ORCID Profile
0000-0002-0233-9484
Current Organisations
Cardiff University
,
Deakin University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Materials Engineering | Composite and Hybrid Materials | Polymers and Plastics | Theory and Design of Materials | Theoretical and Computational Chemistry not elsewhere classified | Medicinal and Biomolecular Chemistry | Macromolecular and Materials Chemistry | Membrane and Separation Technologies | Biologically Active Molecules | Reaction Kinetics and Dynamics | Bioprocessing, Bioproduction and Bioproducts | Analytical Biochemistry | Nanobiotechnology | Condensed Matter Physics not elsewhere classified
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in Engineering | Expanding Knowledge in the Chemical Sciences | Service Industries Standards and Calibrations | Expanding Knowledge in the Physical Sciences | Nutraceuticals and Functional foods |
Related Links
Publications
Predictions of Pattern Formation in Amino Acid Adlayers at the In Vacuo Graphene Interface: Influence of Termination State
Publisher: Wiley
Date: 30-10-2019
Abstract: Controlled self-assembly of biomolecules on graphene offers a pathway for realizing its full potential in biological applications. Microscopy has revealed the self-assembly of amino acid adlayers into dimer rows on nonreactive substrates. However, neither the spontaneous formation of these patterns, nor the influence of amino acid termination state on the formation of patterns has been directly resolved to date. Molecular dynamics simulations, with the ability to reveal atomic level details and exert full control over the termination state, are used here to model initially disordered adlayers of neutral, zwitterionic, and neutral-zwitterionic mixtures for two types of amino acids, tryptophan and methionine, adsorbed on graphene in vacuo. The simulations of the zwitterion-containing adlayers exhibit the spontaneous emergence of dimer row ordering, mediated by charge-driven intermolecular interactions. In contrast, adlayers containing only neutral species do not assemble into ordered patterns. It is also found that the presence of trace amounts of water reduces the interamino acid interactions in the adlayers, but does not induce or disrupt pattern formation. Overall, the findings reveal the balance between the lateral interamino acid interactions and amino acid-graphene interactions, providing foundational insights for ultimately realizing the predictable pattern formation of biomolecules adsorbed on unreactive surfaces.
A robust and reproducible procedure for cross-linking thermoset polymers using molecular simulation
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C5SM02788H
Abstract: Our reliable and reproducible cross-linking procedure ranges from careful equilibration of the liquid polymer precursor to calculating the thermo-mechanical properties of the cross-linked polymer. Our approach can be used to cure not only pure thermoset polymers, but also thermoset-based composite materials.
Investigation of the influence of surface defects on peptide adsorption onto carbon nanotubes
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C003417G
Abstract: The number of possible applications that interface carbon nanotubes with biological systems is rapidly growing, and with these advances comes a need for characterisation of such interfaces. Molecular simulation is one such approach, and many recent ex les exist where simulation has been used to investigate the atomic-scale details of the interface between biomolecules and carbon nanotubes (CNTs). However, these studies have been confined to the realm of pristine CNTs. Here, we build on our previous work and use molecular simulation to consider the adsorption on to defective CNTs of peptide sequences known to bind to the CNT surface [Wang et al., Nat. Mater., 2003, 2, 196]. Two types of idealised chemical defects are considered, along with two different distributions of these defects on the CNT surface. We find that the densely-packed defect distribution yields relatively little engagement with the peptides. Spreading the defects out along the nanotube increases the degree of contact with the peptide, without affecting the binding strength of the peptide-CNT interface in most cases. Both types of defect tend to act more as physical barriers to peptide mobility than as a source of attractive interactions. The resulting physical confinement of the peptide did not affect all sequences in the same way two of the four sequences were found to be more sensitive to the presence of defects. This study has implications for the practical usage of CNTs in a wide range of biological contexts, where well-dispersed, functionalised nanotubes are required.
Atomistic simulations of calcium aluminosilicate interfaced with liquid water
Publisher: AIP Publishing
Date: 11-09-2023
DOI: 10.1063/5.0164817
From graphene to graphene oxide: the importance of extended topological defects
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D1CP04316A
Abstract: By microscopy, spectroscopy, and modelling we show that extended topological defects are ubiquitous in oxygen functionalised graphene, whether from gas-phase or wet-chemical oxidation, and play a critical role in limiting its reduction and stiffness.
Theoretical study of the water tetramer
Publisher: AIP Publishing
Date: 05-1997
DOI: 10.1063/1.473681
Abstract: We report rearrangement mechanisms and new stationary points for the water tetramer and deduce the associated tunneling splitting patterns and nuclear spin weights when different processes are assumed to be feasible. The basis sets employed for the ab initio calculations are double-zeta plus polarization (DZP) and DZP with additional diffuse functions (DZP+diff), and results have been obtained within both the Hartree–Fock (HF) and density functional theory frameworks employing the Becke exchange and the Lee–Yang–Parr correlation functionals (BLYP). The results are compared with those found for a relatively sophisticated empirical rigid-body intermolecular potential. One direct degenerate rearrangement of the cyclic global minimum was characterized in the HF calculations, but disappears when density functional theory is applied. The latter mechanism involves a larger barrier than pathways mediated by higher index saddle points belonging to the torsional space. In principle, doublet splittings could result from tunneling via a number of possible routes, and further calculations will be needed to elucidate the dynamics for this system.
Facet-Specific Adsorption of Tripeptides at Aqueous Au Interfaces: Open Questions in Reconciling Experiment and Simulation
Publisher: American Chemical Society (ACS)
Date: 07-04-2017
DOI: 10.1021/ACS.LANGMUIR.6B04558
Abstract: The adsorption of three homo-tripeptides, HHH, YYY, and SSS, at the aqueous Au interface is investigated, using molecular dynamics simulations. We find that consideration of surface facet effects, relevant to experimental conditions, opens up new questions regarding interpretations of current experimental findings. Our well-tempered metadynamics simulations predict the rank ordering of the tripeptide binding affinities at aqueous Au(111) to be YYY > HHH > SSS. This ranking differs with that obtained from existing experimental data which used surface-immobilized Au nanoparticles as the target substrate. The influence of Au facet on these experimental findings is then considered, via our binding strength predictions of the relevant amino acids at aqueous Au(111) and Au(100)(1 × 1). The Au(111) interface supports an amino acid ranking of Tyr > HisA ≃ HisH > Ser, matching that of the tripeptides on Au(111), while the ranking on Au(100) is HisA > Ser ≃ Tyr ≃ HisH, with only HisA showing non-negligible binding. The substantial reduction in Tyr amino acid affinity for Au(100) vs Au(111) offers one possible explanation for the experimentally observed weaker adsorption of YYY on the nanoparticle-immobilized substrate compared with HHH. In a separate set of simulations, we predict the structures of the adsorbed tripeptides at the two aqueous Au facets, revealing facet-dependent differences in the adsorbed conformations. Our findings suggest that Au facet effects, where relevant, may influence the adsorption structures and energetics of biomolecules, highlighting the possible influence of the structural model used to interpret experimental binding data.
Simulation of the hydration structure of glycyl-alanine
Publisher: Informa UK Limited
Date: 04-2007
Peptide Sequence Effects Control the Single Pot Reduction, Nucleation, and Growth of Au Nanoparticles
Publisher: American Chemical Society (ACS)
Date: 15-08-2016
Archetypal energy landscapes
Publisher: Springer Science and Business Media LLC
Date: 08-1998
DOI: 10.1038/29487
Synergistic interfacial effects of ionic liquids as sizing agents and surface modified carbon fibers
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C7TA10516A
Abstract: This paper presents investigations into the use of ionic liquids as sizing agents for carbon fibers in epoxy matrices.
ContactAngleCalculator: An Automated, Parametrized, and Flexible Code for Contact Angle Estimation in Visual Molecular Dynamics
Publisher: American Chemical Society (ACS)
Date: 16-05-2022
Abstract: Accurate, fast, and flexible approaches for contact angle estimation in molecular dynamics simulations are of great importance for characterization of surface wettability, especially for machine learning approaches which would usually require thousands of computational contact angle evaluations for training and prediction purposes. However, evaluation of the contact angle from molecular simulations is typically a human-intensive process, which hinders the required fast throughput. To address this challenge, here a flexible and automated contact angle estimation tool, ContactAngleCalculator, is developed to meet these new requirements. In contrast to the current widely used computational approaches that are laborious and human intensive, this code is based on the concepts of the coarse-graining technique and equivalent contact area and volume of the droplet. Once the parameters are determined for a target liquid, it can automatically estimate the contact angle of different time points of one case or multiple cases by only one click. This tool is targeted for integration with machine learning methods, in which it can substantially streamline and reduce human labor and time in a computational contact angle estimation.
Exact exchange and Wilson-Levy correlation: a pragmatic device for studying complex weakly-bonded systems
Publisher: Royal Society of Chemistry (RSC)
Date: 2005
DOI: 10.1039/B415563G
Abstract: The Wilson-Levy (WL) correlation functional is used together with Hartree-Fock (HF) theory to evaluate interaction energies at intermediate separations (i.e. around equilibrium separation) for several weakly-bonded systems. The HF+WL approach reproduces binding trends for all complexes studied: selected rare-gas dimers, isomers of the methane dimer, benzene dimer and naphthalene dimer, and base-pair stacking structures for pyrimidine, cytosine, uracil and guanine dimers. These HF+WL data are contrasted against results obtained from some popular functionals (including B3LYP and PBE), as well as two newly-developed functionals, X3LYP and xPBE. The utility of HF+WL, with reference to exact-exchange (EXX) density-functional theory, is discussed in terms of a suggested EXXWL exchange-correlation functional.
Aqueous citrate: a first-principles and force-field molecular dynamics study
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3RA42437E
Controlling the Orientation and Viscoelasticity of Materials-Binding Peptides on Hexagonal Boron Nitride Using Fatty Acids
Publisher: American Chemical Society (ACS)
Date: 10-09-2021
First-principles molecular dynamics simulations of NH4+ and CH3COO- adsorption at the aqueous quartz interface
Publisher: AIP Publishing
Date: 11-12-2012
DOI: 10.1063/1.4769727
Abstract: The ability to exert molecular-level control at the aqueous interface between biomolecules and inorganic substrates is pivotal to advancing applications ranging from sustainable manufacturing to targeted therapeutics. Progress is hindered by a lack of structural information of these interfaces with atomic resolution. Molecular simulation is one approach to obtain such data, but can be limited by the reliability of the force-field used. First-principles simulations, in principle, can provide insights into such aqueous interfaces, but are resource-intensive, limiting previous first-principles studies to approximate the environment of liquid water. Here, we use Car-Parrinello simulations to investigate adsorption of two charged adsorbates that are functional groups common to all amino-acids—ethanoate and ammonium—at the interface between hydroxylated quartz and liquid water, directly incorporating full solvation effects at the interface. Our findings reveal the stable character of carboxylate-quartz binding, as well as the surprisingly indifferent nature of ammonium-quartz interactions, in liquid water.
Comparative Study of Materials-Binding Peptide Interactions with Gold and Silver Surfaces and Nanostructures: A Thermodynamic Basis for Biological Selectivity of Inorganic Materials
Publisher: American Chemical Society (ACS)
Date: 29-08-2014
DOI: 10.1021/CM501529U
Dramatic size effects and evidence of structural isomers in the reactions of rhodium clusters, Rhn±, with nitrous oxide
Publisher: Royal Society of Chemistry (RSC)
Date: 2007
DOI: 10.1039/B618299B
Abstract: The reactions of gas phase rhodium clusters, Rhn+/- (n<30), with nitrous oxide, N2O, have been investigated under single collision conditions by Fourier transform ion cyclotron resonance mass spectrometry. The only significant reaction observed is the sequential generation of oxides. Absolute rate constants for the reactions of all clusters have been determined and, in the case of the cationic clusters especially, they exhibit large fluctuations as a function of cluster size with local minima observed for n=5, 19, 28. Striking similarities are observed with the variation in rate constants for these clusters in reactions with small hydrocarbons (C. Adlhart and E. Uggerud, J. Chem. Phys., 2005, 123, 214709). Corresponding size effects are also observed but are less marked in the reactions of the anionic clusters. The reactions of several clusters exhibit marked deviations from simple pseudo-first-order kinetics suggesting the presence of multiple isomeric forms: Rh11+, Rh12+ and Rh8- exhibit characteristic biexponential decays which are interpreted in terms of the existence of different structural forms of the cluster which have markedly different reactivity. By contrast, Rh6+, Rh7+ and Rh8+ show rates which apparently increase with time, probably due to collisional activation. Thermalisation of the clusters prior to reaction by exposure to pulses of argon results in changes to the kinetics of these anomalous systems which can be explained in terms of collision induced isomerisation.
