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].

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.

Cellulose Iβ 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 Iβ microfibril model, comprising 36 chains of 40 glucosyl residues, with an infinite sheet of pristine graphene.

Polyguluronate simulations shed light onto the therapeutic action of OligoG CF-5/20.

Chronic mucoid P. aeruginosa cystic fibrosis (CF) lung infections are associated with the development of a biofilm composed of anionic acetylated exopolysaccharide (EPS) alginate, electrostatically stabilised by extracellular Ca ions. OligoG CF-5/20, a low molecular weight guluronate rich oligomer, is emerging as a novel therapeutic capable of disrupting mature P.

Atomic-scale interactions between quorum sensing autoinducer molecules and the mucoid P. aeruginosa exopolysaccharide matrix.

Mucoid Pseudomonas aeruginosa is a prevalent cystic fibrosis (CF) lung coloniser whose chronicity is associated with the formation of cation cross-linked exopolysaccharide (EPS) matrices, which form a biofilm that acts as a diffusion barrier, sequestering cationic and neutral antimicrobials, and making it extremely resistant to pharmacological challenge. Biofilm chronicity and virulence of the colony is regulated by quorum sensing autoinducers (QSAIs), small signalling metabolites that pass between bacteria, through the biofilm matrix, regulating genetic responses on a population-wide scale. The nature of how these molecules interact with the EPS is poorly understood, despite the fact that they must pass through EPS matrix to reach neighbouring bacteria.

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

amino benzoic acid (PABA) has two well-characterised α- and β-polymorphic forms and, whilst both crystallise in the monoclinic space group 2/, 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 β-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 β-form but also that low solution supersaturations might be needed for it to preferentially nucleate.

Atomistic Simulation of Water Incorporation and Mobility in Silk Fibroin.

silk fibroin (SF) is a biopolymer that can be processed into materials with attractive properties (e.g., biocompatibility and degradability) for use in a multitude of technical and medical applications (including textiles, sutures, drug delivery devices, tissue scaffolds, etc.

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 3-helix conformation, which has been observed to be the most abundant secondary structure in unfolded peptides and proteins compared to α-helix and β-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.

A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase.

Copper-containing nitrite reductases (CuNiRs) play a key role in the global nitrogen cycle by reducing nitrite (NO₂) to nitric oxide, a reaction that involves one electron and two protons. In typical two-domain CuNiRs, the electron is acquired from an external electron-donating partner. The recently characterised (NiR) system is a three-domain CuNiR, where the cupredoxin domain is tethered to a heme domain that can function as the electron donor.

Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.

High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed.

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.

Active-site protein dynamics and solvent accessibility in native copper nitrite reductase.

Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (Asp and His) involved in the nitrite-reduction mechanism of this enzyme.

Understanding gas capacity, guest selectivity, and diffusion in porous liquids.

Porous liquids are a new class of material that could have applications in areas such as gas separation and homogeneous catalysis. Here we use a combination of measurement techniques, molecular simulations, and control experiments to advance the quantitative understanding of these liquids. In particular, we show that the cage cavities remain unoccupied in the absence of a suitable guest, and that the liquids can adsorb large quantities of gas, with gas occupancy in the cages as high as 72% and 74% for Xe and SF, respectively.

Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations.

DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme.

Study of interactions between polymer nanoparticles and cell membranes at atomistic levels.

Knowledge of how the structure of nanoparticles and the interactions with biological cell membranes is important not only for understanding nanotoxicological effects on human, animal health and the environment, but also for better understanding of nanoparticle fabrication for biomedical applications. In this work, we use molecular modelling techniques, namely molecular dynamics (MD) simulations, to explore how polymer nanoparticles interact with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid cell membranes. Two different polymers have been considered: 100 monomer units of polyethylene (approx.

Structural behaviour of 2-hydroxypropyl-beta-cyclodextrin in water: molecular dynamics simulation studies.

Purpose: To investigate the effect of 2-hydroxypropyl side group substitutions on the structure of beta-cyclodextrin (CD) in water.

Methods: Molecular dynamics simulations were carried out on four HPBCDs that broadly represent a range of degree of substitutions in order to investigate the effect of substitution of beta-cyclodextrin with 2-hydroxypropyl groups at various O2 and O6 positions of the glucose units.

Results: The 2-hydroxypropyl side groups located at the O2 positions widen the cavity entrance at the secondary OH position of the CD molecule.

Molecular dynamics using atomic-resolution structure reveal structural fluctuations that may lead to polymerization of human Cu-Zn superoxide dismutase.

Mutations of the gene encoding Cu-Zn superoxide dismutase (SOD1) cause 20% of the familial cases of the progressive neurodegenerative disease ALS. A growing body of evidence suggests that in familial ALS (FALS) it is the molecular behavior of the metal-depleted SOD1 dimer that leads to a gain of toxic properties by misfolding, unfolding, and aggregation. Structural studies have so far provided static snapshots on the behavior of the wild-type enzyme and some of the FALS mutants.

Atomistic studies of surface adhesions using molecular-dynamics simulations.

The existing theoretical descriptions of continuum surface adhesions, such as the JKR (Johnson-Kendall-Roberts) model, have been very useful for the interpretation of particle contacts of sizes down to micrometre length-scales. However, the continuum model is expected to fail at atomic length-scales, where discrete atomistic interactions become significant. The crossover length-scales at which the macroscopic phenomena begin to manifest themselves, and how they occur, are equally baffling and remain poorly understood.