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Adam Arnold Skelton

Adam Arnold Skelton

PhD in Chemistry
Data scientist in transport consultancy

About

59
Publications
12,653
Reads
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1,191
Citations
Additional affiliations
March 2018 - present
University of KwaZulu-Natal
Position
  • Fellow
February 2018 - present
Univeristy of Liverpool
Position
  • Research Associate
November 2012 - February 2018
University of KwaZulu-Natal
Position
  • Lecturer
Education
June 2004 - May 2008
The University of Warwick
Field of study
  • Chemistry

Publications

Publications (59)
Article
Pentazole having the molecular formula HN5 is an archetypical five-membered homocyclic inorganic aromatic molecule consisting of five nitrogen atoms. A hydrogen atom is bonded to one of the nitrogens. Even though the molecule does not contain a carbon it appears last in the series of the heterocyclic azole family; the family containing one to five...
Article
pKas of P(1)-H deprotonation of all phosphole group compounds, phosphole (C4H4PH), 1,2 and 1,3-diphospholes (C3H3PPH), 1,2,3, and 1,2,4-triphospholes (C2H2P2PH), tetraphosphole (CHP3PH), and pentaphosphole (P4PH) are determined by DFT calculations. We have compared these to the pKas of the analogue azole group compounds and the factors that cause t...
Article
Full-text available
A computational methodology that couples the acidity (Ka) and density functional theory (DFT) calculations has been developed to explain the pH-dependent drug loading and releasing by mesoporous silica nanoparticles. The...
Article
It is well known that benzoic acid distributes itself between chloroform and water. The partition coefficients (Kp) of seven different benzoic acids in chloroform/water are documented in the literature. Plausible hydrogen bonded structures of these seven benzoic acids with the two immiscible solvents were envisaged and the DFT calculation for these...
Article
Full-text available
Pharmaceuticals (PhACs) are a class of emerging contaminants of global concern due to their ubiquitous nature, persistence and capability of affecting humans and aquatic lives negatively even at very low concentrations. Conventional wastewater treatment procedures are generally inadequate for removing these contaminants. Photocatalysis, an advance...
Article
Smart antimicrobial surfaces are a powerful tool to prevent bacterial colonisation at surfaces. In this work, we report a successful strategy for the functionalisation of polydimethylsiloxane (PDMS) surfaces, widely used in medical devices, with salicylic acid (SA), a biocide approved for use in humans. Antimicrobial PDMS surfaces were fabricated v...
Article
Full-text available
Alzheimer’s disease is the most common form of dementia, that affects millions of people worldwide. According to the widely accepted amyloid cascade hypothesis, misfolding and aggregation of Aβ peptides is the principal cause of Alzheimer’s disease. In the present mini-review, we have discussed the different structures of Aβ protein from monomer to...
Article
Full-text available
The pH-dependent adsorption of ibuprofen (IBP) onto acid-functionalized multiwalled carbon nanotubes (CNT-COOH), was investigated by batch adsorption experiments, quantum mechanics (QM) and molecular mechanics (MM) simulation. A force field was developed and applied for monitoring interactions between IBP and CNT-COOH. Our simulations relied on the...
Article
Three new ruthenium(II) complexes [(η⁶-p-cymene)RuX(L)]PF6 (X = Cl (1), Br (2) and I (3)) with 9-ethyl-N-(pyridin-2-ylmethylene)9H-carbazole-3-amine (L) have been prepared and characterised by elemental analysis and different spectral techniques (NMR studies, IR and HR-Mass spectroscopy). The molecular structure of the [(η⁶-p-cymene)RuI(L)]PF6 (3)...
Article
Full-text available
Herein, we present a theoretical model that combines classical pK a theory with quantum mechanical calculations to predict the extent of interaction between acid/base dependent species at a full range of pH conditions. To demonstrate the theoretical model, we have predicted the drug loading and release for a pH-responsive drug delivery system consi...
Article
Full-text available
A parametric study of ReaxFF for molecular dynamics simulation of graphitization of amorphous carbon was conducted. The responses to different initial amorphous carbon configurations, simulation time steps, simulated temperatures, and ReaxFF parameter sets were investigated. The results showed that time step shorter than 0.2 fs is sufficient for th...
Article
The use of plant extracts provides a biologically inspired route for the synthesis of nanoparticles, which have received a significant interest worldwide. ZnO nanomaterials have been one of the most comprehensively researched materials for decades and still hold attention of researchers in the field of biosensing. In the present study, a systematic...
Article
Full-text available
The solution conditions such as the ion concentration and pH have a profound effect on the behaviour of the silica/water interface, which dictates many of the surface properties of mesoporous silica nanoparticles (MSNs) and their utility in a range of nanotechnology applications. The interaction of water molecules with a model silica surface, α-qua...
Article
Alzheimer’s disease is the most common form of dementia and is considered to be caused by the conformational change of Aβ monomers, from their native monomeric states, to form Aβ oligomers/aggregates in the brain. Turn formation in Aβ monomer has been suggested to be the nucleation step for Aβ misfolding. In the present work, we have performed a se...
Article
In our earlier article¹, we had shown the application of Hammett equation of finding the site of attack. The application is based on the relative position of substituent on the aromatic ring from the center of the reaction. We had shown why we have to use σm value for σp and σp value for σm value, when we use Hammett’s plot. In the present article...
Article
Full-text available
1,4,7 triazacyclononane-1,4,7 triacetic acid (NOTA) is a key bifunctional chelator utilized for the complexation of metal ions in radiopharmaceutical applications; the ability of these chelators depends on the strength of their binding with ions. The focus of the present work is to evaluate the complexation of Cu2+, Ga3+, Sc3+ and In3+ radiometal i...
Article
The ligand, 4′-(4-hydroxyphenyl)-2,2′:6′,2″-terpyridine, was bonded to multiwalled carbon nanotubes to afford nitrogen-functionalized carbon nanotubes (MWCNT-ttpy). This material was compared with acid-functionalized multiwalled carbon nanotubes (MWCNT-COOH) for the removal of Pb²⁺ and Zn²⁺ from aqueous solution. The comparison was conducted both e...
Article
1, 4, 7, 10-tetraazacyclododecane-1, 4, 7, 10-tetracetic acid (DOTA) is an important chelator for radiolabeling of pharmaceuticals. The ability of alkali metals found in the body to complex with DOTA and compete with radio metal ions can alter the radiolabeling process. Non-covalent interactions between DOTA complexed with alkali metals Li⁺, Na⁺, K...
Article
This work involves the experimental and theoretical study of the nucleophilic substitution of meta- and para-substituted benzyl bromides with benzylamine. Conductometric rate experiments confirm the applicability of the Hammett linear free-energy relationship to this system. To gain a deep understanding of the physical chemistry at play, a quantum...
Article
Abstract Hammett and Taft equations in their most basic forms are linear free energy relationships between standard free energies of two reaction series. Therefore any chemical or physical property inherently associated with any of the thermodynamic property like enthalpy H, free energy G, internal energy E or entropy S are subjected to substituent...
Article
1,4,7 triazacyclononane-1,4,7 triacetic acid (NOTA) is a key chelator for radiolabelling pharmaceuticals. The ability of alkali metals in the human body to complex with NOTA and compete with radiometals can influence the radiolabelling process. The focus of the present work is to evaluate the NOTA?alkali metal complexation with density functional t...
Article
Recent experimental data elucidated that 12-crown-4 ether molecule can disrupt Aβ40 fibrils but the mechanism of disruption remains elusive. We have performed a series of all-atom molecular dynamics simulations to study the molecular mechanism of Aβ40 fibril disruption by 12-crown-4. In the present study we have used the Aβ40 fibril trimer as it is...
Article
MMP-9 is an attractive target for the development of new anticancer drugs. In the current study, pharmacophore modeling was employed using two highly active and selective gelatinase inhibitors obtained from two X- ray crystal structures PDB IDs: 2OVX and 2OW1 to identify novel selective MMP-9 inhibitors. The derived model was refined manually and a...
Article
Full-text available
The structure and dynamics of B. circulans b-1,4-xylanase (BCX) were comparatively studied utilizing molecular dynamics. Simulations of the free enzyme, non-covalently bound, and covalently bound xylobiose intermediate were conducted and post-dynamically studied to comprehend structural changes adopted during a reaction. Results showed that (a) cov...
Article