Sulfur K beta x-ray emission from carbonyl sulfide: Variations with polarization and excitation energy at the S K threshold
Publisher: American Physical Society (APS)
Date: 04-1998
Peptide-Directed PdAu Nanoscale Surface Segregation: Toward Controlled Bimetallic Architecture for Catalytic Materials
Publisher: American Chemical Society (ACS)
Date: 13-09-2016
Abstract: Bimetallic nanoparticles are of immense scientific and technological interest given the synergistic properties observed when two different metallic species are mixed at the nanoscale. This is particularly prevalent in catalysis, where bimetallic nanoparticles often exhibit improved catalytic activity and durability over their monometallic counterparts. Yet despite intense research efforts, little is understood regarding how to optimize bimetallic surface composition and structure synthetically using rational design principles. Recently, it has been demonstrated that peptide-enabled routes for nanoparticle synthesis result in materials with sequence-dependent catalytic properties, providing an opportunity for rational design through sequence manipulation. In this study, bimetallic PdAu nanoparticles are synthesized with a small set of peptides containing known Pd and Au binding motifs. The resulting nanoparticles were extensively characterized using high-resolution scanning transmission electron microscopy, X-ray absorption spectroscopy, and high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Structural information obtained from synchrotron radiation methods was then used to generate model nanoparticle configurations using reverse Monte Carlo simulations, which illustrate sequence dependence in both surface structure and surface composition. Replica exchange with solute tempering molecular dynamics simulations were also used to predict the modes of peptide binding on monometallic surfaces, indicating that different sequences bind to the metal interfaces via different mechanisms. As a testbed reaction, electrocatalytic methanol oxidation experiments were performed, wherein differences in catalytic activity are clearly observed in materials with identical bimetallic composition. Taken together, this study indicates that peptides could be used to arrive at bimetallic surfaces with enhanced catalytic properties, which could be leveraged for rational bimetallic nanoparticle design using peptide-enabled approaches.
An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture
Publisher: Elsevier BV
Date: 07-2015
Simulation-ready graphene oxide structures with hierarchical complexity: a modular tiling strategy
Publisher: IOP Publishing
Date: 25-01-2023
Abstract: Graphene oxide (GO) sheet structures are highly variable and depend on preparation conditions. The use of molecular simulation is a complementary strategy to explore how this complexity influences the ion transport properties of GO membranes. However, despite recent advances, computational models of GO typically lack the required complexity as suggested by experiment. The labor required to create such an ensemble of such structural models with the required complexity is impractical without recourse to automated approaches, but no such code currently can meet this challenge. Here, a modular tiling concept is introduced, along with the HierGO suite of code an automated approach to producing highly complex hierarchically-structured models of GO with a high degree of control in terms of holes and topological defects, and oxygen-group placement, that can produce simulation-ready input files. The benefits of the code are exemplified by modeling and contrasting the properties of three types of GO membrane stack the widely-modeled Lerf–Klinowski structure, and two types of highly heterogeneous GO sheet reflecting differing processing conditions. The outcomes of this work clearly demonstrate how the introduction of the complexity modeled here leads to new insights into the structure roperty relationships of GO with respect to permeation pathways of water, ions and molecular agents that are inaccessible using previously-considered models.
Exploring the influence of organic species on pre- and post-nucleation calcium carbonate
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2FD20052J
Modulation of Peptide–Graphene Interfaces via Fatty Acid Conjugation
Publisher: Wiley
Date: 30-11-2021
Structure of the electrical double layer at aqueous gold and silver interfaces for saline solutions
Publisher: Elsevier BV
Date: 12-2014
DOI: 10.1016/J.JCIS.2014.08.045
Abstract: We report the structure of the electrical double layer, determined from molecular dynamics simulations, for a range of saline solutions (NaCl, KCl, MgCl2 and CaCl2) at both 0.16 and 0.60 mol kg(-1) on different facets of the gold and silver aqueous interfaces. We consider the Au/Ag(111), native Au/Ag(100) and reconstructed Au(100)(5×1) facets. For a given combination of metallic surface and facet, some variations in density profile are apparent across the different cations in solution, with the corresponding chloride counterion profiles remaining broadly invariant. All density profiles at the higher concentration are predicted to be very similar to their low-concentration counterparts. We find that each electrolyte responds differently to the different metallic surface and facets, particularly those of the alent metal ions. Our findings reveal marked differences in density profiles between facets for a given metallic interface for both Mg(2+) and Ca(2+), with Na(+) and K(+) showing much less distinction. Mg(2+) was the only ion for which we find evidence of materials-dependent differences in interfacial solution structuring between the Ag and Au.
Controlled synthesis of highly-branched plasmonic gold nanoparticles through peptoid engineering
Publisher: Springer Science and Business Media LLC
Date: 13-06-2018
DOI: 10.1038/S41467-018-04789-2
Abstract: In nature, specific biomolecules interacting with mineral precursors are responsible for the precise production of nanostructured inorganic materials that exhibit complex morphologies and superior performance. Despite advances in developing biomimetic approaches, the design rules for creating sequence-defined molecules that lead to the synthesis of inorganic nanomaterials with predictable complex morphologies are unknown. Herein we report the design of sequence-defined peptoids for controlled synthesis of highly branched plasmonic gold particles. By engineering peptoid sequences and investigating the resulting particle formation mechanisms, we develop a rule of thumb for designing peptoids that predictively enabled the morphological evolution from spherical to coral-shaped nanoparticles. Through a combination of hyperspectral UV-Vis extinction microscopy and three-photon photoemission electron microscopy, we demonstrate that the in idual coral-shaped gold nanoparticles exhibit a plasmonic enhancement as high as 10 5 -fold. This research significantly advances our ultimate vision of predictive bio-inspired materials synthesis using sequence-defined synthetic molecules that mimic proteins and peptides.
A multipole‐based water potential with implicit polarization for biomolecular simulations
Publisher: Wiley
Date: 10-09-2008
DOI: 10.1002/JCC.21111
Abstract: A new water potential, DMIP (distributed multipoles, implicit polarization), is constructed using distributed multipoles to describe the electrostatic interactions, while accounting for polarization implicitly. In this procedure, small clusters are randomly s led from atomistic simulations of bulk water using the AMOEBA (Ren and Ponder, J Comput Chem 2002, 23, 1497) potential. The multipole moments of the central water in each cluster are obtained from ab initio densities for each cluster, and the moments are then averaged over all clusters. Properties of bulk water calculated using DMIP compare favorably with existing data from AMOEBA simulations and experiment, with a conservative estimate of reduction in compute time of roughly 40%. The implicit force-field is also shown to work compatibly with existing polarizable multipole-based force-fields for biomolecules.
Solution Study of Engineered Quartz Binding Peptides Using Replica Exchange Molecular Dynamics
Publisher: American Chemical Society (ACS)
Date: 22-10-2010
DOI: 10.1021/BM100646Z
Abstract: We use replica-exchange molecular dynamics (REMD) to interrogate molecular structures and properties of four engineered dodecapeptides (in solution, in the absence of a surface) that have been shown to bind to quartz with different propensities. We find that all of the strong-binding peptides feature some polyproline type II secondary structure, have less conformational freedom, and feature fewer intrapeptide hydrogen bonds compared with the weak binder. The regions of contiguous proline content in a given sequence appear to play a role in fostering some of these properties of the strong binders. For preliminary insights into quartz binding, we perform lattice-matching studies between a grid corresponding with the quartz (100) surface and the strong-binding peptide REMD structures. Our findings indicate a commonality among the putative contact residues, even for peptide structures with very different backbone conformations. Furthermore, interpeptide interactions in solution are studied. Our preliminary findings indicate that the strong-binder interpeptide contacts are dominated by weak, nonspecific hydrophobic interactions, while the weak-binding peptide shows more variable behavior due to the distribution of charged residues. In summary, the solution structures of peptides appear to be significant. We propose that these differences in their intra- and interpeptide interactions can influence their propensity to bind onto a solid substrate.
Probing the structures of gas-phase rhodium cluster cations by far-infrared spectroscopy
Publisher: AIP Publishing
Date: 07-12-2010
DOI: 10.1063/1.3509778
Abstract: The geometric structures of small cationic rhodium clusters Rh \\documentclass[12pt]{minimal}\\begin{document}$_n^+$\\end{document}n+ (n = 6–12) are investigated by comparison of experimental far-infrared multiple photon dissociation spectra with spectra calculated using density functional theory. The clusters are found to favor structures based on octahedral and tetrahedral motifs for most of the sizes considered, in contrast to previous theoretical predictions that rhodium clusters should favor cubic motifs. Our findings highlight the need for further development of theoretical and computational methods to treat these high-spin transition metal clusters.
Biomolecular Material Recognition in Two Dimensions: Peptide Binding to Graphene, h-BN, and MoS2 Nanosheets as Unique Bioconjugates
Publisher: American Chemical Society (ACS)
Date: 08-10-2019
DOI: 10.1021/ACS.BIOCONJCHEM.9B00593
Abstract: Two-dimensional nanosheet-based materials such as graphene, hexagonal boron nitride, and MoS
Atomistic modelling of the interaction between peptides and carbon nanotubes
Publisher: Informa UK Limited
Date: 20-01-2007
Identifying Affinity Classes of Inorganic Materials Binding Sequences via a Graph-Based Model
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 2015
Electronic Properties of a Graphene Device with Peptide Adsorption: Insight from Simulation
Publisher: American Chemical Society (ACS)
Date: 02-08-2013
DOI: 10.1021/AM401731C
Abstract: In this work, to explain doping behavior of single-layer graphene upon HSSYWYAFNNKT (P1) and HSSAAAAFNNKT (P1-3A) adsorption in field-effect transistors (GFETs), we applied a combined computational approach, whereby peptide adsorption was modeled by molecular dynamics simulations, and the lowest energy configuration was confirmed by density functional theory calculations. On the basis of the resulting structures of the hybrid materials, electronic structure and transport calculations were investigated. We demonstrate that π-π stacking of the aromatic residues and proximate peptide backbone to the graphene surface in P1 have a role in the p-doping. These results are consistent with our experimental observation of the GFET's p-doping even after a 24-h annealing procedure. Upon substitution of three of the aromatic residues to Ala in (P1-3A), a considerable decrease from p-doping is observed experimentally, demonstrating n-doping as compared to the nonadsorbed device, yet not explained based on the atomistic MD simulation structures. To gain a qualitative understanding of P1-3A's adsorption over a longer simulation time, which may differ from aromatic amino acid residues' swift anchoring on the surface, we analyzed equilibrated coarse-grain simulations performed for 500 ns. Desorption of the Ala residues from the surface was shown computationally, which could in turn affect charge transfer, yet a full explanation of the mechanism of n-doping will require elucidation of differences between various aromatic residues as dependent on peptide composition, and inclusion of effects of the substrate and environment, to be considered in future work.
Epoxy-gold nanoparticle nanocomposites with enhanced thermo-mechanical properties: An integrated modelling and experimental study
Publisher: Elsevier BV
Date: 04-2019
Beyond the ring flip: A molecular signature of the glass–rubber transition in tetrafunctional epoxy resins
Publisher: Elsevier BV
Date: 10-2020
Evaluation of a liaison and diversion Court Mental Health Service for defendants with neurodevelopmental disorders
Publisher: Elsevier BV
Date: 12-2021
Optical Control of Nanoparticle Catalysis Influenced by Photoswitch Positioning in Hybrid Peptide Capping Ligands
Publisher: American Chemical Society (ACS)
Date: 06-09-2018
Abstract: Here, we present an in-depth analysis of structural factors that modulate peptide-capped nanoparticle catalytic activity via optically driven structural reconfiguration of the biointerface present at the particle surface. Six different sets of peptide-capped Au nanoparticles were prepared, in which an azobenzene photoswitch was incorporated into one of two well-studied peptide sequences with known affinity for Au, each at one of three different positions: the N- or C-terminus or mid-sequence. Changes in the photoswitch isomerization state induce a reversible structural change in the surface-bound peptide, which modulates the catalytic activity of the material. This control of reactivity is attributed to changes in the amount of accessible metallic surface area available to drive the reaction. This research specifically focuses on the effect of the peptide sequence and photoswitch position in the biomolecule, from which potential target systems for on/off reactivity have been identified. Additionally, trends associated with photoswitch position for a peptide sequence (Pd4) have been identified. Integrating the azobenzene at the N-terminus or central region results in nanocatalysts with greater reactivity in the trans and cis conformations, respectively, however, positioning the photoswitch at the C-terminus gives rise to a unique system that is reactive in the trans conformation and partially deactivated in the cis conformation. These results provide a fundamental basis for new directions in nanoparticle catalyst development to control activity in real time, which could have significant implications in the design of catalysts for multistep reactions using a single catalyst. Additionally, such a fine level of interfacial structural control could prove to be important for applications beyond catalysis, including biosensing, photonics, and energy technologies that are highly dependent on particle surface structures.
