Adam A. Skelton

Bio: Adam A. Skelton is an academic researcher from University of KwaZulu-Natal. The author has contributed to research in topics: Molecular dynamics & Mesoporous silica. The author has an hindex of 18, co-authored 52 publications receiving 1158 citations. Previous affiliations of Adam A. Skelton include University of Dayton & University of Warwick.

Simulations of the Quartz(1011)/Water Interface: A Comparison of Classical Force Fields, Ab Initio Molecular Dynamics, and X-ray Reflectivity Experiments

Abstract: Classical molecular dynamics (CMD) simulations of the (1011) surface of quartz interacting with bulk liquid water are performed using three different classical force fields, Lopes et al., ClayFF, ...

Interplay of Sequence, Conformation, and Binding at the Peptide−Titania Interface as Mediated by Water

Abstract: The initial stages of the adsorption of a hexapeptide at the aqueous titania interface are modeled using atomistic molecular dynamics simulations. This hexapeptide has been identified by experiment [Sano, K. I.; Shiba, K. J. Am. Chem. Soc. 2003, 125, 14234] to bind to Ti particles. We explore the current hypothesis presented by these authors that binding at this peptide−titania interface is the result of electrostatic interactions and find that contact with the surface appears to take place via a pair of oppositely charged groups in the peptide. Our data indicate that the peptide may initially recognize the water layers at the interface, not the titania surface itself, via these charged groups. We also report results of simulations for hexapeptide sequences with selected single-point mutations for alanine and compare these behaviors with those suggested from observed binding affinities from existing alanine scan experiments. Our results indicate that factors in addition to electrostatics also contribute, ...

Ion pairing with linoleic acid simultaneously enhances encapsulation efficiency and antibacterial activity of vancomycin in solid lipid nanoparticles

Abstract: Ion pairing of a fatty acid with an antibiotic may be an effective strategy for formulation optimization of a nanoantibiotic system. The aim of this study was therefore to explore the potential of linoleic acid (LA) as an ion pairing agent to simultaneously enhance encapsulation efficiency and antibacterial activity of triethylamine neutralized vancomycin (VCM) in solid lipid nanoparticles (SLNs). The prepared VCM-LA2 conjugate was characterized by Fourier transform-infrared (FT-IR) spectroscopy, logP and binding energy calculations. The shifts in the FT-IR frequencies of COOH, NH2 and CO functionalities, an increase in logP value (1.37) and a lower interaction energy between LA and VCM (-125.54 kcal/mol) confirmed the formation of the conjugate. SLNs were prepared by a hot homogenization and ultrasonication method, and characterized for size, polydispersity index (PI), zeta potential (ZP), entrapment efficiency (%EE), surface morphology and physical stability. In vitro antibacterial activity studies against Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) were conducted. Size, PI and ZP for VCM-LA2_SLNs were 102.7±1.01, 0.225±0.02 and -38.8±2.1 (mV) respectively. SLNs were also stable at 4 °C for 3 months. %EE for VCM-HCl_SLNs and VCM-LA2_SLNs were 16.81±3.64 and 70.73±5.96 respectively, indicating a significant improvement in encapsulation of the drug through ion pairing with LA. Transmission electron microscopy images showed spherical nanoparticles with sizes in the range of 95-100 nm. After 36 h, VCM-HCl showed no activity against MRSA. However, the minimum inhibitory concentration for VCM-HCl_SLNs and VCM-LA2_SLNs were 250 and 31.25 μg/ml respectively against S. aureus, while against MRSA it was 500 and 15.62 μg/ml respectively. This confirms the enhanced antibacterial activity of VCM-LA2_SLNs over VCM-HCl_SLNs. These findings therefore suggest that VCM-LA2_SLNs is a promising nanoantibiotic system for effective treatment against both sensitive and resistant S. aureus infections.

Computer Simulations of Quartz (101)–Water Interface over a Range of pH Values

Abstract: The original force field for clay materials (ClayFF) developed by Cygan et al. (J. Phys. Chem. B 2004, 108, 1255) is modified to describe negative charging of the (101) quartz surface above its point of zero charge (pH ≈ 2.0–4.5). The modified force field adopts the scaled natural bond orbital charges derived by the quantum mechanical calculations which are used to obtain the desired surface charge density and to determine the delocalization of the charge after deprotonation of surface silanol groups. Classical molecular dynamics simulations (CMD) of the (101) surface of α-quartz with different surface charge densities (0, −0.03, −0.06, and −0.12 C m–2) are performed to evaluate the influence of the negative surface charge on interfacial water and adsorption of Na+, Rb+, and Sr2+ ions. The CMD results are compared with ab initio calculations, X-ray experiment, and the triple-layer model. The modified force field can be easily implemented in common molecular dynamics packages and used for simulations of in...

Comment on "structure and dynamics of liquid water on rutile TiO 2(110)"

Abstract: Liu and co-workers [Phys. Rev. B 82, 161415 (2010)] discussed the long-standing debate regarding whether H${}_{2}$O molecules on the defect-free (110) surface of rutile (\ensuremath{\alpha}-TiO${}_{2}$) sorb associatively, or there is dissociation of some or all first-layer water to produce hydroxyl surface sites. They conducted static density functional theory (DFT) and DFT molecular dynamics (DFT-MD) investigations using a range of cell configurations and functionals. We have reproduced their static DFT calculations of the influence of crystal slab thickness on water sorption energies. However, we disagree with several assertions made by these authors: (a) that second-layer water structuring and hydrogen bonding to surface oxygens and adsorbed water molecules are ``weak''; (b) that translational diffusion of water molecules in direct contact with the surface approaches that of bulk liquid water; and (c) that there is no dissociation of adsorbed water at this surface in contact with liquid water. These assertions directly contradict our published work, which compared synchrotron x-ray crystal truncation rod, second harmonic generation, quasielastic neutron scattering, surface charge titration, and classical MD simulations of rutile (110) single-crystal surfaces and (110)-dominated powders in contact with bulk water, and (110)-dominated rutile nanoparticles with several monolayers of adsorbed water.

I and i

Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

A molecular perspective of water at metal interfaces

Abstract: Water/solid interfaces are relevant to a broad range of physicochemical phenomena and technological processes such as corrosion, lubrication, heterogeneous catalysis and electrochemistry. Although many fields have contributed to rapid progress in the fundamental knowledge of water at interfaces, detailed molecular-level understanding of water/solid interfaces comes mainly from studies on flat metal substrates. These studies have recently shown that a remarkably rich variety of structures form at the interface between water and even seemingly simple flat surfaces. In this Review we discuss the most exciting work in this area, in particular the emerging physical insight and general concepts about how water binds to metal surfaces. We also provide a perspective on outstanding problems, challenges and open questions.

Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments

Abstract: Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments / Albert Rimola;Dominique Costa;Mariona Sodupe;Jean-François Lambert;Piero Ugliengo. In: CHEMICAL REVIEWS. ISSN 0009-2665. STAMPA. 113:6(2013), pp. 4216-4313. Original Citation: Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments