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Molecular dynamics procedures have been used to investigate the conformation and mobility of n-alkyl ligands immobilized onto an amorphous silica surface, analogous to those utilized with silica-based RP-HPLC sorbents. Molecular models were constructed for n-octyl and n-octadecyl bonded phases with ligand densities of 1.64, 2.67, and 3.69 [micro]mol/[m.sup.2] for each ligand length. The hydrocarbon layer thickness, gauche - trans statistics, end-to-end distance distribution of the n-alkyl chains, and diffusion coefficients of individual atoms in the n-alkyl ligands were determined for each system. The results have been compared with data previously obtained with an n-butyl bonded phase. The conformation of the chains, their positions with respect to the surface, and the chain mobilities were characterized as a function of ligand length and surface density. The results demonstrated that the most ordered part of the chain is always the segment that is anchored closest to the silica surface. With decreasing density, the ligands become more bent, with more gauche defects occurring in the middle and at the free end of the chains. This behavior leads to a dramatic decrease in the thickness of the hydrocarbon layer at minimum surface loading. Potentially, this behavior could result in stronger surface interactions with a prospective solute. These simulation studies also indicate that both short and long n-alkyl ligands can layer over the surface at lower ligand density, thus creating additional protection of unreacted surface silanols, with this effect being more pronounced for the longer n-alkyl chains. In terms of ligand dynamics, the simulated structures indicated that the n-octyl chain exhibits the highest overall mobility at all studied densities, while the n-octadecyl ligands possess the lowest motional freedom. The degree of mobility for any length ligand decreased with increasing surface density. The mobility of individual carbon atoms within the chains also increased with distance from the silica surface for all ligand lengths and densities. These simulated properties of n-alkyl ligands immobilized onto a silica surface correlated well with other results obtained by FTIR or 13C-cross polarization magic angle spinning NMR experimental methods and statistical predictions of the behavior of immobilized chains.

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 (>0.04 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 (<0.004 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. [ABSTRACT FROM AUTHOR]

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. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

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 (HOCS[sup -, sub 2]) and its adsorption characteristics on the pyrite FeS[sub 2](110) and (111) surfaces. Molecular calculations revealed that HOCS[sup -, sub 2] and CH[sub 3]CH[sub 2]OCS[sup -, sub 2] 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 FeS[sub 2] surfaces. Results from DFT calculations suggest that HOCS[sup -, sub 2] 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 FeS[sub 2] surfaces, which contain low-coordinate Fe sites and sites in proximity to cleaved S-S bonds. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 a-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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

A course of identical molecular dynamics simulations were utilized to identify and compare possible systematic effects of multiple forcefields on the structure and dynamics of chain B of insulin. The results showed that the all-atom CHARMM27 and united-atom GROMOS 43A1 forcefields were most suitable to study dynamic behavior of chain B of insulin.

A series of simulations are conducted on insulin chain-B under different electric field and applied stress conditions. The application of thermal stress has increased the conformational mobility of the termini regions, although to a much lesser extent than in the isolated chain-B and throughout the simulations, the B9-B19 [alpha]-helical core is maintained.

The interaction of neutral and charged fullerenes with model silica and polyester surfaces is examined by using molecular dynamics simulations. Functionalization of the polyester surface has prevented the [C.sub.60] from approaching as close to the polyester surface and fluorination has led to improved resistance to positively charged fullerenes, compared to the unmodified polyester.

The relative stabilities and properties of different arrangements of S on Fe(110) at a 1/3 monolayer coverage is compared using density functional theory calculations. For all studied arrangements, S is absorbed in the three high-symmetry adsorption sites, 4-fold hollow, 3-fold hollow, bridge and atop sites.

A study on molecular dynamics simulations on insulin chain-B under the influence of both static and oscillating electric fields ranging from 10(super 7) to 10(super 9) V/m was conducted. Both the 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 study examined the adhesion of graphite to functionalized polyester surfaces using a range of qualitative and quantitative measures of theoretical adhesion. The theoretical results suggested one mechanism to reduce adhesion to carbonaceous solids, which is to increase atomic roughness using strongly hydrophilic or alternatively strongly hydrophobic substituents.

The effects of adsorbed S at different coverages on the adhesion of Fe(110) surfaces in the match and mismatch is examined using density functional theory (DFT). S is adsorbed in the atop, bridge, and 4-fold hollow sites on one side of the inter face in c(2 x 2) and p(1 x 1) arrangements, corresponding to coverages of 1/2 an 1 monolayer.