ORCID Profile
0000-0002-4033-5150
Current Organisation
RMIT University
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
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)
Theoretical and Computational Chemistry | Theory and Design of Materials | Theoretical and Computational Chemistry not elsewhere classified | Theoretical And Computational Chemistry Not Elsewhere Classified | Materials Engineering | Macromolecular and Materials Chemistry | Nanomaterials | Biological And Medical Chemistry | Physical Chemistry Of Macromolecules | Condensed Matter Physics not elsewhere classified | Physical Chemistry Not Elsewhere Classified | Pyrometallurgy | Metals and Alloy Materials | Condensed Matter Physics—Other | Biomolecular modelling and design | Nanotechnology | Condensed Matter Physics | Atmospheric Sciences | Polymers | Composite Materials | Alloy Materials | Medicinal and biomolecular chemistry | Nanomaterials | Structural Biology (incl. Macromolecular Modelling) | Biophysics | Climate Change Processes | Innovation and Technology Management | Macromolecular Chemistry Not Elsewhere Classified | Nanotechnology | Manufacturing Processes and Technologies (excl. Textiles) | Biosensor Technologies | Biomaterials | Theory and design of materials | Biomedical Engineering | Biomaterials | Radiation And Matter | Quantum Chemistry | Theory Of Materials | Cellular Interactions (incl. Adhesion, Matrix, Cell Wall) | Interdisciplinary Engineering Not Elsewhere Classified | Condensed Matter Modelling and Density Functional Theory | Nanobiotechnology | Plasmas And Electrical Discharges
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Chemical Sciences | Expanding Knowledge in Engineering | Chemical sciences | Physical sciences | Biological sciences | Coated Metal and Metal-Coated Products | Paints | Expanding Knowledge in the Medical and Health Sciences | Expanding Knowledge in Technology | Basic Iron and Steel Products | Expanding Knowledge in the Physical Sciences | Expanding Knowledge in the Biological Sciences | Health related to ageing | Physical and Chemical Conditions of Water in Fresh, Ground and Surface Water Environments (excl. Urban and Industrial Use) | Clinical health not specific to particular organs, diseases and conditions | Management of Solid Waste from Manufacturing Activities | Prevention—biologicals (e.g. vaccines) | Organs, diseases and abnormal conditions not elsewhere classified | Climate Change Models | Other | Metals (composites, coatings, bonding, etc.) | Diagnostic methods | Sheet metal products | Health policy evaluation | Polymeric materials (e.g. paints) | Public health not elsewhere classified |
Related Links
Publications
First-principles studies of the structural and electronic properties of pyrite
Publisher:
American Physical Society (APS)
Date:
11-01-2002
Publisher: American Physical Society (APS)
Date: 11-01-2002
Density-functional theory studies of xanthate adsorption on the pyrite FeS2(110) and (111) surfaces
Publisher: AIP Publishing
Date: 18-03-2003
DOI: 10.1063/1.1556076
Abstract: We have used the density functional theory (DFT) method with a plane wave-pseudopotential basis to compute the structure and properties of a model xanthate molecule (HOCS2−) and its adsorption characteristics on the pyrite FeS2(110) and (111) surfaces. Molecular calculations revealed that HOCS2− and CH3CH2OCS2− have similar head group electronic structure and, therefore, the use of the model xanthate is a justifiable approximation in simulations of xanthate head group attachment to FeS2 surfaces. Results from DFT calculations suggest that HOCS2− readily undergoes dissociation at the fourfold coordinated surface Fe on the (110) surface, and the bridging S of the (111) surface. These results suggest that xanthate may undergo chemisorption at defect sites on real FeS2 surfaces, which contain low-coordinate Fe sites and sites in proximity to cleaved S–S bonds.
Surface presentation of functional peptides in solution determines cell internalization efficiency of TAT conjugated nanoparticles
Publisher: American Chemical Society (ACS)
Date: 28-08-2014
DOI: 10.1021/NL5021848
Particle engineering enabled by polyphenol-mediated supramolecular networks
Publisher: Springer Science and Business Media LLC
Date: 23-09-2020
DOI: 10.1038/S41467-020-18589-0
Abstract: We report a facile strategy for engineering erse particles based on the supramolecular assembly of natural polyphenols and a self-polymerizable aromatic dithiol. In aqueous conditions, uniform and size-tunable supramolecular particles are assembled through π–π interactions as mediated by polyphenols. Owing to the high binding affinity of phenolic motifs present at the surface, these particles allow for the subsequent deposition of various materials (i.e., organic, inorganic, and hybrid components), producing a variety of monodisperse functional particles. Moreover, the solvent-dependent disassembly of the supramolecular networks enables their removal, generating a wide range of corresponding hollow structures including capsules and yolk–shell structures. The versatility of these supramolecular networks, combined with their negligible cytotoxicity provides a pathway for the rational design of a range of particle systems (including core–shell, hollow, and yolk–shell) with potential in biomedical and environmental applications.
Refinements in the collection of energy filtered diffraction patterns from disordered materials
Publisher: Elsevier BV
Date: 07-2005
DOI: 10.1016/J.ULTRAMIC.2005.01.002
Abstract: In this paper a method for collecting electron diffraction patterns using a Gatan imaging filter is presented. The method enables high-quality diffraction data to be measured at scattering angles comparable to those that can be obtained using X-ray and neutron diffraction. In addition, the method offers the capability for examining small regions of s le in, for ex le, thin films and nano-structures. Using X-ray, neutron and electron diffraction data collected from the same s le, we demonstrate quantitative agreement between all three. We also present a novel method for obtaining the single scattering contribution to the total diffracted intensity by collecting data at various electron wavelengths. This approach allows pair distribution functions to be determined from electron diffraction in cases where there exists significant multiple scattering.
Engineering Flexible Metal‐Phenolic Networks with Guest Responsiveness via Intermolecular Interactions
Publisher: Wiley
Date: 24-03-2023
Abstract: Flexible metal‐organic materials are of growing interest owing to their ability to undergo reversible structural transformations under external stimuli. Here, we report flexible metal‐phenolic networks (MPNs) featuring stimuli‐responsive behavior to erse solute guests. The competitive coordination of metal ions to phenolic ligands of multiple coordination sites and solute guests (e.g., glucose) primarily determines the responsive behavior of the MPNs, as revealed experimentally and computationally. Glucose molecules can be embedded into the dynamic MPNs upon mixing, leading to the reconfiguration of the metal‐organic networks and thus changes in their physicochemical properties for targeting applications. This study expands the library of stimuli‐responsive flexible metal‐organic materials and the understanding of intermolecular interactions between metal‐organic materials and solute guests, which is essential for the rational design of responsive materials for various applications.
Block Length-Dependent Protein Fouling on Poly(2-oxazoline)-Based Polymersomes: Influence on Macrophage Association and Circulation Behavior.
Publisher: Wiley
Date: 07-06-2022
Abstract: Polymersomes are vesicular structures self-assembled from hiphilic block copolymers and are considered an alternative to liposomes for applications in drug delivery, immunotherapy, biosensing, and as nanoreactors and artificial organelles. However, the limited availability of systematic stability, protein fouling (protein corona formation), and blood circulation studies h ers their clinical translation. Poly(2-oxazoline)s (POx) are valuable antifouling hydrophilic polymers that can replace the current gold-standard, poly(ethylene glycol) (PEG), yet investigations of POx functionality on nanoparticles are relatively sparse. Herein, a systematic study is reported of the structural, dynamic and antifouling properties of polymersomes made of poly(2-methyl-2-oxazoline)-block-poly(dimethylsiloxane)-block-poly(2-methyl-2-oxazoline) (PMOXA-b-PDMS-b-PMOXA). The study relates in vitro antifouling performance of the polymersomes to atomistic molecular dynamics simulations of polymersome membrane hydration behavior. These observations support the experimentally demonstrated benefit of maximizing the length of PMOXA (degree of polymerization (DP) > 6) while keeping PDMS at a minimal length that still provides sufficient membrane stability (DP > 19). In vitro macrophage association and in vivo blood circulation evaluation of polymersomes in zebrafish embryos corroborate these findings. They further suggest that single copolymer presentation on polymersomes is outperformed by blends of varied copolymer lengths. This study helps to rationalize design rules for stable and low-fouling polymersomes for future medical applications.
Microstructure of an industrial char by diffraction techniques and Reverse Monte Carlo modelling
Publisher: Elsevier BV
Date: 2004
Effects of oxidation, pH and lipids on amyloidogenic peptide structure: implications for fibril formation?
Publisher: Springer Science and Business Media LLC
Date: 04-09-2008
DOI: 10.1007/S00249-008-0363-3
Abstract: We have performed experimental and computational studies to investigate the influences of phospholipids, methionine oxidation and acidic pH on amyloid fibril formation by a peptide derived from human apolipoprotein C-II (apoC-II), a known component of proteinaceous atherosclerotic plaques. Fibril growth monitored by thioflavin T fluorescence revealed inhibition under lipid-rich and oxidising conditions. We subsequently performed fully-solvated atomistic molecular dynamics (MD) simulations of the peptide monomer to study its conformations under both fibril favouring (neutral and low pH) and inhibiting (lipid-rich and oxidising) conditions. Examination of the chain topology, backbone hydrogen-bonding patterns and aromatic sidechain orientations of the peptide under different conditions reveals that, while the peptide adopts similar structures under the fibril-favouring conditions, significantly different structures are obtained under fibril-disruptive conditions. Based on our results, we advance hypotheses for the roles of peptide conformation on aggregation and fibrillisation propensities.
Regional DFT—Electronic Stress Tensor Study of Aluminum Nanostructures for Hydrogen Storage
Publisher: AIP
Date: 2009
DOI: 10.1063/1.3108389
Exploring the binding sites and proton diffusion on insulin amyloid fibril surfaces by naphthol-based photoacid fluorescence and molecular simulations
Publisher: Springer Science and Business Media LLC
Date: 24-07-2017
DOI: 10.1038/S41598-017-06030-4
Abstract: The diffusion of protons along biological surfaces and the interaction of biological structures with water are fundamental areas of interest in biology and chemistry. Here, we examine the surface of insulin amyloid fibrils and follow the binding of small molecules (photoacids) that differ according to the number and location of their sulfonic groups. We use transient fluorescence combined with a spherically-symmetric diffusion theory to show that the binding mode of different photoacids determines the efficiency of proton dissociation from the photoacid and the dimensionality of the proton’s diffusion. We use molecular dynamics simulations to examine the binding mode and mechanism of the photoacids and its influence on the unique kinetic rates and diffusion properties of the photoacid’s dissociated proton, where we also suggest a proton transfer process between one of the photoacids to proximal histidine residues. We show that the photoacids can be used as fluorescent markers for following the progression of amyloidogenic processes. The detailed characterisation of different binding modes to the surface of amyloid fibrils paves the way for better understanding of the binding mechanism of small molecules to amyloid fibrils.
Single-step homogeneous immunoassays utilizing epitope-tagged gold nanoparticles: On the mechanism, feasibility, and limitations
Publisher: American Chemical Society (ACS)
Date: 15-08-2014
DOI: 10.1021/CM500535P
Understanding and Designing the Gold-Bio Interface: Insights from Simulations
Publisher: Wiley
Date: 23-03-2016
Abstract: Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.
Exploring the folding free energy landscape of insulin using bias exchange metadynamics
Publisher: American Chemical Society (ACS)
Date: 25-02-2009
DOI: 10.1021/JP809776V
Abstract: The bias exchange metadynamics (BE-META) technique was applied to investigate the folding mechanism of insulin, one of the most studied and biologically important proteins. The BE-META simulations were performed starting from an extended conformation of chain B of insulin, using only eight replicas and seven reaction coordinates. The folded state, together with the intermediate states along the folding pathway were identified and their free energy was determined. Three main basins were found separated from one another by a large free energy barrier. The characteristic native fold of chain B was observed in one basin, while the other two most populated basins contained "molten-globule" conformations stabilized by electrostatic and hydrophobic interactions, respectively. Transitions between the three basins occur on the microsecond time scale. The implications and relevance of this finding to the folding mechanisms of insulin were investigated.
Density functional theory study of hydrogen adsorption on Al12 cages
Publisher: American Physical Society (APS)
Date: 02-05-2007
Layer-by-Layer Self-Assembly of Polymer Films and Capsules through Coiled-Coil Peptides
Publisher: American Chemical Society (ACS)
Date: 13-03-2026
Residue-Specific Solvation-Directed Thermodynamic and Kinetic Control over Peptide Self-Assembly with 1D/2D Structure Selection
Publisher: American Chemical Society (ACS)
Date: 23-01-2019
Surface enhanced Raman scattering artificial nose for high dimensionality fingerprinting
Publisher: Springer Science and Business Media LLC
Date: 10-01-2020
DOI: 10.1038/S41467-019-13615-2
Abstract: Label-free surface-enhanced Raman spectroscopy (SERS) can interrogate systems by directly fingerprinting their components’ unique physicochemical properties. In complex biological systems however, this can yield highly overlapping spectra that hinder s le identification. Here, we present an artificial-nose inspired SERS fingerprinting approach where spectral data is obtained as a function of sensor surface chemical functionality. Supported by molecular dynamics modeling, we show that mildly selective self-assembled monolayers can influence the strength and configuration in which analytes interact with plasmonic surfaces, ersifying the resulting SERS fingerprints. Since each sensor generates a modulated signature, the implicit value of increasing the dimensionality of datasets is shown using cell lysates for all possible combinations of up to 9 fingerprints. Reliable improvements in mean discriminatory accuracy towards 100% are achieved with each additional surface functionality. This arrayed label-free platform illustrates the wide-ranging potential of high-dimensionality artificial-nose based sensing systems for more reliable assessment of complex biological matrices.