Biointerface Structural Effects on the Properties and Applications of Bioinspired Peptide-Based Nanomaterials
Publisher: American Chemical Society (ACS)
Date: 29-08-2017
DOI: 10.1021/ACS.CHEMREV.7B00139
Abstract: Peptide sequences are known to recognize and bind different nanomaterial surfaces, which has resulted in the screening and identification of hundreds of peptides with the ability to bind to a wide range of metallic, metal oxide, mineral, and polymer substrates. These biomolecules are able to bind to materials with relatively high affinity, resulting in the generation of a complex biointerface between the biotic and abiotic components. While the number of material-binding sequences is large, at present, quantitative materials-binding characterization of these peptides has been accomplished only for a relatively small number of sequences. Moreover, it is currently very challenging to determine the molecular-level structure(s) of these peptides in the materials adsorbed state. Despite this lack of data related to the structure and function of this remarkable biointerface, several of these peptide sequences have found extensive use in creating functional nanostructured materials for assembly, catalysis, energy, and medicine, all of which are dependent on the structure of the in idual peptides and collective biointerface at the material surface. In this Review, we provide a comprehensive overview of these applications and illustrate how the versatility of this peptide-mediated approach for the growth, organization, and activation of nanomaterials could be more widely expanded via the elucidation of biointerfacial structure roperty relationships. Future directions and grand challenges to realize these goals are highlighted for both experimental characterization and molecular-simulation strategies.
Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design
Publisher: American Chemical Society (ACS)
Date: 07-11-2017
DOI: 10.1021/ACSSENSORS.7B00435
Abstract: We report on the predicted structural disruption of an adenosine-binding DNA aptamer adsorbed via noncovalent interactions on aqueous graphene. The use of surface-adsorbed biorecognition elements on device substrates is needed for integration in nanofluidic sensing platforms. Upon analyte binding, the conformational change in the adsorbed aptamer may perturb the surface properties, which is essential for the signal generation mechanism in the sensor. However, at present, these graphene-adsorbed aptamer structure(s) are unknown, and are challenging to experimentally elucidate. Here we use molecular dynamics simulations to investigate the structure and analyte-binding properties of this aptamer, in the presence and absence of adenosine, both free in solution and adsorbed at the aqueous graphene interface. We predict this aptamer to support a variety of stable binding modes, with direct base-graphene contact arising from regions located in the terminal bases, the centrally located binding pockets, and the distal loop region. Considerable retention of the in-solution aptamer structure in the adsorbed state indicates that strong intra-aptamer interactions compete with the graphene-aptamer interactions. However, in some adsorbed configurations the analyte adenosines detach from the binding pockets, facilitated by strong adenosine-graphene interactions.
Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6CP02323A
Abstract: First-principles calculations on nanoscale-sized noble metal nanoparticles demonstrate that planes, edges and vertices show different noncovalent adsorption propensities depending on the adsorbate functional group.
Synchrotron activation radiotherapy: Effects of dose-rate and energy spectra to tantalum oxide nanoparticles selective tumour cell radiosentization enhancement
Publisher: IOP Publishing
Date: 02-2020
Chemistry of (and on) Transition Metal Clusters: A Fourier Transform Ion Cyclotron Resonance Study of the Reaction of Niobium Cluster Cations with Nitric Oxide
Publisher: SAGE Publications
Date: 04-2009
DOI: 10.1255/EJMS.945
Abstract: The reactions of niobium cluster cations, Nb + n ( n = 2–19), with nitric oxide have been investigated using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR). The overall reaction rate constants are found to be in reasonable agreement with collision rates calculated using the surface charge capture model. The dominant reaction for small clusters ( n 9) involves reaction-induced fragmentation resulting in the loss of either NbO or NbN. By contrast, the main reaction observed for the larger clusters ( n 11) is sequential NO chemisorption. Clusters n = 9, 10 exhibit both extremes of behaviour and are the only clusters upon which there is evidence of NO decomposition with N 2 loss observed whenever multiple NO molecules are co-adsorbed. The rate constants for each process have been determined as a function of cluster size.
Tristearin bilayers: structure of the aqueous interface and stability in the presence of surfactants
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5RA09192F
Abstract: Molecular dynamics simulations predict that sodium dodecylbenzene sulphonate surfactant molecules embed themselves in a tristearin bilayer, packing commensurate with the hexagonally packed lattice formed by the acyl tails of tristearin.
Triggering nanoparticle surface ligand rearrangement via external stimuli: light-based actuation of biointerfaces
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5NR02311D
Abstract: Bio-molecular non-covalent interactions provide a powerful platform for material-specific self-organization in aqueous media. Here, we introduce a strategy that integrates a synthetic optically-responsive motif with a materials-binding peptide to enable remote actuation. Specifically, we linked a photoswitchable azobenzene moiety to either terminus of a Au-binding peptide. We employed these hybrid molecules as capping agents for synthesis of Au nanoparticles. Integrated experiments and molecular simulations showed that the hybrid molecules maintained both of their functions, i.e. binding to Au and optically-triggered reconfiguration. The azobenzene unit was optically switched reversibly between trans and cis states while adsorbed on the particle surface. Upon switching, the conformation of the peptide component of the molecule also changed. This highlights the interplay between the surface adsorption and conformational switching that will be pivotal to the creation of actuatable nanoparticle bio-interfaces, and paves the way toward multifunctional peptide hybrids that can produce stimuli responsive nanoassemblies.
Elucidating the influence of polymorph-dependent interfacial solvent structuring at chitin surfaces
Publisher: Elsevier BV
Date: 10-2016
DOI: 10.1016/J.CARBPOL.2016.05.116
Abstract: Interfacial solvent structuring is thought to be influential in mediating the adsorption of biomolecules at aqueous materials interfaces. However, despite the enormous potential for exploitation of aqueous chitin interfaces in industrial, medical and drug-delivery applications, little is known at the molecular-level about such interfacial solvent structuring for chitin. Here we use molecular simulation to predict the structure of the [100] and [010] interfaces of α-chitin and β-chitin dihydrate in contact with liquid water and saline solution. We find the α-chitin [100] interface supports lateral high-density regions in the first water layer at the interface, which are also present, but not as pronounced, for β-chitin. The lateral structuring of interfacial ions at the saline/chitin interface is also more pronounced for α-chitin compared with β-chitin. Our findings provide a foundation for the systematic design of biomolecules with selective binding affinity for different chitin polymorphs.
Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation
Publisher: American Chemical Society (ACS)
Date: 25-09-2017
DOI: 10.1021/ACS.LANGMUIR.7B02480
Abstract: We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.
Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides
Publisher: Elsevier BV
Date: 09-2019
DOI: 10.1016/J.NBT.2019.04.001
Abstract: The interactions between biomolecules and solid surfaces play an important role in designing new materials and applications which mimic nature. Recently, solid-binding peptides (SBPs) have emerged as potential molecular building blocks in nanobiotechnology. SBPs exhibit high selectivity and binding affinity towards a wide range of inorganic and organic materials. Although these peptides have been widely used in various applications, there is a need to understand the interaction mechanism between the peptide and its material substrate, which is challenging both experimentally and theoretically. This review describes the main characterisation techniques currently available to study SBP-surface interactions and their contribution to gain a better insight for designing new peptides for tailored binding.
Ductile thermoset polymers via controlling network flexibility
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C4CC10192H
Abstract: We report the design and synthesis of a polymer structure from a cross-linkable epoxy–ionic liquid system which behaves like a hard and brittle epoxy thermoset, perfectly ductile thermoplastic and an elastomer, all depending on controllable network compositions.
Determination of Kamlet-Taft parameters for selected solvate ionic liquids (vol 18, pg 13153, 2016)
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6CP90177H
Abstract: Correction for 'Determination of Kamlet–Taft parameters for selected solvate ionic liquids' by Daniel J. Eyckens et al. , Phys. Chem. Chem. Phys. , 2016, 18 , 13153–13157.
Biomolecular Adsorption at Aqueous Silver Interfaces: First-Principles Calculations, Polarizable Force-Field Simulations, and Comparisons with Gold
Publisher: American Chemical Society (ACS)
Date: 14-10-2013
DOI: 10.1021/LA402839Q
Abstract: The molecular simulation of biomolecules adsorbed at noble metal interfaces can assist in the development of bionanotechnology applications. In line with advances in polarizable force fields for adsorption at aqueous gold interfaces, there is scope for developing a similar force field for silver. One way to accomplish this is via the generation of in vacuo adsorption energies calculated using first-principles approaches for a wide range of different but biologically relevant small molecules, including water. Here, we present such first-principles data for a comprehensive range of bio-organic molecules obtained from plane-wave density functional theory calculations using the vdW-DF functional. As reported previously for the gold force field, GolP-CHARMM (Wright, L. B. Rodger, P. M. Corni, S. Walsh, T. R. GolP-CHARMM: first-principles based force-fields for the interaction of proteins with Au(111) and Au(100). J. Chem. Theory Comput. 2013, 9, 1616-1630), we have used these data to construct a a new force field, AgP-CHARMM, suitable for the simulation of biomolecules at the aqueous Ag(111) and Ag(100) interfaces. This force field is derived to be consistent with GolP-CHARMM such that adsorption on Ag and Au can be compared on an equal footing. Our force fields are used to evaluate the water overlayer stability on both silver and gold, finding good agreement with known behaviors. We also calculate and compare the structuring (spatial and orientational) of liquid water adsorbed at both silver and gold. Finally, we report the adsorption free energy of a range of amino acids at both the Au(111) and Ag(111) aqueous interfaces, calculated using metadynamics. Stronger adsorption on gold was noted in most cases, with the exception being the carboxylate group present in aspartic acid. Our findings also indicate differences in the binding free energy profile between silver and gold for some amino acids, notably for His and Arg. Our analysis suggests that the relatively stronger structuring of the first water layer on silver, relative to gold, could give rise to these differences.
Single Amino Acid Modifications for Controlling the Helicity of Peptide-Based Chiral Gold Nanoparticle Superstructures
Publisher: American Chemical Society (ACS)
Date: 13-03-2023
DOI: 10.1021/JACS.3C00827
The Influence of Water and Metal Salt on the Transport and Structural Properties of 1-Octyl-3-methylimidazolium Chloride
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/CH14240
Abstract: The addition of diluents to ionic liquids (ILs) has recently been shown to enhance the transport properties of ILs. In the context of electrolyte design, this enhancement allows the realisation of IL-based electrolytes for metal–air batteries and other storage devices. It is likely that diluent addition not only impacts the viscosity of the IL, but also the ion–ion interactions and structure. Here, we investigate the nano-structured 1-methyl-3-octylimidazolium chloride (OMImCl) with varying water concentrations in the presence of two metal salts, zinc chloride and magnesium chloride. We find that the choice of metal salt has a significant impact on the structure and transport properties of the system this is explained by the water structuring and destructing properties of the metal salt.
Oxides of small Rhodium clusters: Theoretical investigation of experimental reactivities
Publisher: AIP Publishing
Date: 23-09-2008
DOI: 10.1063/1.2981810
Abstract: Density functional theory is used to investigate the structures of cationic rhodium cluster oxides, Rh6Om+ (m=1,4). On the monoxide and dioxide, the oxygen atoms occupy bridge sites, while on trioxide and tetroxide clusters, high-coordination sites are favored. A range of spin multiplicities are investigated for each cluster, with high spin multiplicities found to be less favored for the oxides compared with the naked metal clusters. The dissociation of nitric oxide on low-energy isomers of Rh6O4+ is investigated and found to be unfavorable compared to molecular adsorption due to a combination of thermodynamic and kinetic factors. These calculations are consistent with, and help to account for, the experimentally observed reactivity of rhodium and rhodium oxide clusters with nitric oxide [M. S. Ford et al., Phys. Chem. Chem. Phys. 7, 975 (2005)].
