulations in ceramics. Both modified Steinhardt local order and connectivity topology analysis techniques provide results that are both translationally and rotationally invariant and which do not rely on a particular choice of a reference structure. We illustrate the methods with new analyses of molecular dynamics simulations of single cascades in the pyrochlores Gd(2)Ti(2)O(7) and Gd(2)Zr(2)O(7) similar to those reported previously (Todorov et al 2006 J. Phys.: Condens. Matter 18 2217). Results from the Steinhardt and topology analyses are consistent, while often providing complementary information, since the Steinhardt parameters are sensitive to changes in angular arrangement even when the overall topological connectivity is fixed. During the highly non-equilibrium conditions at the start of the cascade, both techniques reveal significant localized transient structural changes and variation in the cation connectivity. After a few picoseconds, the connectivity is largely fixed, while the order parameters continue to change. In the zirconate there is a shift to the anion disordered system while in the titanate there is substantial reversion and healing back to the parent pyrochlore structure.

Monte Carlo simulation of segregation in ceramic thin films.

A Monte Carlo exchange technique is used to study segregation in thin ceramic films with application to MgO/MnO. The approach is not restricted to the dilute limit. Surface concentrations as a function of temperature and film composition are determined directly from the simulations. For all compositions studied (Mn(chi)Mg(1-chi)O, 0 < or = chi < or = 1) the (001) surface is Mn(2+) rich; the occupancy of sites by Mn(2+) decreases rapidly with depth. The ratio of the number of Mn(2+) to Mg(2+) ions at the surface decreases as a function of temperature. The calculated enthalpies of segregation of Mn(2+) for the thin film are strongly dependent on the total Mn(2+) concentration at small Mn(2+) concentrations, with the enthalpy of segregation varying by a factor of two with surface coverage.