Surface heterogeneity: A friend or foe of protein adsorption-insights from theoretical simulations
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6FD00050A
Abstract: A lack in the detailed understanding of mechanisms through which proteins adsorb or are repelled at various solid/liquid interfaces limits the capacity to rationally design and produce more sophisticated surfaces with controlled protein adsorption in both biomedical and industrial settings. To date there are three main approaches to achieve anti biofouling efficacy, namely chemically adjusting the surface hydrophobicity and introducing various degrees of surface roughness, or a combination of both. More recently, surface nanostructuring has been shown to have an effect on protein adsorption. However, the current resolution of experimental techniques makes it difficult to investigate these three phase systems at the molecular level. In this molecular dynamics study we explore in all-atom detail the adsorption process of one of the most surface active proteins, EAS hydrophobin, known for its versatile ability to self-assemble on both hydrophobic and hydrophilic surfaces forming stable monolayers that facilitate further biofilm growth. We model the adsorption of this protein on organic ligand protected silica surfaces with varying degrees of chemical heterogeneity and roughness, including fully homogenous hydrophobic and hydrophilic surfaces for comparison. We present a detailed characterisation of the functionalised surface structure and dynamics for each of these systems, and the effect the ligands have on interfacial water, the adsorption process and conformational rearrangements of the protein. Results suggest that the ligand arrangement that produces the highest hydrophilic chain mobility and the lack of significant hydrophobic patches shows the most promising anti-fouling efficacy toward hydrophobin. However, the presence on the protein surface of a flexible loop with hipathic character (the Cys3–Cys4 loop) is seen to facilitate EAS adsorption on all surfaces by enabling the protein to match the surface pattern.
Molecular Mechanism of Stabilization of Thin Films for Improved Water Evaporation Protection
Publisher: American Chemical Society (ACS)
Date: 11-11-2013
DOI: 10.1021/LA402275P
Abstract: All-atom molecular dynamics simulations and experimental characterization have been used to examine the structure and dynamics of novel evaporation-suppressing films where the addition of a water-soluble polymer to an ethylene glycol monooctadecyl ether monolayer leads to improved water evaporation resistance. Simulations and Langmuir trough experiments demonstrate the surface activity of poly(vinyl pyrrolidone) (PVP). Subsequent MD simulations performed on the thin films supported by the PVP sublayer show that, at low surface pressures, the polymer tends to concentrate at the film/water interface. The simulated atomic concentration profiles, hydrogen bonding patterns, and mobility analyses of the water-polymer-monolayer interfaces reveal that the presence of PVP increases the atomic density near the monolayer film, improves the film stability, and reduces the mobility of interfacial waters. These observations explain the molecular basis of the improved efficacy of these monolayer olymer systems for evaporation protection of water and can be used to guide future development of organic thin films for other applications.
Membrane Permeating Macrocycles: Design Guidelines from Machine Learning
Publisher: American Chemical Society (ACS)
Date: 30-09-2022
Abstract: The ability to predict cell-permeable candidate molecules has great potential to assist drug discovery projects. Large molecules that lie beyond the Rule of Five (bRo5) are increasingly important as drug candidates and tool molecules for chemical biology. However, such large molecules usually do not cross cell membranes and cannot access intracellular targets or be developed as orally bioavailable drugs. Here, we describe a random forest (RF) machine learning model for the prediction of passive membrane permeation rates developed using a set of over 1000 bRo5 macrocyclic compounds. The model is based on easily calculated chemical features/descriptors as independent variables. Our random forest (RF) model substantially outperforms a multiple linear regression model based on the same features and achieves better performance metrics than previously reported models using the same underlying data. These features include: (1) polar surface area in water, (2) the octanol-water partitioning coefficient, (3) the number of hydrogen-bond donors, (4) the sum of the topological distances between nitrogen atoms, (5) the sum of the topological distances between nitrogen and oxygen atoms, and (6) the multiple molecular path count of order 2. The last three features represent molecular flexibility, the ability of the molecule to adopt different conformations in the aqueous and membrane interior phases, and the molecular "chameleonicity." Guided by the model, we propose design guidelines for membrane-permeating macrocycles. It is anticipated that this model will be useful in guiding the design of large, bioactive molecules for medicinal chemistry and chemical biology applications.
Fluorinated Metal–Organic Coatings with Selective Wettability
Publisher: American Chemical Society (ACS)
Date: 25-06-2021
DOI: 10.1021/JACS.1C04396
Monte Carlo based modeling of carbon nanostructured surfaces
Publisher: American Physical Society (APS)
Date: 13-09-2005
Simulations of nanoindentation of polymer surfaces: Effects of surface cross-linking on adhesion and hardness
Publisher: American Chemical Society (ACS)
Date: 12-11-2010
DOI: 10.1021/JP9087546
Fate of Liposomes in the Presence of Phospholipase C and D: From Atomic to Supramolecular Lipid Arrangement
Publisher: American Chemical Society (ACS)
Date: 06-08-2018
Effects of Size and Functionalization on the Structure and Properties of Graphene Oxide Nanoflakes: An in Silico Investigation
Publisher: American Chemical Society (ACS)
Date: 20-09-2018
Electric field effects on insulin chain-B conformation
Publisher: American Chemical Society (ACS)
Date: 04-11-2005
DOI: 10.1021/JP052742Q
Abstract: The response of proteins to different forms of stress continues to be a topic of major interest, especially with the proliferation of electromagnetic devices conjectured to have detrimental effects on human health. In this paper, we have performed molecular dynamics simulations on insulin chain-B under the influence of both static and oscillating electric fields, ranging from 10(7) to 10(9) V/m. We have found that both variants have an effect on the normal behavior of the protein, with oscillating fields being more disruptive to the structure as compared to static fields of similar effective strength. The application of a static field had a stabilizing effect on the secondary structure, restricting the inherent flexibility that is crucial for insulin's biological activity.
Hydration Layer Structure of Biofouling-Resistant Nanoparticles
Publisher: American Chemical Society (ACS)
Date: 18-10-2018
Abstract: Hydrophilic surface chemistries can strongly bind water to produce surfaces that are highly resistant to protein adsorption and fouling. The interfacial bound water and its distinct properties have intrigued researchers for decades, yet the relationship between the water three-dimensional structure and function in antifouling coatings remains elusive. Here, we use hydrophilic, epoxy organosilane modified silica nanoparticles to demonstrate cheap, robust, and practically applied coatings that we discover have broad-ranging, ultralow fouling properties when challenged by various proteins, bacteria, and fungal spores. To understand their excellent antifouling properties, frequency modulation-atomic force microscopy is used to directly observe the interfacial water structure at subatomic resolution, which we validate using all-atom molecular dynamic simulations that strikingly predict similar structures of water layers on the original and ultralow fouling surfaces. The convergence of experimental and modeling data reveals that suitably spaced, flexible chains with hydrophilic groups interact with water molecules to produce a connective, quasi-stable layer, consisting of dynamic interfacial water, that provides a basis for antifouling performance of ultrathin, hydrophilic surface chemistries.
Design of Lipid-Based Nanocarriers via Cation Modulation of Ethanol-Interdigitated Lipid Membranes
Publisher: American Chemical Society (ACS)
Date: 28-09-2021
Inhibition of peptide aggregation by lipids: Insights from coarse-grained molecular simulations
Publisher: Elsevier BV
Date: 02-2011
DOI: 10.1016/J.JMGM.2010.11.001
Abstract: The amyloidogenic peptide apolipoprotein C-II(60-70) is known to exhibit lipid-dependent aggregation behaviour. While the peptide rapidly forms amyloid fibrils in solution, fibrillization is completely inhibited in the presence of lipids. In order to obtain molecular-level insights into the mechanism of lipid-dependent fibril inhibition, we have employed molecular dynamics simulations in conjunction with a coarse-grained model to study the aggregation of an amyloidogenic peptide, apoC-II(60-70), in the absence and presence of a short-chained lipid, dihexanoylphosphatidylcholine (DHPC). Simulation of a solution of initially dispersed peptides predicts the rapid formation of an elongated aggregate with an internal hydrophobic core, while charged sidechains and termini are solvent-exposed. Inter-peptide interactions between aromatic residues serve as the principal driving force for aggregation. In contrast, simulation of a mixed peptide-DHPC solution predicts markedly reduced peptide aggregation kinetics, with subsequent formation of a suspension of aggregates composed of smaller peptide oligomers partially inserted into lipid micelles. Both effects are caused by strong interactions between the aromatic residues of the peptide with the lipid hydrophobic tails. This suggests that lipid-induced aggregate inhibition is partly due to the preferential binding of peptide aromatic sidechains with lipid hydrophobic tails, reducing inter-peptide hydrophobic interactions. Furthermore, our simulations suggest that the morphology of peptide aggregates is strongly dependent on their local lipid environment, with greater contacts with lipids resulting in the formation of more elongated aggregates. Finally, we find that peptides disrupt lipid self-assembly, which has possible implications for explaining the cytotoxicity of peptide oligomers.
The Enigma of Amyloid Forming Proteins: Insights From Molecular Simulations
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/CH19059
Abstract: Molecular level insight into the interplay between protein sequence, structure, and conformational dynamics is crucial for the comprehensive understanding of protein folding, misfolding, and aggregation phenomena that are pertinent to the formation of amyloid fibrils implicated in several degenerative diseases. Computational modelling provides insight into protein behaviour at spatial and temporal resolution still largely outside the reach of experiments. Herein we present an account of our theoretical modelling research conducted in collaboration with several experimental groups where we explored the effects of local environment on the structure and aggregation propensity of several types of amyloidogenic peptides and proteins, including apolipoprotein C-II, insulin, amylin, and amyloid-β using a variety of computational approaches.
“Exact” surface free energies of iron surfaces using a modified embedded atom method potential and λ integration
Publisher: AIP Publishing
Date: 10-02-2004
DOI: 10.1063/1.1637334
Abstract: Previously a new universal λ-integration path and associated methodology was developed for the calculation of “exact” surface and interfacial free energies of solids. Such a method is in principle applicable to any intermolecular potential function, including those based on ab initio methods, but in previous work the method was only tested using a relatively simple embedded atom method iron potential. In this present work we apply the new methodology to the more sophisticated and more accurate modified embedded atom method (MEAM) iron potential, where application of other free- energy methods would be extremely difficult due to the complex many-body nature of the potential. We demonstrate that the new technique simplifies the process of obtaining “exact” surface free energies by calculating the complete set of these properties for the low index surface faces of bcc and fcc solid iron structures. By combining these data with further calculations of liquid surface tensions we obtain the first complete set of exact surface free energies for the solid and liquid phases of a realistic MEAM model system. We compare these predictions to various experimental and theoretical results.
Characterization of Metallurgical Chars by Small Angle Neutron Scattering
Publisher: American Chemical Society (ACS)
Date: 06-08-2002
DOI: 10.1021/EF010107N
Lipids Enhance Apolipoprotein C-II-Derived Amyloidogenic Peptide Oligomerization but Inhibit Fibril Formation
Publisher: American Chemical Society (ACS)
Date: 19-06-2009
DOI: 10.1021/JP901051N
Abstract: We investigated the effect of submicellar lipids on amyloid fibril formation. Thioflavin T fluorescence studies showed that submicellar levels of the short-chain phospholipids, dipentanoylphosphatidylcholine and dihexanoylphosphatidylcholine, strongly inhibited amyloid fibril formation by an 11-residue peptide derived from human apolipoprotein C-II (apoC-II(60-70)). In contrast, sedimentation equilibrium analysis of these peptide-lipid mixtures indicated the presence of soluble oligomeric complexes. To acquire insight into the atomic level influences of these lipids on the initial stages of aggregation of the peptide, we performed molecular dynamics (MD) simulations coupled with umbrella s ling to determine dimerization free energies of a number of beta-stranded and random coil dimer complexes, both in the presence and absence of lipids. The simulations indicate that, in contrast to their inhibitory effects on fibril formation, short-chain phospholipids promote the formation and stabilization of dimers by enhancing intersubunit hydrophobic interactions. On the basis of these experimental and computational results, we propose that peptide-bound lipids can inhibit amyloid fibril formation by trapping of dimers and other oligomeric species in erse nonfibril forming conformations, reducing their likelihood of acquiring subunit conformations prone to fibril nucleation and growth. In light of the demonstrated cytotoxicity of amyloid peptide oligomers, our results suggest that, by enhancing the stability of oligomeric peptide species, the presence of solvated lipids may contribute to the cytotoxicity of fibrillogenic proteins and peptides.
Effect of Surface Composition and Atomic Roughness on Interfacial Adhesion between Polyester and Amorphous Carbon
Publisher: American Chemical Society (ACS)
Date: 02-2007
DOI: 10.1021/JP064554L
Density Functional Theory Study of Hydrogen Bonding in Ionic Molecular Materials
Publisher: American Chemical Society (ACS)
Date: 12-09-2006
DOI: 10.1021/JP062239T
Abstract: Crystal structures are usually described in geometric terms. However, it is the energetics of intermolecular interactions that determine the chemical and physical properties of molecular materials.(1) In this paper, we use density functional theory (DFT) in combination with numerical basis sets to analyze the hydrogen bonding interactions in a family of novel ionic molecular materials. We find that the calculated binding energies are consistent with those of other ionic hydrogen bonded systems. We also examine electron density distributions for the systems of interest to gain insight into the nature of the hydrogen bonding interaction and investigate the effects of different aspects of the crystal field on the geometry of the hydrogen bond.
Metal-dependent inhibition of amyloid fibril formation: synergistic effects of cobalt–tannic acid networks
Publisher: Royal Society of Chemistry (RSC)
Date: 2019
DOI: 10.1039/C8NR09221D
Abstract: Cobalt–tannic acid-coated gold nanoparticles are found to better inhibit amyloid fibril formation than other metal-based tannic acid-coated particles.
Adhesion between Graphite and Modified Polyester Surfaces: A Theoretical Study
Publisher: American Chemical Society (ACS)
Date: 19-08-2005
DOI: 10.1021/JP0523524
Abstract: This study examines the adhesion of graphite to functionalized polyester surfaces using a range of qualitative and quantitative measures of theoretical adhesion. Modifications to the polyester surfaces include the addition of hydroxyl, carboxyl, or fluorine substituents with coverages of 0.4 and 0.9 groups per nm(2). In each case, the introduction of substituents to the surface of the polyester was calculated to lead to reduced adhesion to graphite. Effects of surface relaxation on adhesion are studied by employing different simulation protocols. The theoretical results suggest one mechanism to reduce adhesion to carbonaceous solids is to increase atomic roughness using strongly hydrophilic or alternatively strongly hydrophobic substituents.