Structure of Arginine Overlayers at the Aqueous Gold Interface: Implications for Nanoparticle Assembly
Publisher: American Chemical Society (ACS)
Date: 25-06-2014
DOI: 10.1021/AM502119G
Abstract: Adsorption of small biomolecules onto the surface of nanoparticles offers a novel route to generation of nanoparticle assemblies with predictable architectures. Previously, ligand-exchange experiments on citrate-capped gold nanoparticles with the amino acid arginine were reported to support linear nanoparticle assemblies. Here, we use a combination of atomistic modeling with experimental characterization to explore aspects of the assembly hypothesis for these systems. Using molecular simulation, we probe the structural and energetic characteristics of arginine overlayers on the Au(111) surface under aqueous conditions at both low- and high-coverage regimes. In the low-density regime, the arginines lie flat on the surface. At constant composition, these overlayers are found to be lower in energy than the densely packed films, although the latter case appears kinetically stable when arginine is adsorbed via the zwitterion group, exposing the charged guanidinium group to the solvent. Our findings suggest that zwitterion-zwitterion hydrogen bonding at the gold surface and minimization of the electrostatic repulsion between adjacent guanidinium groups play key roles in determining arginine overlayer stability at the aqueous gold interface. Ligand-exchange experiments of citrate-capped gold nanoparticles with arginine derivatives agmatine and N-methyl-l-arginine reveal that modification at the guanidinium group significantly diminishes the propensity for linear assembly of the nanoparticles.
Thermal conductivities and mechanical properties of epoxy resin as a function of the degree of cross-linking
Publisher: Elsevier BV
Date: 12-2021
Facet Selectivity of Binding on Quartz Surfaces: Free Energy Calculations of Amino-Acid Analogue Adsorption
Publisher: American Chemical Society (ACS)
Date: 20-01-2012
DOI: 10.1021/JP209554G
Ab initio derived force‐field parameters for molecular dynamics simulations of deprotonated amorphous‐SiO2/water interfaces
Publisher: Wiley
Date: 23-12-2011
An efficient high-throughput grafting procedure for enhancing carbon fiber-to-matrix interactions in composites
Publisher: Elsevier BV
Date: 12-2018
Blocking Directional Lithium Diffusion in Solid-State Electrolytes at the Interface: First-Principles Insights into the Impact of the Space Charge Layer
Publisher: American Chemical Society (ACS)
Date: 06-12-2022
Tuning Materials-Binding Peptide Sequences toward Gold- and Silver-Binding Selectivity with Bayesian Optimization
Publisher: American Chemical Society (ACS)
Date: 06-11-2021
Abstract: Peptide sequence engineering can potentially deliver materials-selective binding capabilities, which would be highly attractive in numerous biotic and abiotic nanomaterials applications. However, the number of known materials-selective peptide sequences is small, and identification of new sequences is laborious and haphazard. Previous attempts have sought to use machine learning and other informatics approaches that rely on existing data sets to accelerate the discovery of materials-selective peptides, but too few materials-selective sequences are known to enable reliable prediction. Moreover, this knowledge base is expensive to expand. Here, we combine a comprehensive and integrated experimental and modeling effort and introduce a Bayesian Effective Search for Optimal Sequences (BESOS) approach to address this challenge. Through this combined approach, we significantly expand the data set of Au-selective peptide sequences and identify an additional Ag-selective peptide sequence. Analysis of the binding motifs for the Ag-binders offers a roadmap for future prediction with machine learning, which should guide identification of further Ag-selective sequences. These discoveries will enable wider and more versatile integration of Ag nanoparticles in biological platforms.
Practical atomistic models of carbon fiber surfaces with tuneable topology and topography
Publisher: Elsevier BV
Date: 11-2021
Moisture Ingress at the Molecular Scale in Hygrothermal Aging of Fiber–Epoxy Interfaces
Publisher: American Chemical Society (ACS)
Date: 23-11-2020
Prediction of chain-growth polymerisation of vinyl ester resin structure at the carbon fibre interface
Publisher: Elsevier BV
Date: 02-2022
MOLECULAR AUGER RATES USING A STATISTICAL-MODEL AND AB-INITIO WAVE-FUNCTIONS
Publisher: IOP Publishing
Date: 14-10-1994
Organic-Silica Interactions in Saline: Elucidating the Structural Influence of Calcium in Low-Salinity Enhanced Oil Recovery
Publisher: Springer Science and Business Media LLC
Date: 08-09-2017
DOI: 10.1038/S41598-017-10327-9
Abstract: Enhanced oil recovery using low-salinity solutions to sweep sandstone reservoirs is a widely-practiced strategy. The mechanisms governing this remain unresolved. Here, we elucidate the role of Ca 2+ by combining chemical force microscopy (CFM) and molecular dynamics (MD) simulations. We probe the influence of electrolyte composition and concentration on the adsorption of a representative molecule, positively-charged alkylammonium, at the aqueous electrolyte/silica interface, for four electrolytes: NaCl, KCl, MgCl 2 , and CaCl 2 . CFM reveals stronger adhesion on silica in CaCl 2 compared with the other electrolytes, and shows a concentration-dependent adhesion not observed for the other electrolytes. Using MD simulations, we model the electrolytes at a negatively-charged amorphous silica substrate and predict the adsorption of methylammonium. Our simulations reveal four classes of surface adsorption site, where the prevalence of these sites depends only on CaCl 2 concentration. The sites relevant to strong adhesion feature the O − silica site and Ca 2+ in the presence of associated Cl − , which gain prevalence at higher CaCl 2 concentration. Our simulations also predict the adhesion force profile to be distinct for CaCl 2 compared with the other electrolytes. Together, these analyses explain our experimental data. Our findings indicate in general how silica wettability may be manipulated by electrolyte concentration.
Probing the Molecular Mechanisms of Quartz-Binding Peptides
Publisher: American Chemical Society (ACS)
Date: 25-05-2010
DOI: 10.1021/LA100049S
Abstract: Understanding the mechanisms of biomineralization and the realization of biology-inspired inorganic materials formation largely depends on our ability to manipulate peptide/solid interfacial interactions. Material interfaces and biointerfaces are critical sites for bioinorganic synthesis, surface diffusion, and molecular recognition. Recently adapted biocombinatorial techniques permit the isolation of peptides recognizing inorganic solids that are used as molecular building blocks, for ex le, as synthesizers, linkers, and assemblers. Despite their ubiquitous utility in nanotechnology, biotechnology, and medicine, the fundamental mechanisms of molecular recognition of engineered peptides binding to inorganic surfaces remain largely unknown. To explore propensity rules connecting sequence, structure, and function that play key roles in peptide/solid interactions, we combine two different approaches: a statistical analysis that searches for highly enriched motifs among de novo designed peptides, and, atomistic simulations of three experimentally validated peptides. The two strong and one weak quartz-binding peptides were chosen for the simulations at the quartz (100) surface under aqueous conditions. Solution-based peptide structures were analyzed by circular dichroism measurements. Small and hydrophobic residues, such as Pro, play a key role at the interface by making close contact with the solid and hindering formation of intrapeptide hydrogen bonds. The high binding affinity of a peptide may be driven by a combination of favorable enthalpic and entropic effects, that is, a strong binder may possess a large number of possible binding configurations, many of which having relatively high binding energies. The results signify the role of the local molecular environment among the critical residues that participate in solid binding. The work herein describes molecular conformations inherent in material-specific peptides and provides fundamental insight into the atomistic understanding of peptide/solid interfaces.
Sequence-Dependent Structure/Function Relationships of Catalytic Peptide-Enabled Gold Nanoparticles Generated under Ambient Synthetic Conditions
Publisher: American Chemical Society (ACS)
Date: 17-12-2015
DOI: 10.1021/JACS.5B09529
Abstract: Peptide-enabled nanoparticle (NP) synthesis routes can create and/or assemble functional nanomaterials under environmentally friendly conditions, with properties dictated by complex interactions at the biotic/abiotic interface. Manipulation of this interface through sequence modification can provide the capability for material properties to be tailored to create enhanced materials for energy, catalysis, and sensing applications. Fully realizing the potential of these materials requires a comprehensive understanding of sequence-dependent structure/function relationships that is presently lacking. In this work, the atomic-scale structures of a series of peptide-capped Au NPs are determined using a combination of atomic pair distribution function analysis of high-energy X-ray diffraction data and advanced molecular dynamics (MD) simulations. The Au NPs produced with different peptide sequences exhibit varying degrees of catalytic activity for the exemplar reaction 4-nitrophenol reduction. The experimentally derived atomic-scale NP configurations reveal sequence-dependent differences in structural order at the NP surface. Replica exchange with solute-tempering MD simulations are then used to predict the morphology of the peptide overlayer on these Au NPs and identify factors determining the structure/catalytic properties relationship. We show that the amount of exposed Au surface, the underlying surface structural disorder, and the interaction strength of the peptide with the Au surface all influence catalytic performance. A simplified computational prediction of catalytic performance is developed that can potentially serve as a screening tool for future studies. Our approach provides a platform for broadening the analysis of catalytic peptide-enabled metallic NP systems, potentially allowing for the development of rational design rules for property enhancement.
Equilibrium Conformational Ensemble of the Intrinsically Disordered Peptide n16N: Linking Subdomain Structures and Function in Nacre
Publisher: American Chemical Society (ACS)
Date: 20-11-2014
DOI: 10.1021/BM501263S
Abstract: n16 is a framework protein family associated with biogenic mineral stabilization, thought to operate at three key interfaces in nacre: protein/β-chitin, protein rotein, and protein/CaCO3. The N-terminal half of this protein, n16N, is known to be active in conferring this mineral stabilization and organization. While some details relating to the stabilization and organization of the mineral are known, the molecular mechanisms that underpin these processes are not yet established. To provide these molecular-scale details, here we explore current hypotheses regarding the possible subdomain organization of n16N, as related to these three interfaces in nacre, by combining outcomes of Replica Exchange with Solute Tempering molecular dynamics simulations with NMR experiments, to investigate the conformational ensemble of n16N in solution. We verify that n16N lacks a well-defined secondary structure, both with and without the presence of Ca(2+) ions, as identified from previous experiments. Our data support the presence of three different, functional subdomains within n16N. Our results reveal that tyrosine, chiefly located in the center of the peptide, plays a multifunctional role in stabilizing conformations of n16N, for intrapeptide and possibly interpeptide interactions. Complementary NMR spectroscopy data confirm the participation of tyrosine in this stabilization. The C-terminal half of n16N, lacking in tyrosine and highly charged, shows substantive conformational ersity and is proposed as a likely site for nucleation of calcium carbonate. Finally, dominant structures from our predicted conformational ensemble suggest the presentation of key residues thought to be critical to the selective binding to β-chitin surfaces.
Accelerated lithium-ion diffusion via a ligand ‘hopping’ mechanism in lithium enriched solvate ionic liquids
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D3CP04666D
Elucidating the influence of materials-binding peptide sequence on Au surface interactions and colloidal stability of Au nanoparticles
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C6NR07890G
Abstract: Peptide-mediated synthesis and assembly of nanostructures opens new routes to functional inorganic/organic hybrid materials. However, understanding of the many factors that influence the interaction of biomolecules, specifically peptides, with metal surfaces remains limited. Understanding of the relationship between peptide sequence and resulting binding affinity and configurations would allow predictive design of peptides to achieve desired peptide/metal interface characteristics. Here, we measured the kinetics and thermodynamics of binding on a Au surface for a series of peptide sequences designed to probe specific sequence and context effects. For ex le, context effects were explored by making the same mutation at different positions in the peptide and by rearranging the peptide sequence without changing the amino acid content. The degree of peptide-surface contact, predicted from advanced molecular simulations of the surface-adsorbed structures, was consistent with the measured binding constants. In simulations, the ensemble of peptide backbone conformations showed little change with point mutations of the anchor residues that dominate interaction with the surface. Peptide-capped Au nanoparticles were produced using each sequence. Comparison of simulations with nanoparticle synthesis results revealed a correlation between the colloidal stability of the Au nanoparticles and the degree of structural disorder in the surface-adsorbed peptide structures for this family of sequences. These findings suggest new directions in the optimization and design of biomolecules for in situ peptide-based nanoparticle growth, binding, and dispersion in aqueous media.