A new series of ten poly-functionalized pyrano[2,3-d]pyrimidine formimidate derivatives were successfully synthesized. All the synthesized compounds were characterized by 1H NMR, 13C NMR, HRMS, and FT-IR spectral analysis. All the synthesized compounds were evaluated for their antimicrobial activity by using the well plate method and MIC by the bro...
Article
Full-text available
Non-linear Hammett relationship was applied to surface tensions (γ) and dipole moments (μ) of some meta and para substituted phenols. The non-linearity of log γ versus Hammett G correlation was explained in terms of Eötvös constant, Ramsay-Shields equation, Trouton's rule, order of association, sandwich type molecular pairs and number of hydrogen b...
Article
Full-text available
Quantum mechanical calculations were performed to study the conformational behavior and complexation between a sodium cation and a diazacrown (diaza-18-crown-6) using density functional theory (DFT), Møller-Plesset (MP2) and molecular mechanics methods. A goal of this work is to gain a fundamental understanding of the interplay between water molecu...
Article
Full-text available
Quantum mechanical calculations were performed to study the conformational behavior and complexation between a sodium cation and a diazacrown (diaza-18-crown-6) using density functional theory (DFT), Møller-Plesset (MP2) and molecular mechanics methods. A goal of this work is to gain a fundamental understanding of the interplay between water molecu...
Article
Full-text available
All-atom molecular dynamics is used to investigate the transport of Na(+) across a 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayer facilitated by a diazacrown hydraphile. Specifically, the free energy of Na(+) passing through the bilayer is calculated using the adaptive biasing force method to study the free energy associated with the increa...
Article
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...
Article
Full-text available
The design of stable and inexpensive artificial enzymes with potent catalytic activity is a growing field in peptide science. The first step in this design process is to understand the key factors that can affect the conformational preference of an enzyme and correlate them with its catalytic activity. In this work, molecular dynamics simulations i...
Article
Full-text available
Phytochemicals of Catharanthus roseus Linn. and Tylophora indica have been known for their inhibition of malarial parasite, Plasmodium falciparum in cell culture. Resistance to Chloroquine (CQ), a widely used antimalarial is due to the CQ resistance transporter (CRT) system. The present study deals with computational modeling of Plasmodium falcipar...
Article
The rates of reactions of para- and meta-substituted benzylamines with benzyl bromide were measured using conductivity technique in methanol medium. The reaction followed a total second-order path. The end product of the reaction is identified as dibenzylamine (X-C6H4CH2NHCH2C6H5) (where X = 4-OCH3, 4-CH3, H, 4-Cl, 4-CF3, 3-CF3, 4-NO2). Electron-wi...
Article
Full-text available
Simple 5-membered heterocycles and two of their N-methylated derivatives with two hetero atoms viz. pyrazole, isoxazole isothiozole and 1-methylpyrazole and with one hetero atom viz. pyrrole, furan, thiophene and N-methylpyrrole have shown a discriminative behavior toward surface tension, EÖTVÖS constants (k), order of association (x). This was exp...
Article
Published X-ray crystallographic structures for glycoside hydrolases (GHs) from 39 different families are surveyed according to some rigorous selection criteria and the distances separating 208 pairs of catalytic carboxyl groups (20 α-retaining, 87 β-retaining, 38 α-inverting and 63 β-inverting) are analysed. First, the average of all four inter-ca...
Article
Full-text available
Pharmacophore-based virtual screening is being widely used to discover new drug candidates. Building a pharmacophore model based on a known inhibitor that is unbound to the target could be misleading and result in mining for the wrong hits. Results presented herein confirm that pharmacophore models based on unbound and bound ligand confirmations pr...
Article
Full-text available
Association behavior of mono, di and tri-hydric alcohols having three carbon skeleton in a straight chain was studied based on surface tension (γ) data, EÖTVÖS constants (k), order of association (x), hydrogen bond acceptor (H a)-donor (H d) counts and Trouton's rule. It is to be understood from the title that alcohols used were 1-propanol, 2-propa...
Article
Full-text available
Molecular dynamics simulations were performed to gain insight into the channel-forming capabilities of the SCMTR class of anion channels. These results support pore formation by the experimentally predicted single-surface dimeric SCMTR configuration. Simulated currents of 11.1 pA and 3.7 pA were reported for simulations involving a charge imbalance...