Quantum Monte Carlo Study of Water Molecule: A Preliminary Investigation
Publisher: CSIRO Publishing
Date: 2004
DOI: 10.1071/CH04135
Abstract: The Quantum Monte Carlo (QMC) technique[1] offers advantages of good scaling with system size (number of electrons) and an ability to uniformly recover over 90% of the electron correlation energy, compared to the more conventional quantum chemistry approaches. For the water molecule in its ground state, it has been shown[2] that the QMC method gives results that are comparable in accuracy to those obtained by the best available conventional methods, while at the same time using much more modest basis sets than is necessary with these methods. Furthermore, the effect of the orbitals needed for these QMC calculations (which may be obtained from either Hartree–Fock or Density Functional Theory) has been investigated. Both the advantages and disadvantages of the QMC method are discussed.
Monolayer Structure and Evaporation Resistance: A Molecular Dynamics Study of Octadecanol on Water
Publisher: American Chemical Society (ACS)
Date: 03-03-2010
DOI: 10.1021/JP909544A
Abstract: This study examines intermolecular interactions of a monolayer of octadecanol (CH(3)(CH(2))(17)OH) on water as a function of surface density and temperature, using classical molecular dynamics simulations. We observe increased interaction between the alkyl chains (van der Waals) and hydroxyl groups (H-bonding) with increased surface density, which leads to increased order and packing within the monolayer. We also identified clear trends in the intermolecular interactions, ordering and packing of the monolayer molecules as a function of temperature. The observed trends can be closely related to features of the current empirical theories of evaporation resistance.
Ordering surfaces on the nanoscale: Implications for protein adsorption
Publisher: American Chemical Society (ACS)
Date: 05-01-2011
DOI: 10.1021/JA108285U
Abstract: Monolayer-protected metal nanoparticles (MPMNs) are a newly discovered class of nanoparticles with an ordered, striped domain structure that can be readily manipulated by altering the ratio of the hydrophobic to hydrophilic ligands. This property makes them uniquely suited to systematic studies of the role of nanostructuring on biomolecule adsorption, a phenomenon of paramount importance in biomaterials design. In this work, we examine the interaction of the simple, globular protein cytochrome C (Cyt C) with MPMN surfaces using experimental protein assays and computational molecular dynamics simulations. Experimental assays revealed that adsorption of Cyt C generally increased with increasing surface polar ligand content, indicative of the dominance of hydrophilic interactions in Cyt C-MPMN binding. Protein-surface adsorption enthalpies calculated from computational simulations employing rigid-backbone coarse-grained Cyt C and MPMN models indicate a monotonic increase in adsorption enthalpy with respect to MPMN surface polarity. These results are in qualitative agreement with experimental results and suggest that Cyt C does not undergo significant structural disruption upon adsorption to MPMN surfaces. Coarse-grained and atomistic simulations furthermore elucidated the important role of lysine in facilitating Cyt C adsorption to MPMN surfaces. The hipathic character of the lysine side chain enables it to form close contacts with both polar and nonpolar surface ligands simultaneously, rendering it especially important for interactions with surfaces composed of adjacent nanoscale chemical domains. The importance of these structural characteristics of lysine suggests that proteins may be engineered to specifically interact with nanomaterials by targeted incorporation of unnatural amino acids possessing dual affinity to differing chemical motifs.
Adsorption of NO and NO2 on the ZnO(2 over(1, ̄) over(1, ̄) 0) surface: A DFT study
Publisher: Elsevier BV
Date: 12-2009
Computer simulation of structure and properties of crosslinked polymers: application to epoxy resins
Publisher: Elsevier BV
Date: 02-2002
First-principles study of metallic iron interfaces
Publisher: Elsevier BV
Date: 04-2002
Comparison of global-minimum-energy conformations of phospholipids
Publisher: Elsevier BV
Date: 11-1991
Effect of sulfur coverage on Fe(110) adhesion: A DFT study
Publisher: American Chemical Society (ACS)
Date: 05-2005
DOI: 10.1021/JP045069Y
Abstract: The effect of adsorbed S at different coverages on the adhesion of Fe(110) surfaces in match and mismatch is examined using density functional theory (DFT). S is adsorbed in atop, bridge, and 4-fold hollow sites on one side of the interface in c(2 x 2) and p(1 x 1) arrangements, corresponding to coverages of 1/2 and 1 monolayer, respectively. The calculated adhesion energy values at different interfacial separations are fitted to the universal binding energy relation, and the effect of the S coverages on the adhesive strength is analyzed. The effect of relaxation of the interfaces at equilibrium is also investigated, and the resulting interfacial structures and related magnetic and charge density properties are compared.
Density functional theory modelling of ZnO (1 0 over(1, ̄) 0) and ZnO (2 over(1, ̄) over(1, ̄) 0) surfaces: Structure, properties and adsorption of N2 O
Publisher: Elsevier BV
Date: 02-2010
DFT study of H adsorption on magnesium-doped aluminum clusters
Publisher: American Chemical Society (ACS)
Date: 17-02-2010
DOI: 10.1021/JP911013T
Abstract: In this study we use density functional theory (DFT) to investigate the properties and H adsorption characteristics of structural isomers of the magnesium-doped aluminum cluster, Al(12)Mg. Our results show that the exohedral structure (exo-MgAl(12)) is significantly lower in energy (1.59 eV) than the endohedral structure (endo-Al(12)Mg) however, the exohedral structure shows significant structural distortion. Our calculations demonstrate that H binds favorably to both exohedral and endohedral structures. Generally, binding energies for H to both clusters range from approximately 2.3 to 2.5 eV with atop positions slightly favored, except for addition directly to the exohedral Mg atom, where the binding energy drops to 1.92 eV. We include a DFT molecular dynamics study of the endo-Al(12)Mg and endo-Al(12)MgH clusters which revealed the isomerization to the respective exostructures at finite temperatures (100-600 K). Interestingly, hydrogen adsorption appears to enhance the isomerization.
Density-functional theory studies of pyrite FeS2 () and () surfaces
Publisher: Elsevier BV
Date: 11-2002
Investigation of lignin-water interactions by molecular simulation
Publisher: Informa UK Limited
Date: 10-2002
Molecular Interactions behind the Synergistic Effect in Mixed Monolayers of 1-Octadecanol and Ethylene Glycol Monooctadecyl Ether
Publisher: American Chemical Society (ACS)
Date: 22-03-2013
DOI: 10.1021/JP401027C
Abstract: Mixed monolayers of 1-octadecanol (C18OH) and ethylene glycol monooctadecyl ether (C18E1) were studied to assess their evaporation suppressing performance. An unexpected increase in performance and stability was found around the 0.5:0.5 bicomponent mixture and has been ascribed to a synergistic effect of the monolayers. Molecular dynamics simulations have attributed this to an additional hydrogen bonding interaction between the monolayer and water, due to the exposed ether oxygen of C18E1 in the mixed system compared to the same ether oxygen in the pure C18E1 system. This interaction is maximized around the 0.5:0.5 ratio due to the particular interfacial geometry associated with this mixture.
Nanomaterials in biological environment: A review of computer modelling studies
Publisher: Springer Science and Business Media LLC
Date: 14-12-2011
DOI: 10.1007/S00249-010-0651-6
Abstract: Nanotechnology is set to impact a vast range of fields, including computer science, materials technology, engineering/manufacturing and medicine. As nanotechnology grows so does exposure to nanostructured materials, thus investigation of the effects of nanomaterials on biological systems is paramount. Computational techniques can allow investigation of these systems at the nanoscale, providing insight into otherwise unexaminable properties, related to both the intentional and unintentional effects of nanomaterials. Herein, we review the current literature involving computational modelling of nanoparticles and biological systems. This literature has highlighted the common modes in which nanostructured materials interact with biological molecules such as membranes, peptides roteins and DNA. Hydrophobic interactions are the most favoured, with π-stacking of the aromatic side-chains common when binding to a carbonaceous nanoparticle or surface. van der Waals forces are found to dominate in the insertion process of DNA molecules into carbon nanotubes. Generally, nanoparticles have been observed to disrupt the tertiary structure of proteins due to the curvature and atomic arrangement of the particle surface. Many hydrophobic nanoparticles are found to be able to transverse a lipid membrane, with some nanoparticles even causing mechanical damage to the membrane, thus potentially leading to cytotoxic effects. Current computational techniques have revealed how some nanoparticles interact with biological systems. However, further research is required to determine both useful applications and possible cytotoxic effects that nanoparticles may have on DNA, protein and membrane structure and function within biosystems.
Applications: general discussion
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6FD90051H
The structure of disordered carbon solids studied using a hybrid reverse Monte Carlo algorithm
Publisher: IOP Publishing
Date: 15-04-2005
An Active Site Inhibitor Induces Conformational Penalties for ACE2 Recognition by the Spike Protein of SARS-CoV-2
Publisher: American Chemical Society (ACS)
Date: 03-03-2021
Rational design of monolayers for improved water evaporation mitigation
Publisher: Elsevier BV
Date: 12-2012
Translocation of silica nanospheres through giant unilamellar vesicles (GUVs) induced by a high frequency electromagnetic field
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1RA05459G
Abstract: Membrane model systems capable of mimicking live cell membranes were used for the first time in studying the effects arising from electromagnetic fields (EMFs) of 18 GHz where membrane permeability was observed following exposure.
Polymorphism in disease-related apolipoprotein C-II amyloid fibrils: a structural model for rod-like fibrils
Publisher: Wiley
Date: 09-06-2018
DOI: 10.1111/FEBS.14517
Abstract: Human apolipoprotein (apo) C-II is one of several plasma apolipoproteins that form amyloid deposits in vivo and is an independent risk factor for cardiovascular disease. Lipid-free apoC-II readily self-assembles into twisted-ribbon amyloid fibrils but forms straight, rod-like amyloid fibrils in the presence of low concentrations of micellar phospholipids. Charge mutations exerted significantly different effects on rod-like fibril formation compared to their effects on twisted-ribbon fibril formation. For instance, the double mutant, K30D-D69K apoC-II, readily formed twisted-ribbon fibrils, while the rate of rod-like fibril formation in the presence of micellar phospholipid was negligible. Structural analysis of rod-like apoC-II fibrils, using hydrogen-deuterium exchange and NMR analysis showed exchange protection consistent with a core cross-β structure comprising the C-terminal 58-76 region. Molecular dynamics simulations of fibril arrangements for this region favoured a parallel cross-β structure. X-ray fibre diffraction data for aligned rod-like fibrils showed a major meridional spacing at 4.6 Å and equatorial spacings at 9.7, 23.8 and 46.6 Å. The latter two equatorial spacings are not observed for aligned twisted-ribbon fibrils and are predicted for a model involving two cross-β fibrils in an off-set antiparallel structure with four apoC-II units per rise of the β-sheet. This model is consistent with the mutational effects on rod-like apoC-II fibril formation. The lipid-dependent polymorphisms exhibited by apoC-II fibrils could determine the properties of apoC-II in renal amyloid deposits and their potential role in the development of cardiovascular disease.
Hydrogen/Deuterium Exchange and Molecular Dynamics Analysis of Amyloid Fibrils Formed by a D69K Charge-Pair Mutant of Human Apolipoprotein C-II
Publisher: American Chemical Society (ACS)
Date: 03-08-2015
DOI: 10.1021/ACS.BIOCHEM.5B00535
Abstract: Plasma apolipoproteins form hipathic α helices in lipid environments but in the lipid-free state show a high propensity to form β structure and self-associate into amyloid fibrils. The widespread occurrence of apolipoproteins in amyloid plaques suggests disease-related roles, specifically in atherosclerosis. To reconcile the dual abilities of apolipoproteins to form either α helices or cross-β sheet structures, we examined fibrils formed by human apolipoprotein C-II (apoC-II). A structural model for apoC-II fibrils shows a cross-β core with parallel β strands, including a buried K30-D69 charge pair. We investigated the effect of abolishing this charge pair in mutant D69K apoC-II. Fluorescence studies indicated more rapid fibril formation and less solvent accessibility of tryptophan (W26) in D69K apoC-II fibrils than in wild-type (WT) fibrils. X-ray diffraction data of aligned D69K apoC-II fibrils yielded a typical cross-β structure with increased β sheet spacing compared to that of WT fibrils. Hydrogen/deuterium (H/D) exchange patterns were similar for D69K apoC-II fibrils compared to WT fibrils, albeit with an overall reduction in the level of slow H/D exchange, particularly around residues 29-32. Molecular dynamics simulations indicated reduced β strand content for a model D69K apoC-II tetramer compared to the WT tetramer and confirmed an expansion of the cross-β spacing that contributed to the formation of a stable charge pair between K69 and E27. The results highlight the importance of charge-pair interactions within the apoC-II fibril core, which together with numerous salt bridges in the flexible connecting loop play a major role in the ability of lipid-free apoC-II to form stable cross-β fibrils.
On simulation methods to compute surface and interfacial free energies of disordered solids
Publisher: AIP Publishing
Date: 29-04-2002
DOI: 10.1063/1.1470199
Abstract: We study λ-integration paths, specifically designed for calculating “exact” surface and interfacial free energies of solids at elevated temperatures using molecular dynamics or Monte Carlo simulation methods. We compare various paths with the standard technique of thermodynamic integration by application to the surface free energy for the (100) and (110) faces of alpha iron using embedded atom method (EAM) potentials. We demonstrate which paths are completely reversible at high temperatures and show consistency of results for these paths. The λ-integration paths can be applied with confidence to find equilibrium surface free energies, within the limits of the surface area, intermolecular potentials and other approximations implicit to the simulation methods used.
Gold Nanoparticles: Understanding and Designing the Gold-Bio Interface: Insights from Simulations (Small 18/2016)
Publisher: Wiley
Date: 05-2016
Abstract: Computational modeling is a virtual microscope providing molecular insight into the complex interactions occurring at nano-bio interfaces. The image shows the atomistic landscape of a peptide-adlayer on gold nanoparticles, providing the physicochemical information needed to tailor the design of efficient colorimetric biosensors. The successes and challenges of theoretical simulations in facilitating gold nanomaterial design for biomedicine are reviewed on page 2395 by I. Yarovsky and co-workers.