Surface-Grafted Cellulose in Water: Interfacial Retention and Dynamical Ingress of Moisture
Publisher: American Chemical Society (ACS)
Date: 22-09-2022
Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly
Publisher: Public Library of Science (PLoS)
Date: 16-07-2015
Atomistic Modeling of the Formation of a Thermoset/Thermoplastic Interphase during Co-Curing
Publisher: American Chemical Society (ACS)
Date: 15-05-2018
Halo-substituted azobenzenes adsorbed at Ag(111) and Au(111) interfaces: Structures and optical properties
Publisher: American Physical Society (APS)
Date: 19-05-2017
Relaxation dynamics of C-60
Publisher: AIP Publishing
Date: 22-10-1998
DOI: 10.1063/1.477319
Abstract: The relaxation dynamics of C60 from high-energy isomers to Buckminsterfullerene is examined using a master equation approach. An exhaustive catalog of the C60 fullerene isomers containing only five- and six-membered rings is combined with knowledge of the Stone-Wales rearrangements that connect all such isomers. Full geometry optimizations have been performed for all the minima and the transition states which connect them up to six Stone-Wales steps away from the global minimum. A density-functional tight-binding potential was employed to provide a quantum mechanical description of the bonding. The resulting picture of the potential energy landscape reveals a “weeping willow” structure which offers a clear explanation for the relatively long relaxation times observed experimentally. We also predict the most important transient local minima on the annealing pathway.
Peptide-Mediated Growth and Dispersion of Au Nanoparticles in Water via Sequence Engineering
Publisher: American Chemical Society (ACS)
Date: 03-05-2018
Predictions of Thermo‐Mechanical Properties of Cross‐Linked Polyacrylamide Hydrogels Using Molecular Simulations
Publisher: Wiley
Date: 04-01-2019
Computational chemistry for graphene-based energy applications: progress and challenges
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5NR00690B
Abstract: Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future.
Molecular Design of Inorganic-Binding Polypeptides
Publisher: Springer Science and Business Media LLC
Date: 05-2008
DOI: 10.1557/MRS2008.103
Abstract: Controlled binding and assembly of peptides onto inorganic substrates is at the core of bionanotechnology and biological-materials engineering. Peptides offer several unique advantages for developing future inorganic materials and systems. First, engineered polypeptides can molecularly recognize inorganic surfaces that are distinguishable by shape, crystallography, mineralogy, and chemistry. Second, polypeptides are capable of self-assembly on specific material surfaces leading to addressable molecular architectures. Finally, genetically engineered peptides offer multiple strategies for their functional modification. In this article, we summarize the details and mechanisms involved in combinatorial-polypeptide sequence selection and inorganic-material recognition and affinity, and outline experimental and theoretical approaches and concepts that will help advance this emerging field.
Electrochemical surface modification of carbon fibres by grafting of amine, carboxylic and lipophilic amide groups
Publisher: Elsevier BV
Date: 07-2017
Aziridine Scaffolds for the Detection and Quantification of Hydrogen‐Bonding Interactions through Transition‐State Stabilization
Publisher: Wiley
Date: 22-12-2010
Manipulation of peptide-fatty acid bioconjugates on graphene: effects of fatty acid chain length and attachment point
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D2TB01104B
Abstract: We demonstrate that attachment of fatty acids to graphene-binding peptides modulate interfacial interactions and structures, for enhancing sensing device applicability.
Selective manipulation of peptide orientation on hexagonal boron nitride nanosheets
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1NR00609F
Abstract: Modification of h-BN binding peptides can manipulate peptide orientation and overlayer viscoelasticity.
Infrared-Induced Reactivity of N2O on Small Gas-Phase Rhodium Clusters
Publisher: American Chemical Society (ACS)
Date: 10-03-2011
DOI: 10.1021/JP201171P
Abstract: Far- and mid-infrared multiple photon dissociation spectroscopy has been employed to study both the structure and surface reactivity of isolated cationic rhodium clusters with surface-adsorbed nitrous oxide, Rh(n)N(2)O(+) (n = 4-8). Comparison of experimental spectra recorded using the argon atom tagging method with those calculated using density functional theory (DFT) reveals that the nitrous oxide is molecularly bound on the rhodium cluster via the terminal N-atom. Binding is thought to occur exclusively on atop sites with the rhodium clusters adopting close-packed structures. In related, but conceptually different experiments, infrared pumping of the vibrational modes corresponding with the normal modes of the adsorbed N(2)O has been observed to result in the decomposition of the N(2)O moiety and the production of oxide clusters. This cluster surface chemistry is observed for all cluster sizes studied except for n = 5. Plausible N(2)O decomposition mechanisms are given based on DFT calculations using exchange-correlation functionals. Similar experiments pumping the Rh-O stretch in Rh(n)ON(2)O(+) complexes, on which the same chemistry is observed, confirm the thermal nature of this reaction.
Theoretical study of the water pentamer
Publisher: AIP Publishing
Date: 22-10-1996
DOI: 10.1063/1.471987
Abstract: Geometry optimizations, rearrangement mechanisms, spectral intensities, and tunneling splittings are reported for the water pentamer. Two low energy degenerate rearrangements are identified for the chiral cyclic global minimum which are analogous to processes that lead to observable tunneling splittings in the water trimer. Fourteen different pathways are characterized by ab initio calculations employing basis sets up to double-zeta plus polarization (DZP) quality with subsequent reoptimization of the associated minima using the Becke exchange and the Lee–Yang–Parr correlation functionals (BLYP) with the same basis. All the pathways have been recomputed for a number of different empirical potentials, some of which reproduce the two lowest energy degenerate rearrangements quite well. However, none of the empirical potentials support all the higher energy ab initio minima. Qualitative estimates of the two tunneling splittings associated with the lowest energy pathways suggest that at least one might be observable experimentally the associated splitting patterns and nuclear spin weights are also reported. The corresponding stationary points were finally reoptimized using DZP basis sets plus diffuse functions with the BLYP exchange-correlation functional.
Molecular Dynamics Simulations of the Adsorption and Dynamical Behavior of Single DNA Components on TiO2
Publisher: American Chemical Society (ACS)
Date: 15-11-2011
DOI: 10.1021/JP207950P
Tuning the Structure and Chiroptical Properties of Gold Nanoparticle Single Helices via Peptide Sequence Variation
Publisher: American Chemical Society (ACS)
Date: 05-09-2019
DOI: 10.1021/JACS.9B08798
Abstract: Just as peptide function is determined by the position, sequence, and overall arrangement of constituent amino acids, the optical properties of nanoparticle (NP) assemblies are influenced by the size, dimensions, and arrangement of constituent NPs. In this work, we demonstrate that peptide sequence can be programmed to direct the structure and chiroptical activity of chiral helical gold NP (AuNP)superstructures, a growing class of chiral nanomaterials with potential in sensing, detection, and optics-based applications. Gold-binding peptide conjugate families, C
Molecular Dynamics Studies of the Interactions of Water and Amino Acid Analogues with Quartz Surfaces
Publisher: American Chemical Society (ACS)
Date: 06-01-2009
DOI: 10.1021/LA803324X
Abstract: The interactions of silica surfaces with water and biomolecules are of considerable significance in bio- and nanotechnology and in geochemistry. An important goal in the fields of biomineralization and biomimetics is to fine-tune these interactions for the control, e.g., of assembly of materials at the nanoscale. Here we report molecular dynamics simulations of fully hydroxylated alpha-quartz (1010), (0001), and (0111) surfaces in explicit water. We also present free energy estimates of adsorbing water and analogues of amino acid side chains onto the quartz (1010) surface. We find that at least two layers of structured water form on the surface, which is driven by the formation of a strong hydrogen bond network at the interface. Interestingly, we find that the free energy change to move methane (analogue of the side chain of alanine) from bulk water to the (1010) interface is favorable. We ascribe this to the presence of microscopic voids on the surface, which can accommodate small hydrophobic moieties and shield them from the solvent. These observations draw some useful insights into the possible mechanisms by which biomolecules, in particular peptides and proteins, bind to quartz and other silica surfaces.
Structural isomers and reactivity for Rh-6 and Rh-6(+)
Publisher: American Chemical Society (ACS)
Date: 25-08-2006
DOI: 10.1021/JP062603O
Abstract: The structure, energetics, and interconversion of isomers of Rh(6) and Rh(6)(+) are studied by using density functional theory with Gaussian basis sets, using guess structures derived from basin-hopping simulations, and obtained by using the Sutton-Chen potential. A large range of spin multiplicities is considered for each isomer. Our calculations suggest two low-lying structures as possible structural isomers: a square bipyramid and a trigonal prism. The reactivity of these two candidate structural isomers with respect to adsorption of nitric oxide is studied via location of reaction transition states and calculation of reaction barriers. Similarities and differences with surface reaction studies are highlighted. These data provide powerful evidence that structural isomerism, and not different spin states, is responsible for the observed biexponential reaction kinetics.
Simultaneously increasing the hydrophobicity and interfacial adhesion of carbon fibres: a simple pathway to install passive functionality into composites
Publisher: Royal Society of Chemistry (RSC)
Date: 2019
DOI: 10.1039/C9TA02436K
Abstract: Hydrophobic carbon fibres were developed and show improved interfacial adhesion.
Design Traits for Diblock Copolymer Coating Properties on NaGdF4 Upconversion Nanoparticles
Publisher: American Chemical Society (ACS)
Date: 24-06-2022
Relaxation dynamics and structural isomerism in Nb-10 and Nb-10(+)
Publisher: AIP Publishing
Date: 25-05-2006
DOI: 10.1063/1.2201997
Abstract: The structure, energetics, and interconversion of isomers of Nb10 and Nb10+ are studied using density functional theory with Gaussian basis sets, using guess structures derived from basin-hopping simulations with the Finnis-Sinclair [Philos. Mag. A 50, 45 (1984)] potential. These results are used as input to a master equation approach to model the relaxation of these clusters. Ionization potentials are calculated for all relevant minima, as are the infrared spectra. On the basis of these data, and known experimental results, plausible explanations are given for the biexponential reaction kinetics observed for Nb10 and Nb10+ with respect to small molecule adsorbates. In principle, this approach could be extended to investigate any midsized transition metal cluster that exhibits structural isomerism.
Plasmon-enhanced two-photon-induced isomerization for highly-localized light-based actuation of inorganic/organic interfaces
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C5NR07973J
Abstract: Plasmon-enhanced two-photon isomerization of non-donor/acceptor modified azobenzene on Ag NPs.
Testing the inter-operability of the CHARMM and SPC/Fw force fields for conformational sampling
Publisher: Informa UK Limited
Date: 03-09-2014
Density functional theory calculations of vibrational spectra of rhodium oxide clusters
Publisher: Elsevier BV
Date: 02-2009
Photochemical control of molecular motion associated with pyramidal inversion
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3CC43036G
Abstract: Rates of pyramidal motion in an aziridine are controlled by reversible trans to cis photoisomerisation of an azobenzene unit attached to the ring nitrogen atom. The dynamics of the inversion process and activation parameters are derived by variable temperature NMR, and are supported by ab initio calculations.
Carbon fibre surface chemistry and its role in fibre-to-matrix adhesion
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1TA07151C
Abstract: A key determinant for carbon fibre reinforced polymer (CFRP) performance is their fibre-matrix interactions at the interface and interphase. These allow for stress transfer from the relatively weak and ductile resin to the strong reinforcing fibres.
Calculation of 1D and 2D densities in VMD: A flexible and easy-to-use code
Publisher: Elsevier BV
Date: 09-2021
Rearrangements of the water trimer
Publisher: Royal Society of Chemistry (RSC)
Date: 1996
DOI: 10.1039/FT9969202505
Side-chain effects on the co-existence of emergent nanopatterns in amino acid adlayers on graphene
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0NR01333A
Abstract: The spontaneous emergence of several co-existing ordered nano-motifs in initially spatially randomised amino acid adlayers adsorbed on graphene in vacuo is influenced by side-chain characteristics.