Article
Classical molecular dynamics (MD) simulations were employed to investigate the adsorption behaviors of arginine-glycine-aspartate (RGD) tripeptide onto the negatively charged hydroxylated/nonhydroxylated rutile (110) surfaces, mediated by biologically important cations (Na+ or Ca2+). The simulation results indicate that the inherent nature of catio...
Article
Full-text available
Density functional theory (DFT) calculations using the B3LYP and ωB97XD functionals and Møller-Plesset (MP2) calculations have been used to determine the energy of insertion of seven molecules (CO, N, O, CO, CH, He and HO) into two sizes of polyhedral oligomeric silsesquioxane (POSS) cages, T and T. Geometry optimization results of each molecule in...
Article
Density functional theory (DFT) calculations, including the ab initio molecular dynamics method, atom‐centered density matrix propagation (ADMP), were used to investigate the hydrolysis reaction of a dichlorophosphazene trimer. The model trimer, intermediate structures and the product of the first step of hydrolysis, were optimized using DFT with t...
Article
A novel mechanism for protonating bridging O atoms (Obr) and dissolving silica is proposed that is consistent with experimental data and quantum mechanical simulations of the α-quartz (101)/water interface. The new hypothesis is that H+-transfer occurs through internal surface H-bonds (i.e., SiOH–Obr) rather than surface water H-bonds and that incr...
Article
Full-text available
Liu and co-workers [ Phys. Rev. B 82 161415 (2010)] discussed the long-standing debate regarding whether H2O molecules on the defect-free (110) surface of rutile (α-TiO2) 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 mole...
Article
The binding of a negatively charged residue, aspartic acid (Asp) in tripeptide arginine-glycine-aspartic acid, onto a negatively charged hydroxylated rutile (110) surface in aqueous solution, containing divalent (Mg(2+), Ca(2+), or Sr(2+)) or monovalent (Na(+), K(+), or Rb(+)) cations, was studied by molecular dynamics (MD) simulations. The results...
Article
The dynamics of a single tripeptide Arg-Gly-Asp (RGD) adsorbing onto negatively charged hydroxylated rutile (110) surface in aqueous solution was studied using molecular dynamics (MD) simulations. The results indicate that the adsorbed Na{sup +} ions play an important role in determining the binding geometry of RGD. With an initial 'horseshoe' conf...
Article
Two different terminations of the (1010) surface of quartz (α and β) interacting with water are simulated by classical (CMD) (using two different force fields) and ab initio molecular dynamics (AIMD) and compared with previously published X-ray reflectivity (XR) experiments. Radial distribution functions between hydroxyl and water show good agreeme...
Article
Full-text available
A method for comparing pixelated density profiles (e.g. obtained from molecular dynamics or other computational techniques) with experimental X-ray reflectivity data both directly and quantitatively is described. The conditions under which such a comparison can be made quantitatively (e.g. with errors <1%) are determined theoretically by comparing...
Article
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, and CHARMM water contact angle (CWCA), and compared to ab initio molecular dynamics (AIMD) and X-ray reflectivity (XR) results. The axial densities of the...
Conference Paper
The interaction between water and two surfaces relating to different crystallographic faces of α-quartz have been atomistically modeled using the force-field of Lopes et al. (1). Comparisons with X-ray reflectivity experiments (2) have shown agreement between simulation and experiment for the 10-10 and α-quartz surfaces, supporting the accuracy of...
Article
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 b...
Article
Full-text available
A force-field which describes the interaction between the TiO 2 (110) rutile surface and a modified TIP3P water [P. Mark and L. Nilsson, J. Phys. Chem. A, 105, 9954, (2001)] is tested against periodic density functional theory (PDFT). Optimizations of water on the non-hydroxylated and hydroxylated surfaces are performed using PDFT and the geometrie...

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Projects (5)
Project
Molecular modelling of metal oxide-water and metal oxide/peptide interfaces
Project
Decipher the molecular mechanism of Amyloid fibrils interaction with candidate drug molecules, identify the binding sites, and reveal the conformational perturbations induced by these molecules in Amyloid.