Influence of fatty acid composition on the structure and stability of fatty acid complexes with vitamin E
Publisher: Elsevier BV
Date: 1992
Density functional theory study of the relaxation and energy of iron surfaces
Publisher: Elsevier BV
Date: 07-2002
Solution Conditions Affect the Ability of the K30D Mutation to Prevent Amyloid Fibril Formation by Apolipoprotein C-II: Insights from Experiments and Theoretical Simulations
Publisher: American Chemical Society (ACS)
Date: 29-06-2016
DOI: 10.1021/ACS.BIOCHEM.6B00266
Abstract: Apolipoproteins form hipathic helical structures that bind lipid surfaces. Paradoxically, lipid-free apolipoproteins display a strong propensity to form cross-β structure and self-associate into disease-related amyloid fibrils. Studies of apolipoprotein C-II (apoC-II) amyloid fibrils suggest that a K30-D69 ion pair accounts for the dual abilities to form helix and cross-β structure. Consistent with this is the observation that a K30D mutation prevents fibril formation under standard fibril forming conditions. However, we found that fibril formation by K30D apoC-II proceeded readily at low pH and a higher salt or protein concentration. Structural analysis demonstrated that K30D apoC-II fibrils at pH 7 have a structure similar to that of the wild-type fibrils but are less stable. Molecular dynamics simulations of the wild-type apoC-II fibril model at pH 7 and 3 showed that the loss of charge on D69 at pH 3 leads to greater separation between residues K30 and D69 within the fibril with a corresponding reduction in β-strand content around residue 30. In contrast, in simulations of the K30D mutant model at pH 7 and 3, residues D30 and D69 moved closer at pH 3, accompanied by an increase in β-strand content around residue 30. The simulations also demonstrated a strong dominance of inter- over intramolecular contacts between ionic residues of apoC-II and suggested a cooperative mechanism for forming favorable interactions between the in idual strands under different conditions. These observations demonstrate the important role of the buried K30-D69 ion pair in the stability and solution properties of apoC-II amyloid fibrils.
Metal Surfaces and Interfaces: Properties from Density Functional Theory
Publisher: Wiley
Date: 05-07-2011
Interaction of hydrogen with ZnO nanopowders - Evidence of hydroxyl group formation
Publisher: IOP Publishing
Date: 08-12-2012
DOI: 10.1088/0957-4484/23/1/015705
Abstract: There have been many investigations to reveal the nature of the hydrogen gas and ZnO nanopowder interaction at elevated temperatures, while at present no conclusive description of such an interaction has been confidently reported. In this work, we demonstrate that a hydroxyl group is formed during this interaction, depending on size and relative crystallinity of nanopowders. Our in situ Raman spectroscopy investigations show that the interaction directly affects the intensity of the Raman signal at 483 cm(-1), relative to the peak at 519 cm(-1). Ex situ x-ray diffraction (XRD) and infrared spectroscopy also show extra peaks at 44° and 1618 cm(-1), respectively, after hydrogenation. These peaks were all identified as surface hydroxyl groups, which can be related to the formation of water on the ZnO nanopowder surfaces.
Modular assembly of superstructures from polyphenol-functionalized building blocks
Publisher: Springer Science and Business Media LLC
Date: 10-10-2016
Abstract: The organized assembly of particles into superstructures is typically governed by specific molecular interactions or external directing factors associated with the particle building blocks, both of which are particle-dependent. These superstructures are of interest to a variety of fields because of their distinct mechanical, electronic, magnetic and optical properties. Here, we establish a facile route to a erse range of superstructures based on the polyphenol surface-functionalization of micro- and nanoparticles, nanowires, nanosheets, nanocubes and even cells. This strategy can be used to access a large number of modularly assembled superstructures, including core-satellite, hollow and hierarchically organized supraparticles. Colloidal-probe atomic force microscopy and molecular dynamics simulations provide detailed insights into the role of surface functionalization and how this facilitates superstructure construction. Our work provides a platform for the rapid generation of superstructured assemblies across a wide range of length scales, from nanometres to centimetres.
Effect of frequency on insulin response to electric field stress
Publisher: American Chemical Society (ACS)
Date: 05-2007
DOI: 10.1021/JP067248G
Abstract: There are many unanswered questions regarding the precise way in which proteins respond to external stress. Since the function of proteins is critically linked to their three-dimensional structures, exposure to any form of stress which may induce changes in conformation can potentially initiate severe cellular dysfunction. This is particularly relevant with regard to the increasing presence of electromagnetic devices in today's environment and the possible effects on human health. Previously, we investigated the effect of electric field of various strengths on insulin chain-B under static and oscillating conditions. This paper expands on our previous work by subjecting the peptide to an oscillating electric field of different frequencies. We observed a frequency-dependent effect where the application of lower-frequency oscillating fields resulted in static-field-like behavior of the peptide, whereby the intrinsic flexibility of the protein is constrained, thus potentially restricting access to the protein's active state.
Molecular dynamics study of polyester surfaces and fullerene particles in aqueous environment
Publisher: American Chemical Society (ACS)
Date: 23-10-2008
DOI: 10.1021/JP804840F
Hydration and Dynamics of Ligands Determine the Antifouling Capacity of Functionalized Surfaces
Publisher: American Chemical Society (ACS)
Date: 21-11-2019
Surface Dynamics and Ligand–Core Interactions of Quantum Sized Photoluminescent Gold Nanoclusters
Publisher: American Chemical Society (ACS)
Date: 17-12-2018
DOI: 10.1021/JACS.8B04436
Application of numerical basis sets to hydrogen bonded systems: A density functional theory study
Publisher: AIP Publishing
Date: 08-04-2005
DOI: 10.1063/1.1876152
Abstract: We have investigated and compared the ability of numerical and Gaussian-type basis sets to accurately describe the geometries and binding energies of a selection of hydrogen bonded systems that are well studied theoretically and experimentally. The numerical basis sets produced accurate results for geometric parameters but tended to overestimate binding energies. However, a comparison of the time taken to optimize phosphinic acid dimer, the largest complex considered in this study, shows that calculations using numerical basis sets offer a definitive advantage where geometry optimization of large systems is required.
Atomistic simulation of the sol formation during synthesis of organic/inorganic hybrid materials
Publisher: Informa UK Limited
Date: 10-2002
Applications: general discussion
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6FD90051H
Interaction of hydrogen with zinc oxide nanorods: Why the spacing is important
Publisher: IOP Publishing
Date: 22-02-2011
DOI: 10.1088/0957-4484/22/13/135704
Abstract: Hydrothermally grown ZnO nanorods show high interaction rates with H₂ when the spacing between adjacent nanorods decreases. Density functional theory calculations showed the interaction between nanorod surfaces in-registry is attractive at separations < 5 Å, while it is repulsive for out-of-registry alignments, indicating that uniform nanorods grown with their faces aligned out-of-registry are not likely to fuse due to the repulsion between the surfaces. The separation of 5 Å was found to be sufficient for H₂ to adsorb between the surfaces, resulting in a transfer of charge from H(2) to the surface, consistent with the measured increase in conductivity. This explains the ability of hydrogen to adsorb on closely spaced nanorods.
A structural model for apolipoprotein C-II amyloid fibrils: Experimental characterization and molecular dynamics simulations
Publisher: Elsevier BV
Date: 02-2011
DOI: 10.1016/J.JMB.2010.12.006
Abstract: The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyloid deposits located within atherosclerotic plaques. X-ray diffraction analysis of aligned apoC-II fibrils indicated a simple cross-β-structure composed of two parallel β-sheets. Examination of apoC-II fibrils using transmission electron microscopy, scanning transmission electron microscopy, and atomic force microscopy indicated that the fibrils are flat ribbons composed of one apoC-II molecule per 4.7-Å rise of the cross-β-structure. Cross-linking results using single-cysteine substitution mutants are consistent with a parallel in-register structural model for apoC-II fibrils. Fluorescence resonance energy transfer analysis of apoC-II fibrils labeled with specific fluorophores provided distance constraints for selected donor-acceptor pairs located within the fibrils. These findings were used to develop a simple 'letter-G-like' β-strand-loop-β-strand model for apoC-II fibrils. Fully solvated all-atom molecular dynamics (MD) simulations showed that the model contained a stable cross-β-core with a flexible connecting loop devoid of persistent secondary structure. The time course of the MD simulations revealed that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Our structural model for apoC-II fibrils suggests that apoC-II monomers fold and self-assemble to form a stable cross-β-scaffold containing relatively unstructured connecting loops.
Molecular mapping of poly(methyl methacrylate) super-helix stereocomplexes
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C4SC02971B
Abstract: The structure of the it-/st-poly(methyl methacrylate) (PMMA) triple-helix stereocomplex is composed of a double helix of it-PMMA of 9 units per turn surrounded by a single helix of st-PMMA with an average of 20 units per turn.
Gap junction hemichannel interactions with zwitterionic lipid, anionic lipid, and cholesterol: Molecular simulation studies
Publisher: American Chemical Society (ACS)
Date: 02-02-2011
DOI: 10.1021/BI1004156
Abstract: Interactions with membrane lipids can exert dramatic functional consequences on gap junction proteins. Recent experimental work has highlighted the importance of anionic lipids and cholesterol in facilitating channel activity. In this work, we have employed a coarse-grained molecular model in conjunction with molecular dynamics (MD) simulations to study the interactions between a connexin 26 (Cx26) hemichannel and a number of lipid species, including palmitoyloleoylphosphatidylcholine (POPC), anionic palmitoyloleoylphosphatidic acid (POPA), and cholesterol, in order to identify sites at the protein interface which may exhibit preferential, specific binding to these lipids, as well as determine the characteristics of these interactions. We have also employed an atomistic model of Cx26 embedded in a mixed PA/PC bilayer as a comparison and to elucidate further lipid-protein interactions. Our simulation results suggest enrichment of interfacial PA at the intracellular leaflet at high bulk PA concentrations. PC can form tight binding interactions with the hemichannel, particularly at intersubunit crevices (classical nonannular sites). In mixed bilayers, however, POPA competes with POPC for these sites, displacing the latter in some cases. While the residues responsible for interactions with PC and PA are similar, the latter exhibits a unique property of being capable of forming stable hydrophilic contacts with multiple residues spanning two different adjacent subunits at both leaflets of the bilayer, as opposed to POPC which can only do so at the extracellular side. These results suggest that POPA may be essential to channel function by acting as an intersubunit lipid bridge. Additionally, we propose that the compositional enrichment of POPA at the Cx26 interface may serve important roles in voltage gating. Simulation of a mixed POPC:cholesterol bilayer suggests that the hemichannel enhances the transbilayer mobility of vicinal cholesterols, increasing the likelihood of site-hopping and interleaflet flip-flop transitions.
Ab initio study of S dynamics on iron surfaces
Publisher: Elsevier BV
Date: 02-2007
Effect of aging on interfacial adhesion between polyester and carbon-based particles: A classical molecular dynamics study
Publisher: American Chemical Society (ACS)
Date: 11-04-2007
DOI: 10.1021/JP068239A
Protein flexibility: Multiple molecular dynamics simulations of insulin chain B
Publisher: Elsevier BV
Date: 2006
DOI: 10.1016/J.BPC.2005.08.002
Abstract: Multiple molecular dynamics simulations totaling more than 100 ns were performed on chain B of insulin in explicit solvent at 300 K and 400 K. Despite some in idual variations, a comparison of the protein dynamics of each simulation showed similar trends and most structures were consistent with NMR experimental values, even at the elevated temperature. The importance of packing interactions in determining the conformational transitions of the protein was observed, sometimes resulting in conformations induced by localized hydrophobic interactions. The high temperature simulation generated a more erse range of structures with similar elements of secondary structure and populated conformations to the simulations at room temperature. A broad s ling of the conformational space of insulin chain B illustrated a wide range of conformational states with many transitions at room temperature in addition to the conformational states observed experimentally. The T-state conformation associated with insulin activity was consistently present and a possible mechanism of behavior was suggested.
Origins of the pH-Responsive Photoluminescence of Peptide-Functionalized Au Nanoclusters
Publisher: American Chemical Society (ACS)
Date: 27-10-2022
Abstract: Ultrasmall peptide-protected gold nanoclusters are a promising class of bioresponsive material exhibiting pH-sensitive photoluminescence. We present a theoretical insight into the effect peptide-ligand environment has on pH-responsive fluorescence, with the aim of enhancing the rational design of gold nanoclusters for bioapplications. Employing a hybrid quantum/classical computational methodology, we systematically calculate deprotonation free energies of N-terminal cysteine amine groups in proximity to the inherently fluorescent core of Au
H2 S dissociation on the Fe(1 0 0) surface: An ab initio molecular dynamics study
Publisher: Elsevier BV
Date: 04-2008
A molecular dynamics study of siloxane diffusion in a polyester–melamine solution
Publisher: Elsevier BV
Date: 03-2007
Long-range dipolar order and dispersion forces in polar liquids
Publisher: AIP Publishing
Date: 16-11-2017
DOI: 10.1063/1.5005581
Abstract: Complex solvation phenomena, such as specific ion effects, occur in polar liquids. Interpretation of these effects in terms of structure and dispersion forces will lead to a greater understanding of solvation. Herein, using molecular dynamics, we probe the structure of polar liquids through specific dipolar pair correlation functions that contribute to the potential of mean force that is “felt” between thermally rotating dipole moments. It is shown that unique dipolar order exists at separations at least up to 20 Å for all liquids studied. When the structural order is compared with a dipolar dispersion force that arises from local co-operative enhancement of dipole moments, a strong agreement is found. Lifshitz theory of dispersion forces was compared with the structural order, where the theory is validated for all liquids that do not have significant local dipole correlations. For liquids that do have significant local dipole correlations, specifically liquid water, Lifshitz theory underestimates the dispersion force by a factor of 5–10, demonstrating that the force that leads to the increased structure in liquid water is missed by Lifshitz theory of van der Waals forces. We apply similar correlation functions to an ionic aqueous system, where long-range order between water’s dipole moment and a single chloride ion is found to exist at 20 Å of separation, revealing a long-range perturbation of water’s structure by an ion. Furthermore, we found that waters within the 1st, 2nd, and 3rd solvation shells of a chloride ion exhibit significantly enhanced dipolar interactions, particularly with waters at larger distances of separation. Our results provide a link between structures, dispersion forces, and specific ion effects, which may lead to a more robust understanding of solvation.