Peptide-Driven Exfoliation and Dispersion Mechanisms of Graphene in Aqueous Media
Publisher: American Chemical Society (ACS)
Date: 09-12-2021
DOI: 10.1021/ACS.JPCLETT.1C03558
Abstract: Peptide-mediated exfoliation and suspension of graphene in aqueous media is a promising strategy for bioapplications such as drug delivery, tissue engineering, and biosensors. A few peptide sequences are known as graphene exfoliators/dispersants in water, but the mechanisms underpinning this process remain underexplored. Here, molecular simulations investigate two key steps: sheet exfoliation and subsequent sheet reunification, in aqueous media. Umbrella s ling simulations predict the energy required to separate a graphene sheet from a graphite stack in both the presence/absence of the graphene-exfoliant peptide, P1. The free-energy barrier for reunification of two P1-coated graphene sheets is similarly calculated. Under sonication, the benefit from the relatively lower free-energy barrier associated with exfoliation in the absence of the peptide is negated by its facile reunification postsonication. In contrast, although P1 slightly increases the energy barrier to exfoliation under sonication, the peptides confer high-energy barriers to sheet reunification, thus ensuring stable aqueous graphene dispersions.
DNA Hairpin Adsorption on Gold Surfaces: Temperature and Salt Concentration Effects on Structure
Publisher: CSIRO Publishing
Date: 2020
DOI: 10.1071/CH19533
Toward a modular multi-material nanoparticle synthesis and assembly strategy via bionanocombinatorics: bifunctional peptides for linking Au and Ag nanomaterials
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6CP06135D
Abstract: Materials-binding peptides provide the basis for new nanoparticle assembly strategies.
GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100)
Publisher: American Chemical Society (ACS)
Date: 13-02-2013
DOI: 10.1021/CT301018M
Abstract: Computational simulation of peptide adsorption at the aqueous gold interface is key to advancing the development of many applications based on gold nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, we present a force field, GolP-CHARMM, designed to capture peptide adsorption at both the aqueous Au(111) and Au(100) interfaces. The force field, compatible with the bio-organic force field CHARMM, is parametrized using a combination of experimental and first-principles data. Like its predecessor, GolP (Iori, F. et al. J. Comput. Chem.2009, 30, 1465), this force field contains terms to describe the dynamic polarization of gold atoms, chemisorbing species, and the interaction between sp(2) hybridized carbon atoms and gold. A systematic study of small molecule adsorption at both surfaces using the vdW-DF functional (Dion, M. et al. Phys. Rev. Lett.2004, 92, 246401-1. Thonhauser, T. et al. Phys. Rev. B2007, 76, 125112) is carried out to fit and test force field parameters and also, for the first time, gives unique insights into facet selectivity of gold binding in vacuo. Energetic and spatial trends observed in our DFT calculations are reproduced by the force field under the same conditions. Finally, we use the new force field to calculate adsorption energies, under aqueous conditions, for a representative set of amino acids. These data are found to agree with experimental findings.
Probing diameter-selective solubilisation of carbon nanotubes by reversible cyclic peptides using molecular dynamics simulations
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/B9NR00226J
Abstract: Molecular dynamics simulations are used to explore the encapsulation behaviour of reversible cyclic peptides when adsorbed onto single-walled carbon nanotubes (CNTs) in aqueous solution. Our findings suggest that CNT encapsulation via cyclisation of a single peptide chain is relatively less likely, compared with encapsulation via two-chain complexes. These two-chain complexes comprise pairings of the motifs identified for single-chain adsorption. Our simulation data are compared with existing experimental findings [A. Ortiz-Acevedo et al., J. Am. Chem. Soc., 2005, 127, 9512], for relevant CNT diameters, and are found to be consistent with the experimental results. Our data help to explain the limited diameter selectivity reported by Ortiz-Acevedo et al. These findings should help in the optimisation and future design of peptides capable of enhanced selectivity for specific CNT diameters.
Identification of Parameters Controlling Peptide-Driven Graphene Exfoliation in Aqueous Media
Publisher: American Chemical Society (ACS)
Date: 11-01-2021
Binding Affinities of Amino Acid Analogues at the Charged Aqueous Titania Interface: Implications for Titania-Binding Peptides
Publisher: American Chemical Society (ACS)
Date: 28-10-2014
DOI: 10.1021/LA503312D
Abstract: Despite the extensive utilization of biomolecule-titania interfaces, biomolecular recognition and interactions at the aqueous titania interface remain far from being fully understood. Here, atomistic molecular dynamics simulations, in partnership with metadynamics, are used to calculate the free energy of adsorption of different amino acid side chain analogues at the negatively-charged aqueous rutile TiO2 (110) interface, under conditions corresponding with neutral pH. Our calculations predict that charged amino acid analogues have a relatively high affinity to the titania surface, with the arginine analogue predicted to be the strongest binder. Interactions between uncharged amino acid analogues and titania are found to be repulsive or weak at best. All of the residues that bound to the negatively-charged interface show a relatively stronger adsorption compared with the charge-neutral interface, including the negatively-charged analogue. Of the analogues that are found to bind to the titania surface, the rank ordering of the binding affinities is predicted to be "arginine" > "lysine" ≈ aspartic acid > "serine". This is the same ordering as was found previously for the charge-neutral aqueous titania interface. Our results show very good agreement with available experimental data and can provide a baseline for the interpretation of peptide-TiO2 adsorption data.
Modeling‐Led Materials‐Binding Peptide Design for Hexagonal Boron Nitride Interfaces
Publisher: Wiley
Date: 05-04-2022
Abstract: Peptides that can bind specific nanomaterials with affinity and specificity are attractive for realizing a wide range of applications. Manipulation of biomolecule/2D‐material interfaces via noncovalent interactions in aqueous media has gained intensive attention due to the promising potential for biomolecule‐facilitated 2D‐material exfoliation, dispersion, and organization in water. Such advances have been recently achieved for graphene, where several peptide sequences have demonstrated this capability. However, few peptides are known specific binders of hexagonal boron nitride ( h ‐BN), resulting in a lack of fundamental knowledge regarding biomolecule/ h ‐BN interactions at the aqueous interface. To address this, enhanced s ling techniques are used to complete the set of interfacial adsorption free energies for all 20 amino acids, and a range of tripeptides. Based on these data, a reductionist approach is proposed to design new dodecapeptides anticipated to have stronger binding to h ‐BN compared with a known h ‐BN‐binding peptide, BP7, based on rearrangements of the tripeptide motifs within BP7. This hypothesis is tested using replica exchange with solute tempering molecular dynamics simulations, and the results indicate significantly increased surface contact for the two proposed BP7‐derived sequences. This work provides a rational, economical, and general approach to propose, design, and examine new material‐binding peptides based on their constituent properties.
Biomolecular Recognition Principles for Bionanocombinatorics: An Integrated Approach To Elucidate Enthalpic and Entropic Factors
Publisher: American Chemical Society (ACS)
Date: 14-10-2013
DOI: 10.1021/NN404427Y
Abstract: Bionanocombinatorics is an emerging field that aims to use combinations of positionally encoded biomolecules and nanostructures to create materials and devices with unique properties or functions. The full potential of this new paradigm could be accessed by exploiting specific noncovalent interactions between erse palettes of biomolecules and inorganic nanostructures. Advancement of this paradigm requires peptide sequences with desired binding characteristics that can be rationally designed, based upon fundamental, molecular-level understanding of biomolecule-inorganic nanoparticle interactions. Here, we introduce an integrated method for building this understanding using experimental measurements and advanced molecular simulation of the binding of peptide sequences to gold surfaces. From this integrated approach, the importance of entropically driven binding is quantitatively demonstrated, and the first design rules for creating both enthalpically and entropically driven nanomaterial-binding peptide sequences are developed. The approach presented here for gold is now being expanded in our laboratories to a range of inorganic nanomaterials and represents a key step toward establishing a bionanocombinatorics assembly paradigm based on noncovalent peptide-materials recognition.
Control of Pyramidal Inversion Rates by Redox Switching
Publisher: American Chemical Society (ACS)
Date: 18-10-2006
DOI: 10.1021/JA065325F
Abstract: The dynamics of pyramidal nitrogen inversion can be controlled by reversible redox switching in trans-2,3-diphenylaziridines bearing a suitable 1,4-naphthaquinone substituent. In the reduced form, an intramolecular H-bond significantly raises the inversion barrier slowing this molecular motion by >50-fold. The experimental findings are further supported by DFT calculations.
Pathways to Structure–Property Relationships of Peptide–Materials Interfaces: Challenges in Predicting Molecular Structures
Publisher: American Chemical Society (ACS)
Date: 30-06-2017
DOI: 10.1021/ACS.ACCOUNTS.7B00065
Abstract: An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face challenges in their successful application to model the biotic-abiotic interface, related to several factors. For instance, simulations require a plausible description of the chemistry and the physics of the interface, which comprises two very different states of matter, in the presence of liquid water. Also, it is essential that the conformational ensemble be comprehensively characterized under these conditions this is especially challenging because intrinsically disordered peptides do not typically admit one single structure or set of structures. Moreover, a plausible structural model of the substrate is required, which may require a high level of detail, even for single-element materials such as Au surfaces or graphene. Developing and applying strategies to make credible predictions of the conformational ensemble of adsorbed peptides and using these to construct structure-property relationships of these interfaces have been the goals of our efforts. We have made substantial progress in developing interatomic potentials for these interfaces and adapting advanced conformational s ling approaches for these purposes. This Account summarizes our progress in the development and deployment of interfacial force fields and molecular simulation techniques for the purpose of elucidating these insights at biomolecule-materials interfaces, using ex les from our laboratories ranging from noble-metal interfaces to graphitic substrates (including carbon nanotubes and graphene) and oxide materials (such as titania). In addition to the well-established application areas of plasmonic materials, biosensing, and the production of medical implant materials, we outline new directions for this field that have the potential to bring new advances in areas such as energy materials and regenerative medicine.
A Versatile Computational Procedure for Chain-Growth Polymerization Using Molecular Dynamics Simulations
Publisher: American Chemical Society (ACS)
Date: 25-09-2019
A theoretical study of polyimide flexibility
Publisher: AIP Publishing
Date: 03-2000
DOI: 10.1063/1.480986
Abstract: The flexibility of a model polyimide, pyromellitic-dianhydride 1,4-oxydianiline (PMDA-ODA) is investigated using fully ab initio methods. Hartree–Fock, second-order Møller–Plesset theory (MP2) and density-functional theory (DFT) methods are employed along with both numerical and Gaussian basis sets. A hybrid scheme which combines energies and first derivatives is also used and appraised for this system. Energies of monomer fragments of the polyimide as a function of torsional angle are calculated using geometry optimizations. Extensive comparisons are made with maleanil, a smaller fragment of PMDA-ODA.
Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C4NR00468J
Abstract: Simulations of the aqueous interface between graphitic nanostructures and biomolecules are efficiently realised via the polarisable GRAPPA model.
Severe mental illness, common mental disorders, and neurodevelopmental conditions amongst 9088 lower court attendees in London, UK
Publisher: Springer Science and Business Media LLC
Date: 12-08-2022
DOI: 10.1186/S12888-022-04150-4
Abstract: Court Mental Health Liaison and Diversion Services (CMHLDS) have developed in some countries as a response to the over-representation of mental illness and other vulnerabilities amongst defendants presenting to criminal justice (or correctional) systems. This study examined the characteristics and rates of mental disorder of 9088 defendants referred to CMHLDS. The study analysed service level data, obtained from the National Health Service’s mental health data set, to examine characteristics relating to gender, ethnicity and comorbidity of common mental and neurodevelopmental disorders at five CMHLDS across London between September 2015 and April 2017. The s le included 7186 males (79.1%) and 1719 females (18.9%), the gender of 183 (2%) were not recorded. Of those referred, 6616 (72.8%) presented with an identifiable mental disorder and 503 (5.5%) with a neurodevelopmental disorder (NDD). Significantly higher rates of schizophrenia were reported amongst Black defendants ( n = 681 37.2%) and Asian defendants ( n = 315 29%), while higher rates of depression were found amongst White defendants ( n = 1007 22.1%). Substance misuse was reported amongst 2813 defendants (31%), and alcohol misuse amongst 2111 (23.2%), with significantly high rates of substance and alcohol misuse amongst defendants presenting with schizophrenia or personality disorder. This is one of the largest studies to examine mental health needs and vulnerabilities amongst defendants presenting to CMHLDS. It will enable an improved understanding of the required service designs and resources required to manage the healthcare pathways for people attending CMHLDS.