Density-functional theory of xanthate adsorption on the pyrite FeS2(100) surface
Publisher: Informa UK Limited
Date: 03-2004
Site‐Selective Coordination Assembly of Dynamic Metal‐Phenolic Networks
Publisher: Wiley
Date: 13-07-2022
Abstract: Coordination states of metal‐organic materials are known to dictate their physicochemical properties and applications in various fields. However, understanding and controlling coordination sites in metal‐organic systems is challenging. Herein, we report the synthesis of site‐selective coordinated metal‐phenolic networks (MPNs) using flavonoids as coordination modulators. The site‐selective coordination was systematically investigated experimentally and computationally using ligands with one, two, and multiple different coordination sites. Tuning the multimodal Fe coordination with catechol, carbonyl, and hydroxyl groups within the MPNs enabled the facile engineering of erse physicochemical properties including size, selective permeability (20–2000 kDa), and pH‐dependent degradability. This study expands our understanding of metal‐phenolic chemistry and provides new routes for the rational design of structurally tailorable coordination‐based materials.
Robust and Versatile Coatings Engineered via Simultaneous Covalent and Noncovalent Interactions
Publisher: Wiley
Date: 06-08-2021
Abstract: Interfacial modular assembly has emerged as an adaptable strategy for engineering the surface properties of substrates in biomedicine, photonics, and catalysis. Herein, we report a versatile and robust coating (pBDT‐TA), self‐assembled from tannic acid (TA) and a self‐polymerizing aromatic dithiol (i.e., benzene‐1,4‐dithiol, BDT), that can be engineered on erse substrates with a precisely tuned thickness (5–40 nm) by varying the concentration of BDT used. The pBDT‐TA coating is stabilized by covalent (disulfide) bonds and supramolecular (π‐π) interactions, endowing the coating with high stability in various harsh aqueous environments across ionic strength, pH, temperature (e.g., 100 mM NaCl, HCl (pH 1) or NaOH (pH 13), and water at 100 °C), as well as surfactant solution (e.g., 100 mM Triton X‐100) and biological buffer (e.g., Dulbecco's phosphate‐buffered saline), as validated by experiments and simulations. Moreover, the reported pBDT‐TA coating enables secondary reactions on the coating for engineering hybrid adlayers (e.g., ZIF‐8 shells) via phenolic‐mediated adhesion, and the facile integration of aromatic fluorescent dyes (e.g., rhodamine B) via π interactions without requiring elaborate synthetic processes.
Molecular rationale for the structure of cyclic poly(methyl methacrylate) stereocomplexes
Publisher: IEEE
Date: 02-2014
Facet-Dependent Interactions of Islet Amyloid Polypeptide with Gold Nanoparticles: Implications for Fibril Formation and Peptide-Induced Lipid Membrane Disruption
Publisher: American Chemical Society (ACS)
Date: 13-02-2017
Janus Cyclic Peptides: A New Approach to Amyloid Fibril Inhibition?
Publisher: Public Library of Science (PLoS)
Date: 20-02-2013
Effects of graphitic nanomaterials on the dissociation pathway of amyloidogenic peptide dimer
Publisher: IEEE
Date: 02-2014
Dissociative adsorption of hydrogen molecule on aluminum clusters: Effect of charge and doping
Publisher: American Chemical Society (ACS)
Date: 18-02-2009
DOI: 10.1021/JP809619Q
Abstract: The dissociative chemisorption of molecular hydrogen on charged and neutral aluminum clusters Al12X (X = Mg, Al, Si) was investigated using DFT and a modified G3(MP2)-RAD procedure. Reaction barriers and enthalpies were determined for both neutral and singly charged clusters. The lowest barrier for dissociative adsorption of H2 on a neutral cluster was found for the Al12Mg cluster, whereas the highest barrier was found to be on the closed-shell Al12Si. The interaction of H2 with Al13(+) is found to proceed via an association complex that is 0.07 eV lower in energy than the isolated species and from which the barrier to H2 dissociative adsorption is only 0.16 eV. The most exothermic reaction of H2 with Al12X occurs for the Al13(+)/H2 system. In comparison, reactions with the closed-shell Al13(-) and Al12Si clusters are found to be endothermic. The barriers for H2 desorption from the dihydrogenated clusters are generally quite substantial.
Performance of numerical basis set DFT for aluminum clusters
Publisher: American Chemical Society (ACS)
Date: 10-09-2008
DOI: 10.1021/JP802389B
Abstract: We have investigated and compared the ability of numerical and Gaussian-type basis sets combined with density functional theory (DFT) to accurately describe the geometries, binding energies, and electronic properties of aluminum clusters, Al12XHn (X = Al, Si n = 0, 1, 2). DFT results are compared against high-level benchmark calculations and experimental data where available. Properties compared include geometries, binding energies, ionization potentials, electron affinities, and HOMO-LUMO gaps. Generally, the PBE functional with the double numerical basis set with polarization (DNP) performs very well against experiment and the analytical basis sets for considerably less computational expense.
Ab initio molecular dynamics study of H2 S dissociation on the Fe(110) surface
Publisher: American Chemical Society (ACS)
Date: 05-10-2007
DOI: 10.1021/JP074430O
Identifying the Coiled-Coil Triple Helix Structure of β-Peptide Nanofibers at Atomic Resolution
Publisher: American Chemical Society (ACS)
Date: 29-08-2018
Abstract: Peptide self-assembly represents a powerful bottom-up approach to the fabrication of nanomaterials. β
Toward Cell Membrane Biomimetic Lipidic Cubic Phases: A High-Throughput Exploration of Lipid Compositional Space
Publisher: American Chemical Society (ACS)
Date: 07-12-2019
Quantitative design rules for protein-resistant surface coatings using machine learning
Publisher: Springer Science and Business Media LLC
Date: 22-01-2019
DOI: 10.1038/S41598-018-36597-5
Abstract: Preventing biological contamination (biofouling) is key to successful development of novel surface and nanoparticle-based technologies in the manufacturing industry and biomedicine. Protein adsorption is a crucial mediator of the interactions at the bio – nano -materials interface but is not well understood. Although general, empirical rules have been developed to guide the design of protein-resistant surface coatings, they are still largely qualitative . Herein we demonstrate that this knowledge gap can be addressed by using machine learning approaches to extract quantitative relationships between the material surface chemistry and the protein adsorption characteristics. We illustrate how robust linear and non-linear models can be constructed to accurately predict the percentage of protein adsorbed onto these surfaces using lysozyme or fibrinogen as prototype common contaminants. Our computational models could recapitulate the adsorption of proteins on functionalised surfaces in a test set with an r 2 of 0.82 and standard error of prediction of 13%. Using the same data set that enabled the development of the Whitesides rules, we discovered an extension to the original rules. We describe a workflow that can be applied to large, consistently obtained data sets covering a broad range of surface functional groups and protein types.
Lipid Concentration Effects on the Amyloidogenic apoC-II60-70 Peptide: A Computational Study
Publisher: American Chemical Society (ACS)
Date: 24-05-2010
DOI: 10.1021/JP102142X
Abstract: Molecular dynamics simulations were implemented to investigate the effects of phospholipid concentration on the conformation and dynamics of the amyloidogenic peptide apoC-II(60-70). The results showed a progressive reduction in the solvent accessible surface area of apoC-II(60-70) with increasing lipid concentration, accompanied by increased lipid-peptide interactions. Favorable peptide interaction sites with lipids were found to be the aromatic residues, Tyr63 and Phe67. The high stability of lipid-peptide contacts resulted in reduced conformational flexibility of the peptide. A significant change in the secondary structure of apoC-II(60-70) peptide was observed with increasing lipid concentration. At lower concentrations (1-3 lipids per peptide), the peptide adopted extended beta-strand conformations, caused by contacts with the lipids, which reduced the intramolecular interactions within the peptide. In contrast, a higher lipid concentration (4-6 lipids per peptide) had a restraining effect on the peptide's flexibility by trapping it in a particular conformation. Such behavior can be suggested as inhibiting fibril formation, because of the lipid-induced inability of the peptide to adopt fibril competent conformations. This finding complements our recent ThT fluorescence results, which revealed that the 4:1 lipid to peptide ratio is sufficient to cause fibril inhibition in apoC-II(60-70).
Origins of Structural Elasticity in Metal-Phenolic Networks Probed by Super-Resolution Microscopy and Multiscale Simulations
Publisher: American Chemical Society (ACS)
Date: 29-11-2022
Abstract: Metal-phenolic networks (MPNs) are amorphous materials that can be used to engineer functional films and particles. A fundamental understanding of the heat-driven structural reorganization of MPNs can offer opportunities to rationally tune their properties ( e . g ., size, permeability, wettability, hydrophobicity) for applications such as drug delivery, sensing, and tissue engineering. Herein, we use a combination of single-molecule localization microscopy, theoretical electronic structure calculations, and all-atom molecular dynamics simulations to demonstrate that MPN plasticity is governed by both the inherent flexibility of the metal (Fe III )-phenolic coordination center and the conformational elasticity of the phenolic building blocks (tannic acid, TA) that make up the metal-organic coordination complex. Thermal treatment (heating to 150 °C) of the flexible TA/Fe III networks induces a considerable increase in the number of aromatic π-π interactions formed among TA moieties and leads to the formation of hydrophobic domains. In the case of MPN capsules, 15 min of heating induces structural rearrangements that cause the capsules to shrink (from ∼4 to ∼3 μm), resulting in a thicker (3-fold), less porous, and higher protein ( e.g. , bovine serum albumin) affinity MPN shell. In contrast, when a simple polyphenol such as gallic acid is complexed with Fe III to form MPNs, rigid materials that are insensitive to temperature changes are obtained, and negligible structural rearrangement is observed upon heating. These findings are expected to facilitate the rational engineering of versatile TA-based MPN materials with tunable physiochemical properties for erse applications.
Comb polymers: Are they the answer to monolayer stability?
Publisher: Elsevier BV
Date: 07-2011
Electromagnetic bioeffects: a multiscale molecular simulation perspective
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D1CP05510K
Abstract: We summarise methodologies, challenges and opportunities for theoretical modelling to advance current understanding of electromagnetic bioeffects for biomedicine and industry.
Bioelectromagnetics research within an Australian context: The Australian centre for electromagnetic bioeffects research (ACEBR)
Publisher: MDPI AG
Date: 29-09-2016
Dynamic Performance of Duolayers at the Air/Water Interface. 1. Experimental Analysis
Publisher: American Chemical Society (ACS)
Date: 08-09-2014
DOI: 10.1021/JP5060974
Abstract: Understanding, and improving, the behavior of thin surface films under exposure to externally applied forces is important for applications such as mimicking biological membranes, water evaporation mitigation, and recovery of oil spills. This paper demonstrates that the incorporation of a water-soluble polymer into the surface film composition, i.e., formation of a three-duolayer system, shows improved performance under an applied dynamic stress, with an evaporation saving of 84% observed after 16 h, compared to 74% for the insoluble three-monolayer alone. Canal viscometry and spreading rate experiments, performed using the same conditions, demonstrated an increased surface viscosity and faster spreading rate for the three-duolayer system, likely contributing to the observed improvement in dynamic performance. Brewster angle microscopy and dye-tagged polymers were used to visualize the system and demonstrated that the duolayer and monolayer system both form a homogeneous film of uniform, single-molecule thickness, with the excess material compacting into small floating reservoirs on the surface. It was also observed that both components have to be applied to the water surface together in order to achieve improved performance under dynamic conditions. These findings have important implications for the use of surface films in various applications where resistance to external disturbance is required.
ChemInform Abstract: Ab initio Study of the Structure and Energetics of HONF2 and × ONF2.
Publisher: Wiley
Date: 23-11-2010
Electromagnetic field modulates aggregation propensity of amyloid peptides
Publisher: AIP Publishing
Date: 16-01-2020
DOI: 10.1063/1.5126367
Abstract: Nonthermal effects of the electromagnetic (EM) field in the radio and microwave frequency ranges on basic biological matter are difficult to detect and thus remain poorly understood. In this work, all-atom nonequilibrium molecular dynamics simulations were performed to investigate the molecular mechanisms of an amyloidogenic peptide response to nonionizing radiation of varying field characteristics. The results showed that the EM field induced peptide conformations dependent on the field frequency and strength. At the high field strength (0.7 V/nmrms), the peptide explored a wider conformational space as the frequency increased from 1.0 to 5.0 GHz. At the intermediate strength fields (0.07–0.0385 V/nmrms), the frequencies of 1.0 and 2.5 GHz resulted in the peptide being trapped in specific conformations, with 1.0 GHz enabling both fibril-forming and fibril-inhibiting conformations, while 2.5 GHz led to formation of mostly fibril-forming conformations. In contrast, the 5.0 GHz frequency caused increased peptide dynamics and more extended conformations with fibril-enabling aromatic side-chain arrangement akin to the structures formed under ambient conditions. All the simulated frequencies at low strength fields (0.007–0.0007 V/nmrms) resulted in the formation of amyloid-prone hairpin conformations similar to those formed under the weak static electric field and ambient conditions. These results suggest that specific ranges of EM field parameters produce peptide conformations unfavorable for formation of amyloid fibrils, a phenomenon that can be exploited in treatment and prevention of amyloid diseases. Alternatively, EM field parameters can be selected to modulate the formation of well-ordered peptide assemblies as a rational design strategy for engineering biocompatible materials.
Effect of S contamination on properties of Fe(1 0 0) surfaces
Publisher: Elsevier BV
Date: 09-2005
Nanoscale wetting and fouling resistance of functionalized surfaces: A computational approach
Publisher: American Chemical Society (ACS)
Date: 27-08-2014
DOI: 10.1021/LA500114K
Abstract: A computational modeling methodology has been developed and employed to characterize the nanoscale wettability and antifouling properties of functionalized hard and deformable surfaces, with a specific focus on poly(ethylene glycol) grafted substrates and their resistance to graphitic carbons. Empirical evidence suggests that the antifouling behavior of polyethylene PEG is associated with two main mechanisms: steric repulsions and hydration via formation of a structured water layer. However, there is also little attention paid to the contribution of steric repulsion vs surface hydration. We examine these two mechanisms through a combination of in silico contact angle and force measurements at the nanoscale level. We investigate the properties of the grafted functional chains and the underlying substrate, responsible for resisting surface deposition of graphitic contaminants in aqueous solution. Our results reveal that the fouling-release efficiency is enhanced when PEG chains are grafted onto hard hydrophilic substrates such as silica in contrast to deformable polymer substrates where surface modifications are effectively mitigated during interfacial contact with a hard contaminant. We conclude that the contribution of steric repulsion vs surface hydration to the antifouling ability of surfaces is strongly dependent on the nanoscale structure and deformability of the substrate. This generic method can be applied to examine in idual contribution of steric repulsions and surface hydration to antifouling performance of grafted chains.
Role of hydrogen in dimerizaton of aluminum clusters: A theoretical study
Publisher: American Chemical Society (ACS)
Date: 02-06-2011
DOI: 10.1021/JP201810T
Abstract: We have used density functional theory to investigate how Al(13) cluster dimers can be formed with or without a bridging hydrogen. We have identified several stable dimers in which 0, 1, or 2 hydrogen atoms link two bare clusters together. Each of these structures can adsorb further H atoms in atop sites on the surface of the dimer. Additional dimers were identified with 3 and 4 H atoms linking the clusters but these are only stable in the multihydrogenated form. Reaction profiles for the formation of these dimers from a range of cluster and H atom combinations indicate that the dimer structures are energetically favored over the isolated clusters. This observation may have significant implications for the design of cluster-assembled materials.
Molecular modelling of peptide folding, misfolding and aggregation phenomena
Publisher: Elsevier BV
Date: 05-2010
Adsorption of NO2 on oxygen deficient ZnO(21̄1̄0) for gas sensing applications: A DFT study
Publisher: American Chemical Society (ACS)
Date: 02-09-2010
DOI: 10.1021/JP105733P
Adsorption of atomic nitrogen and oxygen on surface: A density functional theory study
Publisher: IOP Publishing
Date: 18-03-2009
DOI: 10.1088/0953-8984/21/14/144208
Abstract: The adsorption of atomic nitrogen and oxygen on the ([Formula: see text]) crystal face of zinc oxide (ZnO) was studied. Binding energies, workfunction changes, vibrational frequencies, charge density differences and electron localization functions were calculated. It was elucidated that atomic oxygen binds more strongly than nitrogen, with the most stable [Formula: see text] structure exhibiting a binding energy of -2.47 eV, indicating chemisorption onto the surface. Surface reconstructions were observed for the most stable minima of both atomic species. Positive workfunction changes were calculated for both adsorbed oxygen and nitrogen if the adsorbate interacted with zinc atoms. Negative workfunction changes were calculated when the adsorbate interacted with both surface oxygen and zinc atoms. Interactions between the adsorbate and the surface zinc atoms resulted in ionic-type bonding, whereas interactions with oxygen atoms were more likely to result in the formation of covalent-type bonding. The positive workfunction changes correlate with an experimentally observed increase in resistance of ZnO conductometric sensor devices.
Comparison of embedded atom method potentials for small aluminium cluster simulations
Publisher: IOP Publishing
Date: 18-03-2009
DOI: 10.1088/0953-8984/21/14/144206
Abstract: In this paper, we present a comparison of the performance of a series of embedded atom method potentials for the evaluation of bulk and small aluminium cluster geometries and relative energies, against benchmark density functional theory calculations. In general, the non-pairwise potential-B (NP-B), which was parametrized against Al cluster data, performs the best.
An Ab initio study of the structure and energetics of HONF2 and .ONF2
Publisher: Elsevier BV
Date: 08-1993
Self-assembling peptide biomaterials: Insights from spontaneous and enhanced sampling molecular dynamics simulations
Publisher: AIP Publishing
Date: 21-04-2023
DOI: 10.1063/5.0142302
Abstract: Peptide self-assembly is the process by which peptide molecules aggregate into low dimensional (1D, 2D) or 3D ordered materials with potential applications ranging from drug delivery to electronics. Short peptides are particularly good candidates for forming supramolecular assemblies due to the relatively simple structure and ease of modulating their self-assembly process to achieve required material properties. The experimental resolution of fibrous peptide-based nanomaterials as 3D atomic coordinates remains challenging. For surface-mediated peptide assembly in particular, it is typically not feasible to resolve multiple conformationally distinct surface bound peptide structures by experiment. The mechanisms of peptide self-assembly also remain elusive due to the interchange of complex interactions and multiple time and length scales involved in the self-assembly process. Peptide self-assembly in solution, or mediated by surfaces, is driven by specific interactions between the peptides and water, competing interactions within the peptide and/or between peptide aggregate units and, in the latter case, an interplay of the interactions between peptides and solvent molecules for adsorption onto a proximal surface. Computational methodologies have proven beneficial in elucidating the structures formed during peptide self-assembly and the molecular mechanisms driving it, and hence have scope in facilitating the development of functional peptide-based nanomaterials for medical or biotechnological applications. In this perspective, computational methods that have provided molecular insights into the mechanisms of formation of peptide biomaterials, and the all-atom-resolved structures of peptide assemblies are presented. Established and recently emerged molecular simulation approaches are reviewed with a focus on applications relevant to peptide assembly, including all-atom and coarse-grained “brute force” molecular dynamics methods as well as the enhanced s ling methodologies: umbrella s ling, steered and replica exchange molecular dynamics, and variants of metadynamics. These approaches have been shown to contribute all-atom details not yet available experimentally, to advance our understanding of peptide self-assembly processes and biomaterial formation. The scope of this review includes a summary of the current state of the computational methods, in terms of their strengths and limitations for application to self-assembling peptide biomaterials.
Structural analysis of carbonaceous solids using an adapted reverse Monte Carlo algorithm
Publisher: Elsevier BV
Date: 2003
A DFT study of the perovskite and hexagonal phases of BaTiO3
Publisher: Elsevier BV
Date: 09-2005
Effects of mutation on the amyloidogenic propensity of apolipoprotein C-II60-70 peptide
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C0CP00299B
Abstract: Using experimental and computational methods we identified the effects of mutation on the structure and dynamics of the amyloidogenic peptide apoC-II(60-70), in monomeric and oligomeric states. Methionine (Met60) substitutions to hydrophilic Gln, hydrophobic Val, and methionine sulfoxide residues were investigated and the results compared with observations of fibril formation by the wild-type, Met60Gln, Met60Val, and oxidised Met60 (oxi-Met) apoC-II(60-70) peptides. ThT fluorescence measurements showed fibril formation by all peptides, however with different kinetics. The wild-type and Met60Val peptides formed fibrils fastest, while oxi-Met and Met60Gln peptides exhibited significantly longer lag phases. Molecular dynamics simulations showed that the mutated monomers exhibited structural features consistent with fibril-forming propensity, such as β-hairpin conformation and a hydrophobic core. However, important differences to the wild-type were also noted, such as increased structural flexibility (oxi-Met and Met60Gln systems) and a broader distribution of the aromatic angle orientation, which could contribute to the different fibrillation kinetics observed in these peptides. Our results also showed that the critical nucleus size for fibril formation by apoC-II(60-70) may not be very large, since tetrameric oligomers in anti-parallel configuration were very stable within the 100 ns of simulations. The single-point mutations Met60Val and Met60Gln had no significant effect on the structural stability of the tetramer. The rate of fibril formation by apoC-II(60-70) peptides was generally much faster compared to longer apoC-II(56-76) peptides. Also, the effects of amino acid modifications on the kinetics of peptide fibril formation differ from the effects observed for apoC-II(56-76) and full-length apoC-II, suggesting that additional mechanisms are involved in fibril formation by mature apoC-II.
Engineering Flexible Metal‐Phenolic Networks with Guest Responsiveness via Intermolecular Interactions
Publisher: Wiley
Date: 24-03-2023
Abstract: Flexible metal‐organic materials are of growing interest owing to their ability to undergo reversible structural transformations under external stimuli. Here, we report flexible metal‐phenolic networks (MPNs) featuring stimuli‐responsive behavior to erse solute guests. The competitive coordination of metal ions to phenolic ligands of multiple coordination sites and solute guests (e.g., glucose) primarily determines the responsive behavior of the MPNs, as revealed experimentally and computationally. Glucose molecules can be embedded into the dynamic MPNs upon mixing, leading to the reconfiguration of the metal‐organic networks and thus changes in their physicochemical properties for targeting applications. This study expands the library of stimuli‐responsive flexible metal‐organic materials and the understanding of intermolecular interactions between metal‐organic materials and solute guests, which is essential for the rational design of responsive materials for various applications.
Effect of Oxidation and Mutation on the Conformational Dynamics and Fibril Assembly of Amyloidogenic Peptides Derived from Apolipoprotein C-II
Publisher: American Chemical Society (ACS)
Date: 25-09-2009
DOI: 10.1021/JP903842U
Abstract: The oxidation of methionine residues in proteins can inhibit the self-assembly of proteins to form amyloid fibrils. For human apolipoprotein (apo) C-II the oxidation of methionine at position 60 inhibits fibril formation by the mature protein and by the core peptides apoC-II(56-76) and apoC-II(60-70). To investigate the molecular nature of these effects, we carried out fully solvated, all-atom molecular dynamics simulations of the structural changes in apoC-II(56-76) associated with substitutions of oxidized methionine (Met ox) at position 60. The results with apoC-II(56-76) (Met ox) showed less flexibility in structure, leading to a perturbation of the hydrophobic core. Valine substitution at position 60 showed an increased tendency to explore a wide range of conformational space, whereas the behavior of the Gln substitution mutant was similar to the wild-type peptide. These simulations are consistent with kinetic measurements which showed that a Met60Gln substitution within apoC-II(56-76) had little effect on the rate of fibril formation whereas substitution of Met ox or Val at position 60 lead to significant inhibition of peptide fibril formation. The effects of amino acid modification and substitutions on the kinetics of peptide fibril formation differ from the effects observed with full-length apoC-II inferring that additional mechanisms are involved in fibril formation by mature apoC-II.
Reactivity and regioselectivity of aluminum nanoclusters: Insights from regional density functional theory
Publisher: American Chemical Society (ACS)
Date: 07-01-2011
DOI: 10.1021/JP109804Y
High-Throughput Peptide Derivatization toward Supramolecular Diversification in Microtiter Plates
Publisher: American Chemical Society (ACS)
Date: 15-02-2021
Systematic comparison of empirical forcefields for molecular dynamic simulation of insulin
Publisher: American Chemical Society (ACS)
Date: 12-08-2008
DOI: 10.1021/JP076825D
Abstract: The use of atomistic simulation methodologies based on empirical forcefields has enhanced our understanding of many physical processes governing protein structure and dynamics. However, the forcefields used in classical modeling studies are often designed for a particular class of proteins and rely on continuous improvement and validation by comparison of simulations with experimental data. We present a comprehensive comparison of five popular forcefields for simulating insulin. The effect of each forcefield on the conformational evolution and structural properties of the peptide is analyzed in detail and compared with available experimental results. In this study we observed that different forcefields favor different structural trends. However, the all-atom forcefield CHARMM27 and the united-atom forcefield GROMOS 43A1 delivered the best representation of the experimentally observed dynamic behavior of chain B of insulin.
Further studies of iron adhesion: (1 1 1) surfaces
Publisher: Elsevier BV
Date: 08-2002
High-performance liquid chromatography of amino acids, peptides and proteins
Publisher: Elsevier BV
Date: 02-1994
Effect of Water Concentration on Sol Formation in Synthesis of Organic/Inorganic Hybrid Materials
Publisher: Informa UK Limited
Date: 2003
Classical Molecular Dynamics Study of [60]Fullerene Interactions with Silica and Polyester Surfaces
Publisher: American Chemical Society (ACS)
Date: 27-07-2006
DOI: 10.1021/JP0622886
Abstract: This study examines the interaction of neutral and charged fullerenes with model silica and polyester surfaces. Molecular dynamics simulations at 298 K indicate that van der Waals forces are sufficiently strong in most cases to cause physisorption of the neutral fullerene particle onto the surfaces. The fullerenes are unable to penetrate the rigid silica surface but are generally able to at least partially infiltrate the flexible polymer surface by opening surface cavities. The introduction of charge to the fullerene generally leads to an increase in both the separation distance and Work of Separation with silica. However, the charged fullerenes generally exhibit significantly closer and stronger interactions with polyester films, with a distinct tendency to absorb into the "bulk" of the polymer. The separation distance and Work of Separation of C60 with each of the surfaces also depend greatly on the sign, magnitude, and localization of the charge on the particle. Cross-linking of the polyester can improve resistance to the neutral fullerene. Functionalization of the polyester surface (F and OH substituents) has been shown to prevent the C60 from approaching as close to the polyester surface. Fluorination leads to improved resistance to positively charged fullerenes, compared to the unmodified polyester. However, hydroxylation generally enables greater adhesion of charged fullerenes to the surface due to H-bonding and electrostatic attraction.
First principles investigation of H addition and abstraction reactions on doped aluminum clusters
Publisher: American Chemical Society (ACS)
Date: 29-04-2009
DOI: 10.1021/JP810688F
Abstract: We have investigated axial interactions of H(2) with Al(12)X (X = Mg, Al, and Si) clusters and found that homolytic dissociation leading to Al(12)XH and H atom proceeds without a barrier but is an extremely endothermic process. The calculated difference in energy of the addition and abstraction reactions indicates that any Al(12)X-based hydrogen storage technology that involves predissociation of H(2) will be limited by the competing processes. We have also discovered that while there is a modest barrier for dissociation of H(2) on a single Al(12)Mg cluster to give the dihydride, the process occurs spontaneously between two closely spaced Al(12)Mg clusters, resulting in the formation of two Al(12)MgH species. Doping of the cluster with an electropositive atom (Mg) enables the transfer of electron density to the Al cage, which enhances H(2) dissociation. The information gained can contribute to the design of novel solid-state materials made of doped Al clusters, which may ultimately be suitable for catalytic processes.