Structure and Properties of Citrate Overlayers Adsorbed at the Aqueous Au(111) Interface
Publisher: American Chemical Society (ACS)
Date: 12-12-2014
DOI: 10.1021/LA503690T
Abstract: One of the most common means of gold nanoparticle (AuNP) biofunctionalization involves the manipulation of precursor citrate-capped AuNPs via ligand displacement. However, the molecular-level structural characteristics of the citrate overlayer adsorbed at the aqueous Au interface at neutral pH remain largely unknown. Access to atomistic-scale details of these interfaces will contribute much needed insight into how AuNPs can be manipulated and exploited in aqueous solution. Here, the structures of such citrate overlayers adsorbed at the aqueous Au(111) interface at pH 7 are predicted and characterized using atomistic molecular dynamics simulations, for a range of citrate surface densities. We find that the overlayers are disordered in the surface density range considered, and that many of their key characteristics are invariant with surface density. In particular, we predict the overlayers to have 3-D, rather than 2-D, morphologies, with the anions closest to the gold surface being oriented with their carboxylate groups pointing away from the surface. We predict both striped and island morphologies for our overlayers, depending on the citrate surface density, and in all cases we find bare patches of the gold surface are present. Our simulations suggest that both citrate-gold adsorption and citrate-counterion pairing contribute to the stability of these citrate overlayer morphologies. We also calculate the free energy of adsorption at the aqueous Au(111) interface of a single citrate molecule, and compare this with the corresponding value for a single arginine molecule. These findings enable us to predict the conditions under which ligand displacement of surface-adsorbed citrate by arginine may take place. Our findings represent the first steps toward elucidating a more elaborate, detailed atomistic-scale model relating to the biofunctionalization of citrate-capped AuNPs.
Interplay of Sequence, Conformation, and Binding at the Peptide−Titania Interface as Mediated by Water
Publisher: American Chemical Society (ACS)
Date: 10-06-2009
DOI: 10.1021/AM9001666
Abstract: The initial stages of the adsorption of a hexapeptide at the aqueous titania interface are modeled using atomistic molecular dynamics simulations. This hexapeptide has been identified by experiment [Sano, K. I. Shiba, K. J. Am. Chem. Soc. 2003, 125, 14234] to bind to Ti particles. We explore the current hypothesis presented by these authors that binding at this peptide-titania interface is the result of electrostatic interactions and find that contact with the surface appears to take place via a pair of oppositely charged groups in the peptide. Our data indicate that the peptide may initially recognize the water layers at the interface, not the titania surface itself, via these charged groups. We also report results of simulations for hexapeptide sequences with selected single-point mutations for alanine and compare these behaviors with those suggested from observed binding affinities from existing alanine scan experiments. Our results indicate that factors in addition to electrostatics also contribute, with the structural rigidity conferred by proline suggested to play a significant role. Finally, our findings suggest that intrapeptide interaction may provide mechanisms for surface detachment that could be detrimental to binding at the interface.
Dynamical Water Ingress and Dissolution at the Amorphous–Crystalline Cellulose Interface
Publisher: American Chemical Society (ACS)
Date: 08-2021
Energy landscapes: From clusters to biomolecules
Publisher: Wiley
Date: 2000
Using molecular entanglement as a strategy to enhance carbon fiber-epoxy composite interfaces
Publisher: Elsevier BV
Date: 08-2020
Interaction between Polysialic Acid and the MARCKS-ED Peptide at the Molecular Level
Publisher: American Chemical Society (ACS)
Date: 15-05-2020
Achieving regioselective materials binding using multidomain peptides
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D2NR03169H
Abstract: The ability to integrate two disparate materials-binding domains into a single ligand to achieve regiospecific binding would be powerful to direct material assembly however, this has proven challenging to achieve due to cross-materials binding.
Towards an anisotropic bead-spring model for ribbonlike polymers: Monte Carlo simulations of liquid benzene
Publisher: AIP Publishing
Date: 17-07-2003
DOI: 10.1063/1.1586254
Abstract: We present a Monte Carlo study for liquid benzene in the NVT ensemble. The benzene pair potential is described by an anisotropic Gay–Berne model fitted to ab initio interaction energies of the benzene dimer. We investigated the density and structure of liquid benzene at room temperature through the calculation of the carbon–carbon and molecular center–center radial distribution functions as well as the angular-radial distribution function. The simulated results are compared to experimental data and previous theoretical investigations.
First-Principles-Based Force Field for the Interaction of Proteins with Au(100)(5 × 1): An Extension of GolP-CHARMM
Publisher: American Chemical Society (ACS)
Date: 17-11-0011
DOI: 10.1021/JP4061329
Efficient conformational sampling of peptides adsorbed onto inorganic surfaces: insights from a quartz binding peptide
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3CP42921K
Abstract: Harnessing the properties of biomolecules, such as peptides, adsorbed on inorganic surfaces is of interest to many cross-disciplinary areas of science, ranging from biomineralisation to nanomedicine. Key to advancing research in this area is determination of the peptide conformation(s) in its adsorbed state, at the aqueous interface. Molecular simulation is one such approach for accomplishing this goal. In this respect, use of temperature-based replica-exchange molecular dynamics (T-REMD) can yield enhanced s ling of the interfacial conformations, but does so at great computational expense, chiefly because of the need to include an explicit representation of water at the interface. Here, we investigate a number of more economical variations on REMD, chiefly those based on Replica Exchange with Solvent Tempering (REST), using the aqueous quartz-binding peptide S1-(100) α-quartz interfacial system as a benchmark. We also incorporate additional implementation details specifically targeted at improving s ling of biomolecules at interfaces. We find the REST-based variants yield configurational s ling of the peptide-surface system comparable with T-REMD, at a fraction of the computational time and resource. Our findings also deliver novel insights into the binding behaviour of the S1 peptide at the quartz (100) surface that are consistent with available experimental data.
Improved Lithium Diffusion in Anion-Substituted Li7TaO6
Publisher: American Chemical Society (ACS)
Date: 25-05-0099
Emergence of order in self-assembly of the intrinsically disordered biomineralisation peptide n16N
Publisher: Informa UK Limited
Date: 29-11-2018
Predicting biomolecule adsorption on MoS2 nanosheets with high structural fidelity
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D1SC06814H
Abstract: Benchmarked van der Waals density functional theory calculations are used to create a force-field to describe biomolecule interactions at the aqueous MoS 2 interface, which can recover interfacial biomolecule adsorption with high structural fidelity.
Study of boron–nitrogen dative bonds using azetidine inversion dynamics
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3CC36159D
Abstract: A method for probing the strength of B-N dative bonds is reported. The activation parameters for nitrogen inversion in a series of azetidines tethered to boronate esters have been quantified by VT-NMR and the measured barriers correlated with data obtained by (11)B NMR, X-ray crystallography and MP2 calculations.
Tailoring the fibre-to-matrix interface using click chemistry on carbon fibre surfaces
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C7TA00922D
Abstract: A convenient and effective strategy to control the surface chemistry of carbon fibres is presented, comprising electro-chemical reduction of aryl diazonium salts onto the surface, followed by ‘click chemistry’ to tether the desired surface characteristic of choice.
Gradient Line Reaction Paths for Hindered Internal Rotation in H2BNH2 and Inversion in PF3
Publisher: American Chemical Society (ACS)
Date: 02-1997
DOI: 10.1021/JP9628343
An ab initio study of the low energy structures of the naphthalene dimer
Publisher: Elsevier BV
Date: 09-2002
Material composition and peptide sequence affects biomolecule affinity to and selectivity for h-boron nitride and graphene
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0CC02635B
Abstract: Pathways to nanosheet selective binding peptides are presented.
Designing carbon fiber composite interfaces using a ‘graft-to’ approach: Surface grafting density versus interphase penetration
Publisher: Elsevier BV
Date: 05-2019
Interaction of liquid water with the rutile TiO2 (110) surface
Publisher: Informa UK Limited
Date: 04-2007
Achieving flame retardancy and mechanical integrity via phosphites in bio‐based resins
Publisher: Wiley
Date: 22-12-2022
DOI: 10.1002/POL.20210774
Abstract: Bio‐based flame retardant (FR) resins typically exhibit diminished mechanical properties compared with their petroleum‐based counterparts. Recent experiments identified a promising FR phosphorus‐bearing vanillin‐based epoxy resin, EP2, that exhibited superior thermomechanical properties compared to that of petroleum‐based diglycidyl ether of bisphenol A. However, the structure roperty relationships of such phosphorus‐containing bio‐based resins are relatively under‐explored and cannot be resolved via experiments alone. Here, molecular simulations are used to explore these relationships for a resin comprising EP2 cured with 4,4‐diaminodiphenylmethane. The predicted thermomechanical properties are consistent with experimental observations, and critically, the structural analysis reveals the importance of the pendant phosphite group in the monomer as central to maintaining extensive hydrogen‐bonding networks, giving rise to the excellent Young's modulus. This work provides the foundation for knowledge‐based strategies to systematically improve the structure roperty relationships in FR bio‐based epoxy resins.
Communications: The structure of Rh8+ in the gas phase
Publisher: AIP Publishing
Date: 06-01-2010
DOI: 10.1063/1.3285266
Abstract: The geometric structure of the Rh8+ cation is investigated using a combination of far-infrared multiple photon dissociation spectroscopy and density functional theory (DFT) calculations. The energetic ordering of the different structural motifs is found to depend sensitively on the choice of pure or hybrid exchange functionals. Comparison of experimental and calculated spectra suggests the cluster to have a close-packed, bicapped octahedral structure, in contrast to recent predictions of a cubic structure for the neutral cluster. Our findings demonstrate the importance of including some exact exchange contributions in the DFT calculations, via hybrid functionals, when applied to rhodium clusters, and cast doubt on the application of pure functionals for late transition metal clusters in general.
Aqueous Peptide-TiO2 Interfaces: Iso-energetic Binding via either Entropically- or Enthalpically-driven Mechanisms
Publisher: American Chemical Society (ACS)
Date: 11-07-2016
Abstract: A major barrier to the systematic improvement of biomimetic peptide-mediated strategies for the controlled growth of inorganic nanomaterials in environmentally benign conditions lies in the lack of clear conceptual connections between the sequence of the peptide and its surface binding affinity, with binding being facilitated by noncovalent interactions. Peptide conformation, both in the adsorbed and in the nonadsorbed state, is the key relationship that connects peptide-materials binding with peptide sequence. Here, we combine experimental peptide-titania binding characterization with state-of-the-art conformational s ling via molecular simulations to elucidate these structure/binding relationships for two very different titania-binding peptide sequences. The two sequences (Ti-1, QPYLFATDSLIK Ti-2, GHTHYHAVRTQT) differ in their overall hydropathy, yet via quartz-crystal microbalance measurements and predictions from molecular simulations, we show these sequences both support very similar, strong titania-binding affinities. Our molecular simulations reveal that the two sequences exhibit profoundly different modes of surface binding, with Ti-1 acting as an entropically driven binder while Ti-2 behaves as an enthalpically driven binder. The integrated approach presented here provides a rational basis for peptide sequence engineering to achieve the in situ growth and organization of titania nanostructures in aqueous media and for the design of sequences suitable for a range of technological applications that involve the interface between titania and biomolecules.
Benzene adsorption at the aqueous (011) alpha-quartz interface: is surface flexibility important?
Publisher: Informa UK Limited
Date: 11-2013
Effect of calcium ions on peptide adsorption at the aqueous rutile titania (110) interface
Publisher: American Vacuum Society
Date: 31-08-2018
DOI: 10.1116/1.5046531
Abstract: How the presence of Ca2+ ions at the aqueous TiO2 interface influences the binding modes of two experimentally identified titania-binding peptides, Ti-1 and Ti-2, is investigated using replica exchange with solute tempering molecular dynamics simulations. The findings are compared with available experimental data, and the results are contrasted with those obtained under NaCl solution conditions. For Ti-1, Ca2+ ions enhance the adsorption of the negatively charged Asp8 residue in this sequence to the negatively charged surface, via Asp–Ca2+–TiO2 bridging. This appears to generate a nonlocal impact on the adsorption of Lys12 in Ti-1, which then pins the peptide to the surface via direct surface contact. For Ti-2, fewer residues were predicted to adsorb directly to the surface in CaCl2, compared with predictions made for NaCl solution, possibly due to competition between the other peptide residues and Ca2+ ions to adsorb to the surface. This reduction in direct surface contact gives rise to a more extensive solvent-mediated contact for Ti-2. In general, the presence of Ca2+ ions resulted in a loss of conformational ersity of the surface-adsorbed conformational ensembles of these peptides, compared to counterpart data predicted for NaCl solution. The findings provide initial insights into how peptide–TiO2 interactions might be tuned at the molecular level via modification of the salt composition of the liquid medium.