Designing Fluorescent Peptide Sensors with Dual Specificity for the Detection of HIV-1 Protease
Publisher: American Chemical Society (ACS)
Date: 06-10-2015
A cyclic peptide inhibitor of ApoC-II peptide fibril formation: Mechanistic insight from NMR and molecular dynamics analysis
Publisher: Elsevier BV
Date: 03-2012
DOI: 10.1016/J.JMB.2011.12.059
Abstract: The misfolding and aggregation of proteins to form amyloid fibrils is a characteristic feature of several common age-related diseases. Agents that directly inhibit formation of amyloid fibrils represent one approach to combating these diseases. We have investigated the potential of a cyclic peptide to inhibit fibril formation by fibrillogenic peptides from human apolipoprotein C-II (apoC-II). Cyc[60-70] was formed by disulfide cross-linking of cysteine residues added to the termini of the fibrillogenic peptide comprising apoC-II residues 60-70. This cyclic peptide did not self-associate into fibrils. However, substoichiometric concentrations of cyc[60-70] significantly delayed fibril formation by the fibrillogenic, linear peptides apoC-II[60-70] and apoC-II[56-76]. Reduction of the disulfide bond or scrambling the amino acid sequence within cyc[60-70] significantly impaired its inhibitory activity. The solution structure of cyc[60-70] was solved using NMR spectroscopy, revealing a well-defined structure comprising a hydrophilic face and a more hydrophobic face containing the Met60, Tyr63, Ile66 and Phe67 side chains. Molecular dynamics (MD) studies identified a flexible central region within cyc[60-70], while MD simulations of "scrambled" cyc[60-70] indicated an increased formation of intramolecular hydrogen bonds and a reduction in the overall flexibility of the peptide. Our structural studies suggest that the inhibitory activity of cyc[60-70] is mediated by an elongated structure with inherent flexibility and distinct hydrophobic and hydrophilic faces, enabling cyc[60-70] to interact transiently with fibrillogenic peptides and inhibit fibril assembly. These results suggest that cyclic peptides based on amyloidogenic core peptides could be useful as specific inhibitors of amyloid fibril formation.
Nanoscale in silico classification of ligand functionalised surfaces for protein adsorption resistance
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/C9NR10009A
Abstract: Non-specific protein adsorption represents a challenge for the design of efficient and safe nanoparticles for biomedical applications. An in silico method is presented to design ligands imparting protein resistance to functional surfaces.
Dynamic Performance of Duolayers at the Air/Water Interface. 2. Mechanistic Insights from All-Atom Simulations
Publisher: American Chemical Society (ACS)
Date: 04-09-2014
DOI: 10.1021/JP506098D
Abstract: The novel duolayer system, comprising a monolayer of ethylene glycol monooctadecyl ether (C18E1) and the water-soluble polymer poly(vinylpyrrolidone) (PVP), has been shown to resist forces such as wind stress to a greater degree than the C18E1 monolayer alone. This paper reports all-atom molecular dynamics simulations comparing the monolayer (C18E1 alone) and duolayer systems under an applied force parallel to the air/water interface. The simulations show that, due to the presence of PVP at the interface, the duolayer film exhibits an increase in chain tilt, ordering, and density, as well as a lower lateral velocity compared to the monolayer. These results provide a molecular rationale for the improved performance of the duolayer system under wind conditions, as well as an atomic-level explanation for the observed efficacy of the duolayer system as an evaporation suppressant, which may serve as a useful guide for future development for thin films where resistance to external perturbation is desirable.
Effect of substrate on the mechanical response and adhesion of PEGylated surfaces: Insights from all-atom simulations
Publisher: American Chemical Society (ACS)
Date: 04-12-2012
DOI: 10.1021/LA3023375
Abstract: Responsive surfaces show potential for many applications however, the molecular mechanisms of their responsive behavior are often dependent on the nature and properties of the substrate and this dependence is not fully understood. We present a molecular dynamics study on the mechanical response of poly(ethylene glycol) (PEG) grafted on substrates of varying flexibility in "dry" conditions. Our in silico surface loading tests show that when PEG is grafted onto a hard substrate (silica), there is a significant reduction in adhesion to a solid surface, owing to augmented steric repulsions at the interface. However, when the same chains are tethered onto a soft substrate (polyester), interfacial adhesion is strengthened. We find that the deformable substrate allows significant rearrangement of the subsurface and grafted segments during loading. Asperities along the rough soft surface also provide free volume for the tethered chains to occupy, enabling them to carpet the surface and increasing the density at the interface. Our results explain the molecular basis of the mechanical response of PEG when grafted onto hard and soft substrates and provide a rationale for surface protection using PEG.
Density functional theory study of ZnO nanostructures for NO and NO 2 sensing
Publisher: IEEE
Date: 2007
Thermal behavior and molecular simulation of liquid crystalline polymers containing a pentamethylenic spacer
Publisher: Elsevier BV
Date: 06-2003
Effect of external stresses on protein conformation: A computer modelling study
Publisher: Springer Science and Business Media LLC
Date: 04-2004
DOI: 10.1007/S00249-003-0359-Y
Abstract: The increasing use of digital technologies such as mobile phones has led to major health concerns about the effects of non-ionizing pulsed radiation exposure. We believe that the health implications of exposure to radiation cannot be fully understood without establishing the molecular mechanisms of biological effects of pulsed microwaves. We aim to establish methods for studying the molecular mechanisms of protein structural and energetic changes occurring due to external stresses related to non-ionizing radiation by using a combination of experimental and theoretical approaches. In this paper, we present the results from our fully atomistic simulation study of chemical and thermal stress response of a prototype protein, insulin. We performed a series of molecular dynamics simulations of insulin in solution under equilibrium conditions, under chemical stress (imitated by reducing the disulfide bonds in the protein molecule), and under short-lived thermal stress (imitated by increasing simulation temperature for up to 2 ns). The resultant protein conformational behaviour was analysed for various properties with the aim of establishing analysis routines for classification of protein unfolding pathways and associated molecular mechanisms.
Cobalt-Directed Assembly of Antibodies onto Metal–Phenolic Networks for Enhanced Particle Targeting
Publisher: American Chemical Society (ACS)
Date: 10-03-2020
Three-Dimensional Organization of Self-Encapsulating Gluconobacter oxydans Bacterial Cells
Publisher: American Chemical Society (ACS)
Date: 20-11-2017
DFT study of hydrogen adsorption on Al13clusters
Publisher: Informa UK Limited
Date: 05-2005
Effect of sulfur impurity on Fe(110) adhesion: A DFT study
Publisher: American Chemical Society (ACS)
Date: 25-06-2004
DOI: 10.1021/JP049506K
Insights On Protein Structure And Dynamics From Multiple Biased Molecular Dynamics Simulations
Publisher: Elsevier BV
Date: 02-2009
Comparative study of insulin chain-B in isolated and monomeric environments under external stress
Publisher: American Chemical Society (ACS)
Date: 07-06-2008
DOI: 10.1021/JP800350V
Abstract: We have conducted a series of theoretical simulations of insulin chain-B under different electric field conditions. This work extends our previous studies of the isolated chain-B by including chain-A and revealing the effects of chemical stress. For this complete protein, we observed increased stability under ambient conditions and under the application of thermal stress, compared to isolated chain-B. On the other hand, the presence of chain-A enhanced the effects of the applied electric field. Under the static field, the presence of chain-A lowered the strength of the field necessary to stretch the protein. Under the oscillating fields, there was relatively less stretching due to the competitive alignment process of the three helical regions with respect to the field. At high field strengths, we observed that the high frequency oscillating field caused less secondary structure disruption than a lower frequency field of the same strength.
Theoretical study of adhesion between graphite, polyester and silica surfaces
Publisher: Informa UK Limited
Date: 05-2005
Direct dry transfer of chemical vapor deposition graphene to polymeric substrates
Publisher: Elsevier BV
Date: 03-2015
Effect of substrate on the responsive behaviour of functionalised surfaces: Insights from molecular simulation
Publisher: Informa UK Limited
Date: 30-10-2016
Density-functional theory studies of pyrite FeS2() and () surfaces
Publisher: Elsevier BV
Date: 08-2002
Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations
Publisher: Public Library of Science (PLoS)
Date: 05-12-2013
Stereospecific Cyclic Poly(methyl methacrylate) and Its Topology‐Guided Hierarchically Controlled Supramolecular Assemblies
Publisher: Wiley
Date: 25-11-2013
Abstract: In this study, the stereocomplexation between a novel stereospecific cyclic vinyl polymer, that is, cyclic syndiotactic poly(methyl methacrylate) (st-PMMA), with the complementary linear isotactic (it-) PMMA was investigated. Surprising new insight into the effects of the topology (i.e., end groups), size, and tacticity of the assembling components on stereocomplex formation was obtained. Characterization of the stereocomplexes revealed that the self-assembly of cyclic st-PMMAs and linear it-PMMAs resulted in the formation of an unprecedented “polypseudorotaxane-type” supramolecular assembly. This stereocomplex exhibited remarkably different physical properties as compared to the conventional PMMA triple-helix stereocomplex as a result of the restricted topology imposed by the cyclic st-PMMA assembling component.
Cobalt Phosphate Nanostructures for Non-Enzymatic Glucose Sensing at Physiological pH
Publisher: American Chemical Society (ACS)
Date: 13-11-2018
Abstract: Nanostructured materials have potential as platforms for analytical assays and catalytic reactions. Herein, we report the synthesis of electrocatalytically active cobalt phosphate nanostructures (CPNs) using a simple, low-cost, and scalable preparation method. The electrocatalytic properties of CPNs toward the electrooxidation of glucose (Glu) were studied by cyclic voltammetry and chrono erometry in relevant biological electrolytes, such as phosphate-buffered saline (PBS), at physiological pH (7.4). Using CPNs, Glu detection could be achieved over a wide range of biologically relevant concentrations, from 1 to 30 mM Glu in PBS, with a sensitivity of 7.90 nA/mM cm
Surface-water interface induces conformational changes critical for protein adsorption: Implications for monolayer formation of EAS hydrophobin
Publisher: Frontiers Media SA
Date: 16-11-2015
Prediction of liquid crystalline properties of poly(1,4-phenylene sebacate-oxybenzoate) by Monte Carlo simulation
Publisher: Elsevier BV
Date: 02-2005
Surface crosslinking effects on contamination resistance of functionalised polymers
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C2SM27695J
Effects of forcefield and sampling method in all-atom simulations of inherently disordered proteins: Application to conformational preferences of human amylin
Publisher: Public Library of Science (PLoS)
Date: 02-04-190728634
New lambda integration method to compute surface free energies of disordered surfaces
Publisher: AIP Publishing
Date: 08-10-2002
DOI: 10.1063/1.1509059
Abstract: Previously we studied a range of λ-integration paths, specifically designed for calculating surface and interfacial free energies of solids with disordered surfaces or interfaces, using molecular dynamics or Monte Carlo simulation methods. Some of these were successfully applied to the stable low index (100) and (110) Fe bcc surfaces, up to temperatures high enough (1200 K) to induce the onset of surface disorder via the formation of adatoms. Here we apply these same methods to the high energy (111) bcc Fe face, where the “ideal” surface structure was found to be metastable at low temperatures. The results showed that application of paths used in our previous study lead to irreversibility. Hence we further refine the paths with the development of a much more powerful and general path, which we termed the “blanket lambda” path. We show the newest path to be reversible and to provide “exact” surface free energy reference points for the stable and metastable surface structures of the (111) bcc Fe face. We also show this general path to be applicable to the low index (100) and (110) faces.
Influence of the Chain Length and Surface Density on the Conformation and Mobility of n-Alkyl Ligands Chemically Immobilized onto a Silica Surface
Publisher: American Chemical Society (ACS)
Date: 07-1995
DOI: 10.1021/AC00109A038
Comparative study of commonly used molecular dynamics force fields for modeling organic monolayers on water
Publisher: American Chemical Society (ACS)
Date: 21-03-2011
DOI: 10.1021/JP1116867
Abstract: This study compares the performance of the all-atom molecular dynamics force fields OPLS-AA and COMPASS, and the united-atom GROMOS96 ff53a6 force field, for organic monolayers at aqueous interfaces, as a function of surface density, temperature, and system size. Where possible, comparison with experimental data was undertaken and used to scrutinize the performance of each force field. We find close agreement between the all-atom force fields (OPLS and COMPASS) and experiment for the description of organic monolayers on water. However, the united-atom force field 53a6 tends to exhibit poorer agreement than the all-atom force fields.
Electromagnetic-field effects on structure and dynamics of amyloidogenic peptides
Publisher: AIP Publishing
Date: 23-02-0008
DOI: 10.1063/1.4941108
Abstract: Electromagnetic fields (EMFs) are ever-present, and so is the need to better understand their influence on human health and biological matter in general. The interaction between a molecular system and external EMF can alter the structure, and dynamical behaviour, and, hence, biological function of proteins with uncertain health consequences. This urges a detailed investigation of EMF-induced effects on basic protein biophysics. Here, we used all-atom non-equilibrium molecular dynamics simulations to understand and quantify the response mechanisms of the amyloidogenic apoC-II(60-70) peptides to non-ionising radiation by modelling their behaviour under external electromagnetic and electric fields of different strengths. Our simulations show high strength fields (& .04 V/nm) cause structural changes in apoC-II(60-70) due to the peptide dipole alignment along the applied field direction, which disrupts the inherent β-hairpin conformation known to be the intermediate state for fibril formation. The intermediate field-strength range (0.04-0.004 V/nm) causes a significant acceleration in peptide dynamics, which leads to the increased population of structures with fibril-inhibiting characteristics, such as the separated N- and C-termini and colocation of the aromatic residues at the same peptide face. In contrast, lower field strengths (& .004 V/nm) promote the formation of the amyloid-prone hairpin structures relative to the ambient conditions. These findings suggest that intermediate-strength electromagnetic fields could be considered for designing alternative treatments of amyloid diseases, while the very high and low field strengths could be employed for engineering well-ordered fibrillar aggregates for non-medicinal applications.
Effect of S arrangement on Fe(110) properties at 1/3 monolayer coverage: A DFT study
Publisher: American Chemical Society (ACS)
Date: 22-12-2006
DOI: 10.1021/JP054769F
Abstract: Using density functional theory calculations, we compare the relative stabilities and properties of different arrangements of S on Fe(110) at a 1/3 monolayer coverage, including two observed experimentally. For all studied arrangements, S is adsorbed in the three high-symmetry adsorption sites: 4-fold hollow, 3-fold hollow, bridge, and atop sites. The binding energy, work function change, adsorption geometry, charge density distribution, magnetic properties, and density of states are determined and compared. The most stable overlayer arrangement corresponds to the overlayer seen by experiment after dissociative adsorption of H2S and has S adsorbed in 4-fold hollow sites. In the other arrangements, the S atoms are located closer to each other on the surface reducing the stability of the overlayer. S causes a minor adsorbate-induced reconstruction of the Fe surface and quenches the magnetic moment of the Fe atoms it bonds to directly. It adsorbs as an electropositive species, causing a positive work function change and forms polar covalent bonds to the surface.
Site‐Selective Coordination Assembly of Dynamic Metal‐Phenolic Networks
Publisher: Wiley
Date: 13-07-2022
Abstract: Coordination states of metal‐organic materials are known to dictate their physicochemical properties and applications in various fields. However, understanding and controlling coordination sites in metal‐organic systems is challenging. Herein, we report the synthesis of site‐selective coordinated metal‐phenolic networks (MPNs) using flavonoids as coordination modulators. The site‐selective coordination was systematically investigated experimentally and computationally using ligands with one, two, and multiple different coordination sites. Tuning the multimodal Fe coordination with catechol, carbonyl, and hydroxyl groups within the MPNs enabled the facile engineering of erse physicochemical properties including size, selective permeability (20–2000 kDa), and pH‐dependent degradability. This study expands our understanding of metal‐phenolic chemistry and provides new routes for the rational design of structurally tailorable coordination‐based materials.
Amphiphilic amino acids: A key to adsorbing proteins to nanopatterned surfaces?
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C2SC21639F
Influence of Ionic Strength on the Deposition of Metal-Phenolic Networks
Publisher: American Chemical Society (ACS)
Date: 27-09-2017
DOI: 10.1021/ACS.LANGMUIR.7B02692
Abstract: Metal-phenolic networks (MPNs) are a versatile class of self-assembled materials that are able to form functional thin films on various substrates with potential applications in areas including drug delivery and catalysis. Different metal ions (e.g., Fe
Surface defects on ZnO nanowires: Implications for design of sensors
Publisher: IOP Publishing
Date: 19-06-2012
DOI: 10.1088/0953-8984/24/30/305001
Abstract: Surface defects are commonly believed to be fundamentally important to gas-sensor performance. We examine the effect of gas coverage and ethanol orientation on its adsorption on the stoichiometric and oxygen deficient (101(-)0) nanowire surface. Our density functional theory calculations show that ethanol adsorbs in multiple stable configurations at coverages between 1/4 and 1 ML, highlighting the ability of ZnO to detect ethanol. Ethanol prefers to bind to a surface Zn via the adsorbate oxygen atom and, if a surface oxygen atom is in close proximity, the molecule is further stabilized by formation of a hydrogen bond between the hydrogen of the hydroxyl group and the surface oxygen. Two primary adsorption configurations were identified and have different binding strengths that could be distinguished experimentally by the magnitude of their OH stretching frequency. Our findings show that ethanol adsorbed on the oxygen deficient ZnO(101(-)0) surface has a reduced binding strength. This is due to either the lack of a hydrogen bond (due to a deficiency in surface oxygen) or to surface reconstruction that occurs on the defect surface that weakens the hydrogen bond interaction. This reduced binding on the oxygen deficient surface is in contrast to the defect enhanced gas-sensor interaction for other gases. Despite this difference, ethanol still acts as a reducing gas, donating electrons to the surface and decreasing the band gap. We show that multiple adsorbed ethanol molecules prefer to be orientated parallel to each other to facilitate the hydrogen bonding to the defect-free surface for enhanced interaction.
Distinct Bimodal Roles of Aromatic Molecules in Controlling Gold Nanorod Growth for Biosensing
Publisher: Wiley
Date: 26-06-0001
Hydrogen bonding in mixed ligand copper organophosphonates
Publisher: Elsevier BV
Date: 09-2003
Molecular dynamics simulations of a fibrillogenic peptide derived from apolipoprotein C-II
Publisher: Elsevier BV
Date: 11-2007
DOI: 10.1016/J.BPC.2007.08.002
Abstract: The pathway to amyloid fibril formation in proteins involves specific structural changes leading to the combination of misfolded intermediates into oligomeric assemblies. Recent NMR studies showed the presence of "turns" in amyloid peptides, indicating that turn formation may play an important role in the nucleation of the intramolecular folding and possible assembly of amyloid. Fully solvated all-atom molecular dynamics simulations were used to study the structure and dynamics of the apolipoprotein C-II peptide 56 to 76, associated with the formation of amyloid fibrils. The peptide populated an ensemble of turn structures, stabilized by hydrogen bonds and hydrophobic interactions enabling the formation of a strong hydrophobic core which may provide the conditions required to initiate aggregation. Two competing mechanisms discussed in the literature were observed. This has implications in understanding the mechanism of amyloid formation in not only apoC-II and its fragments, but also in other amyloidogenic peptides.
Sulfur adsorption on Fe(1 1 0): A DFT study
Publisher: Elsevier BV
Date: 08-2003
Robust and Versatile Coatings Engineered via Simultaneous Covalent and Noncovalent Interactions
Publisher: Wiley
Date: 06-08-2021
Abstract: Interfacial modular assembly has emerged as an adaptable strategy for engineering the surface properties of substrates in biomedicine, photonics, and catalysis. Herein, we report a versatile and robust coating (pBDT‐TA), self‐assembled from tannic acid (TA) and a self‐polymerizing aromatic dithiol (i.e., benzene‐1,4‐dithiol, BDT), that can be engineered on erse substrates with a precisely tuned thickness (5–40 nm) by varying the concentration of BDT used. The pBDT‐TA coating is stabilized by covalent (disulfide) bonds and supramolecular (π‐π) interactions, endowing the coating with high stability in various harsh aqueous environments across ionic strength, pH, temperature (e.g., 100 mM NaCl, HCl (pH 1) or NaOH (pH 13), and water at 100 °C), as well as surfactant solution (e.g., 100 mM Triton X‐100) and biological buffer (e.g., Dulbecco's phosphate‐buffered saline), as validated by experiments and simulations. Moreover, the reported pBDT‐TA coating enables secondary reactions on the coating for engineering hybrid adlayers (e.g., ZIF‐8 shells) via phenolic‐mediated adhesion, and the facile integration of aromatic fluorescent dyes (e.g., rhodamine B) via π interactions without requiring elaborate synthetic processes.
Intra- and Intersubunit Ion-Pair Interactions Determine the Ability of Apolipoprotein C-II Mutants to Form Hybrid Amyloid Fibrils
Publisher: American Chemical Society (ACS)
Date: 15-03-2017
DOI: 10.1021/ACS.BIOCHEM.6B01146
Abstract: The apolipoprotein family is structurally defined by hipathic α-helical regions that interact with lipid surfaces. In the absence of lipid, human apolipoprotein (apo) C-II also forms well-defined amyloid fibrils with cross-β structure. Formation of this β-structure is accompanied by the burial of two charged residues, K30 and D69, that form an ion-pair within the amyloid fibril core. Molecular dynamics (MD) simulations indicate these buried residues form both intra- and intersubunit ion-pair interactions that stabilize the fibril. Mutations of the ion-pair (either K30D or D69K) reduce fibril stability and prevent fibril formation by K30D apoC-II under standard conditions. We investigated whether mixing K30D apoC-II with other mutants would overcome this loss of fibril forming ability. Co-incubation of equimolar mixtures of K30D apoC-II with wild-type, D69K, or double-mutant (K30D/D69K) apoC-II promoted the incorporation of K30D apoC-II into hybrid fibrils with increased stability. MD simulations showed an increase in the number of intersubunit ion-pair interactions accompanied the increased stability of the hybrid fibrils. These results demonstrate the important role of both intra- and intersubunit charge interactions in stabilizing apoC-II amyloid fibrils, a process that may be a key factor in determining the general ability of proteins to form amyloid fibrils.
Theoretical Nanoscale Design of Self-Cleaning Coatings
Publisher: Jenny Stanford Publishing
Date: 11-07-2011
DOI: 10.1201/B11034-4
ZnO nanostructures for gas sensing: Interaction of NO2 , NO, O, and N with the ZnO(101̄0) surface
Publisher: American Chemical Society (ACS)
Date: 02-06-2010
DOI: 10.1021/JP1016938
Universal simulation method to compute surface and interfacial free energies of disordered solids
Publisher: AIP Publishing
Date: 08-10-2002
DOI: 10.1063/1.1509060
Abstract: Previously we studied λ-integration paths for the calculation of “exact” surface and interfacial free energies that were limited to simulation methods where atomic interactions can be scaled using a multiplicative parameter λ, as is the case for analytical empirical potentials. Here we develop new reversible paths and associated λ-integration methodology to find exact surface and interfacial free energies of solids, that could potentially be used in conjunction with any intermolecular potential function and/or methods such as ab initio simulations, where one cannot trivially scale and sum the slab interactions as is done with “simple” classical intermolecular potentials. As a first step we test our paths and methodology on the (100), (110), and (111) faces of α-iron using embedded atom method interactions. We find accurate agreement with our previous surface free energy calculations for all faces, including the highly disordered (111) face.
Related Organisations
Semenov Institute Of Chemical Physics, Russian Academy Of Sciences
Location: Russian Federation
Related Funding Activities
Surface Ligation Of Nanomaterials For Biomedical Applications
Start Date: 2023
End Date: 2025
Funder: Australian Research Council
View Funded ActivityAustralian Centre For Electromagnetic Bioeffects Research
Start Date: 2018
End Date: 2023
Funder: National Health and Medical Research Council
View Funded ActivityAtomic Scale Precision Engineering Of Cell-material Interfaces
Start Date: 2019
End Date: 2021
Funder: Australian Research Council
View Funded ActivityAustralian Computational Molecular Science Network
Start Date: 2003
End Date: 2003
Funder: Australian Research Council
View Funded ActivityTheoretical Studies Of Molecular Mechanisms Of Abnormal Protein Aggregation
Start Date: 2005
End Date: 2008
Funder: Australian Research Council
View Funded ActivityResponse Of Proteins To External Non-Ionising Radiation: An Experimental And Computer Modelling Investigation
Start Date: 2002
End Date: 2004
Funder: Australian Research Council
View Funded ActivityFundamental Theoretical Study Of Hydrogen Interactions With Novel Nanostructures
Start Date: 2006
End Date: 2008
Funder: Australian Research Council
View Funded ActivityNano-scale Modification Of Paint Surfaces For Contamination Resistance
Start Date: 2003
End Date: 2006
Funder: Australian Research Council
View Funded ActivityDesign And Synthesis Of Transparent Conducting Metal Oxides
Start Date: 2006
End Date: 2009
Funder: Australian Research Council
View Funded ActivityProtein Self-assembly On Surfaces, Interfaces And Nanoparticles
Start Date: 2009
End Date: 2011
Funder: Australian Research Council
View Funded ActivityEngineering Efficient Biomedical Materials And Devices Using Biomolecular Interactions Of Nanoparticles
Start Date: 2014
End Date: 2016
Funder: Australian Research Council
View Funded ActivityARC Research Hub For Australian Steel Manufacturing
Start Date: 2016
End Date: 2020
Funder: Australian Research Council
View Funded ActivityBiodevice Fabrication Through Intelligent Surface Modification
Start Date: 2003
End Date: 2003
Funder: Australian Research Council
View Funded ActivityEnvironmentally Responsive Clean Coatings
Start Date: 2009
End Date: 2012
Funder: Australian Research Council
View Funded ActivityTheoretical Modelling Study Of Thin Film Permeability
Start Date: 2011
End Date: 2013
Funder: Australian Research Council
View Funded ActivityLive Cell Super Resolution Imaging Facility
Start Date: 2020
End Date: 2020
Funder: Australian Research Council
View Funded ActivitySustaining And Strengthening Merit-based Access To National Computational Infrastructure
Start Date: 2019
End Date: 2021
Funder: Australian Research Council
View Funded ActivityA High-performance Cloud Resource For Computational Modelling.
Start Date: 2017
End Date: 2017
Funder: Australian Research Council
View Funded ActivityARC Research Hub For Australian Steel Innovation
Start Date: Start date not available
End Date: End date not available
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP140101888
Start Date: 2014
End Date: 12-2018
Amount: $345,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP110101604
Start Date: 2012
End Date: 12-2014
Amount: $300,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP170100511
Start Date: 06-2017
End Date: 12-2020
Amount: $286,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP0349216
Start Date: 12-2003
End Date: 06-2007
Amount: $344,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP190102290
Start Date: 04-2019
End Date: 04-2022
Amount: $500,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP230100709
Start Date: 2023
End Date: 12-2025
Amount: $396,015.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP0663321
Start Date: 07-2006
End Date: 08-2011
Amount: $234,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP0666883
Start Date: 04-2006
End Date: 06-2010
Amount: $680,000.00
Funder: Australian Research Council
View Funded ActivityIndustrial Transformation Research Hubs - Grant ID: IH130100017
Start Date: 10-2014
End Date: 06-2020
Amount: $5,000,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE170100200
Start Date: 05-2017
End Date: 12-2017
Amount: $635,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP0990511
Start Date: 03-2010
End Date: 12-2013
Amount: $294,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP0984565
Start Date: 07-2009
End Date: 12-2012
Amount: $340,000.00
Funder: Australian Research Council
View Funded ActivitySpecial Research Initiatives - Grant ID: SR0354636
Start Date: 2004
End Date: 12-2004
Amount: $30,000.00
Funder: Australian Research Council
View Funded ActivityIndustrial Transformation Research Hubs - Grant ID: IH200100005
Start Date: 07-2021
End Date: 06-2026
Amount: $5,000,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE190100021
Start Date: 09-2019
End Date: 09-2022
Amount: $4,320,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE200100163
Start Date: 06-2020
End Date: 05-2022
Amount: $700,000.00
Funder: Australian Research Council
View Funded ActivitySpecial Research Initiatives - Grant ID: SR0354583
Start Date: 06-2004
End Date: 12-2004
Amount: $10,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP0562041
Start Date: 09-2005
End Date: 07-2009
Amount: $215,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP0219406
Start Date: 07-2002
End Date: 09-2006
Amount: $250,000.00
Funder: Australian Research Council
View Funded Activity