A Bespoke Force Field To Describe Biomolecule Adsorption at the Aqueous Boron Nitride Interface
Publisher: American Chemical Society (ACS)
Date: 12-11-2019
DOI: 10.1021/ACS.LANGMUIR.9B03121
Abstract: Reliable manipulation of the interface between 2D nanomaterials and biomolecules represents a current frontier in nanoscience. The ability to resolve the molecular-level structures of these biointerfaces would provide a fundamental data set that is needed to enable systematic and knowledge-based progress in this area. These structures are challenging to obtain via experiment alone, and molecular simulations offer a complementary approach to address this problem. Compared with graphene, the interface between hexagonal boron nitride (
Molecular-Level Insights into Biologically Driven Graphite Exfoliation for the Generation of Graphene in Aqueous Media
Publisher: American Chemical Society (ACS)
Date: 10-01-2020
Predicted structures of calcium aluminosilicate glass as a model for stone wool fiber: effects of composition and interatomic potential
Publisher: Elsevier BV
Date: 09-2021
Free Energy Calculations of the Adsorption of Amino Acid Analogues at the Aqueous Titania Interface
Publisher: American Chemical Society (ACS)
Date: 02-12-2010
DOI: 10.1021/JP107859Q
Hydrolysis of the amorphous silica surface. I. Structure and dynamics of the dry surface
Publisher: AIP Publishing
Date: 22-11-2000
DOI: 10.1063/1.1320056
Abstract: Amorphous SiO2 surfaces are generated from bulk–liquid configurations using simulations employing a polarizable-ion model. The surfaces are characterized in terms of the ion environments as a function of depth into the surface. Comparison is made to previous simulation studies and subtle differences are highlighted and attributed to differences in the potential models. The connectivity of the surface sites is established with a view to investigating the hydrolysis of this surface. Dynamical properties are calculated using a simple projected velocity time correlation function and normal mode analysis and compared to the simulated bulk and experimental bulk and surface spectra.
Hydrolysis of the amorphous silica surface. II. Calculation of activation barriers and mechanisms
Publisher: AIP Publishing
Date: 22-11-2000
DOI: 10.1063/1.1320057
Abstract: Using a previously derived model of the dry, amorphous, hydrophilic SiO2 surface, the reactivity of generic defect sites on the surface with respect to water, and the local network rearrangement that accompanies hydrolysis at these sites, is investigated using cluster models. Ab initio methods are used to calculate reaction barriers and reaction pathways. Consequences of the various types of hydrolysis product found are discussed with reference to potential sites for polymer chemisorption on the hydrolyzed, amorphous SiO2 surface.
Improving the description of interactions between Ca2+ and protein carboxylate groups, including gamma-carboxyglutamic acid: revised CHARMM22*parameters
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5RA11268K
Abstract: We show that the CHARMM22* force-field over-binds the interaction between aqueous carboxylates and Ca 2+ , and introduce a modification that can recover experimentally-determined binding free energies for these systems.
Elucidating Polymorph-Selective Bioadsorption on Chitin Surfaces
Publisher: American Chemical Society (ACS)
Date: 13-01-2019
PREDICTION OF MOLECULAR AUGER RATES USING A STATISTICAL-MODEL
Publisher: IOP Publishing
Date: 14-06-1994
Elucidating the mechanisms of nanodiamond-promoted structural disruption of crystallised lipid
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6SM01155A
Abstract: Molecular dynamics simulations predict that a combination of sodium dodecylbenzene sulphonate surfactant molecules and nanodiamonds are able to induce a lowering of the phase transition temperatures of tristearin bilayers.
Exploring Coordination of Neodymium in Ionic Liquid: Insights to Guide Sustainable Recovery
Publisher: American Chemical Society (ACS)
Date: 22-09-2023
Ab initio calculations of normal and resonant x-ray emission spectra for the OCS molecule
Publisher: IOP Publishing
Date: 28-01-1996
Distinct Differences in Peptide Adsorption on Palladium and Gold: Introducing a Polarizable Model for Pd(111)
Publisher: American Chemical Society (ACS)
Date: 07-08-2018
Machine learning-based discovery of vibrationally stable materials
Publisher: Springer Science and Business Media LLC
Date: 11-01-2023
DOI: 10.1038/S41524-022-00943-Z
Abstract: The identification of the ground state phases of a chemical space in the convex hull analysis is a key determinant of the synthesizability of materials. Online material databases have been instrumental in exploring one aspect of the synthesizability of many materials, namely thermodynamic stability. However, the vibrational stability, which is another aspect of synthesizability, of new materials is not known. Applying first principles approaches to calculate the vibrational spectra of materials in online material databases is computationally intractable. Here, a dataset of vibrational stability for ~3100 materials is used to train a machine learning classifier that can accurately distinguish between vibrationally stable and unstable materials. This classifier has the potential to be further developed as an essential filtering tool for online material databases that can inform the material science community of the vibrational stability or instability of the materials queried in convex hulls.
Modeling the Binding Affinity of Peptides for Graphitic Surfaces. Influences of Aromatic Content and Interfacial Shape
Publisher: American Chemical Society (ACS)
Date: 21-05-2009
DOI: 10.1021/JP8087594
Towards an anisotropic bead-spring model for polymers: a Gay-Berne parametrization for benzene
Publisher: Informa UK Limited
Date: 10-09-2002
Sequence control over emergent nano-patterns in dipeptide adlayers at the graphene interface
Publisher: Elsevier BV
Date: 09-2021
Facet selectivity in gold binding peptides: exploiting interfacial water structure
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5SC00399G
Abstract: We demonstrate that surface hydration is a key factor in dictating the free energy of non-covalent peptide-materials recognition.
Enhanced Interfacial Integrity for Chain Growth Polymer Carbon Fiber Composites via Surface-Initiated Polymerization
Publisher: American Chemical Society (ACS)
Date: 07-06-2022
What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5TB00004A
Abstract: Molecular dynamics simulations of the aqueous biomolecule–graphene interface have predicted the free energy of adsorption of amino acids and the structure of peptides.
Testing the transferability of a coarse-grained model to intrinsically disordered proteins
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5CP05652G
Abstract: The coarse-grained PLUM model is shown to capture structural and dimerization behaviour of the intrinsically disordered biomineralisation peptide n16N.
Force fields for water–surface interaction: is reproduction of the experimental water contact angle enough?
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1CC00426C
Abstract: Both the experimental contact angle and structural energetic rankings are needed to revisit and develop force fields for interfacial simulations.
Modelling the nanoscale patterning of nucleic acid base pairs deposited on graphite
Publisher: Informa UK Limited
Date: 06-2008
Design Rules for Enhanced Interfacial Shear Response in Functionalized Carbon Fiber Epoxy Composites
Publisher: American Chemical Society (ACS)
Date: 27-03-2017
Abstract: Carbon-fiber reinforced composites are ideal light-weighting candidates to replace traditional engineering materials. The mechanical performance of these composites results from a complex interplay of influences operating over several length and time scales. The mechanical performance may therefore be limited by many factors, one of which being the modest interfacial adhesion between the carbon fiber and the polymer. Chemical modification of the fiber, via surface grafting of molecules, is one possible strategy to enhance interactions across the fiber-polymer interface. To achieve systematic improvements in these modified materials, the ability to manipulate and monitor the molecular structure of the polymer interphase and the surface grafted molecules in the composite is essential, but challenging to accomplish from a purely experimental perspective. Alternatively, molecular simulations can bridge this knowledge gap by providing molecular-scale insights into the optimal design of these surface-grafted molecules to deliver superior mechanical properties. Here we use molecular dynamics simulations to predict the interfacial shear response of a typical epoxy/carbon-fiber composite for both pristine fiber and a range of surface graftings. We allow for the dynamic curing of the epoxy in the presence of the functionalized surface, including cross-link formation between the grafted molecules and the polymer matrix. Our predictions agree with recently reported experimental data for these systems and reveal the molecular-scale origins of the enhanced interfacial shear response arising from functionalization. In addition to the presence of interfacial covalent bonds, we find that the interfacial structural complexity, resulting from the presence of the grafted molecules, and a concomitant spatial homogeneity of the interphase polymer density are beneficial factors in conferring high interfacial shear stress. Our approach paves the way for computational screening processes to design, test, and rapidly identify viable surface modifications in silico, which would enable rapid systematic progress in optimizing the match between the carbon fiber treatment and the desired thermoset polymer matrix.
Infrared Induced Reactivity on the Surface of Isolated Size-Selected Clusters: Dissociation of N2O on Rhodium Clusters
Publisher: American Chemical Society (ACS)
Date: 15-01-2010
DOI: 10.1021/JA907496C
Abstract: Multiple photon infrared excitation of size-selected Rh(6)N(2)O(+) clusters drives surface chemistry resulting in partially oxidized clusters.
Molecular dynamics simulations of peptide carboxylate hydration
Publisher: Royal Society of Chemistry (RSC)
Date: 2006
DOI: 10.1039/B608672A
Abstract: Aqueous solvation of carboxylate groups, as present in the glycine zwitterion and the dipeptide aspartylalanine, is studied employing a force-field that includes distributed multipole electrostatics and induction contributions (Amoebapro: P. Ren and J. W. Ponder, J. Comput. Chem., 2002, 23, 1497 P. Ren and J. W. Ponder, J. Phys. Chem. B, 2003, 107, 5933 J. W. Ponder and D. A. Case, Adv. Protein Chem., 2003, 66, 27). Radial and orientation distribution functions, as well as hydration numbers, are calculated and compared with existing simulation data derived from Car-Parrinello molecular dynamics (CPMD), and also distributed-charge force-fields. Connections are also made with experimental data for solvation of carboxylates in water. Our findings show that Amoebapro yields carboxylate solvation properties in very good agreement with CPMD results, significantly closer agreement than can be obtained from traditional force-fields. We also demonstrate that the influence of solvation on the conformation of the dipeptide is markedly different using Amoebapro compared with the other force-fields.
A predictive model of interfacial interactions between functionalised carbon fibre surfaces cross-linked with epoxy resin
Publisher: Elsevier BV
Date: 05-2018
Determination of Kamlet-Taft parameters for selected solvate ionic liquids
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6CP01216G
Abstract: The normalised polarity E NT and Kamlet–Taft parameters of recently described solvate ionic liquids, composed of lithium bis(trifluoromethyl)sulfonimide (LiTFSI) in tri- ( G3TFSI ) or tetraglyme ( G4TFSI ) have been determined and compared to the parent glyme ( G3 and G4 ).
Machine Learning-Aided Exploration of Ultrahard Materials
Publisher: American Chemical Society (ACS)
Date: 13-09-2022
Archetypal energy landscapes
Publisher: No publisher found
Date: 1998
DOI: 10.1038/29487}
Probing nano-patterned peptide self-organisation at the aqueous graphene interface
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C7NR06441A
Abstract: The peptide sequence GrBP5, IMVTESSDYSSY, is found experimentally to bind to graphene, and ex situ atomic force microscopy indicates the formation of an ordered over-layer on the graphene substrate. It is unclear if these patterns are stable under aqueous conditions. Here, advanced molecular dynamics simulations suggest this patterning cannot be sustained in aqueous solution and suggest ways to realise pattern formation in water.
Related Organisations
Cardiff University
Location: United Kingdom of Great Britain and Northern Ireland
Related Funding Activities
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Amount: $339,525.00
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View Funded ActivityDiscovery Projects - Grant ID: DP180100094
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View Funded ActivityDiscovery Projects - Grant ID: DP140100165
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Amount: $390,000.00
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View Funded ActivityIndustrial Transformation Training Centres - Grant ID: IC210100040
Start Date: 02-2022
End Date: 02-2027
Amount: $4,997,903.00
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View Funded Activity