Molecular dynamics studies of the STAT3 homodimer:DNA complex: relationships between STAT3 mutations and protein-DNA recognition.

Signal Transducers and Activators of Transcription (STAT) proteins are a group of latent cytoplasmic transcription factors involved in cytokine signaling. STAT3 is a member of the STAT family and is expressed at elevated levels in a large number of diverse human cancers and is now a validated target for anticancer drug discovery.. Understanding the dynamics of the STAT3 dimer interface, accounting for both protein-DNA and protein-protein interactions, with respect to the dynamics of the latent unphosphorylated STAT3 monomer, is important for designing potential small-molecule inhibitors of the activated dimer. Molecular dynamics (MD) simulations have been used to study the activated STAT3 homodimer:DNA complex and the latent unphosphorylated STAT3 monomer in an explicit water environment. Analysis of the data obtained from MD simulations over a 50 ns time frame has suggested how the transcription factor interacts with DNA, the nature of the conformational changes, and ways in which function may be affected. Examination of the dimer interface, focusing on the protein-DNA interactions, including involvement of water molecules, has revealed the key residues contributing to the recognition events involved in STAT3 protein-DNA interactions. This has shown that the majority of mutations in the DNA-binding domain are found at the protein-DNA interface. These mutations have been mapped in detail and related to specific protein-DNA contacts. Their structural stability is described, together with an analysis of the model as a starting-point for the discovery of novel small-molecule STAT3 inhibitors.

Selective Hydrogenation of alpha,beta-Unsaturated Aldehydes and Ketones using Novel Manganese Oxide and Platinum Supported on Manganese Oxide Octahedral Molecular Sieves as Catalysts

The selective hydrogenation of ,-unsaturated aldehydes and ketones has been studied using ketoisophorone and cinnamaldehyde as model substrates using manganese oxide octahedral molecular sieve (OMS-2) based catalysts. For the first time, OMS-2 has been shown to be an efficient and selective hydrogenation catalyst. High selectivities for either the CC or CO double bond at approximate to 100% conversion were achieved by using OMS-2 and platinum supported on OMS-2 catalysts. Density functional theory (DFT) calculations showed that the dissociation of H2 on OMS-2 was water assisted and occurred on the surface Mn of OMS-2(001) that had been modified by an adsorbed H2O molecule. The theoretically calculated activation barrier was in good agreement with the experimentally determined value for the hydrogenation reactions, indicating that H2 dissociation on OMS-2 is likely to be the rate-determining step. A significant increase in the rate of reaction was observed in the presence of Pt as a result of the enhancement of H2 dissociative adsorption and subsequent reaction on the Pt or spillover of the hydrogen to the OMS-2 support. The relative adsorption strengths of ketoisophorone and cinnamaldehyde on the OMS-2 support compared with the Pt were found to determine the product selectivity.

Water-compatible imprinted polymers for selective depletion of riboflavine from beverages

Artificial riboflavin receptors adapted to aqueous environments were studied for their ability to selectively extract riboflavine (Rf) from three types of beverages i.e. milk, beer and a multivitamin mixture. The basic receptor was first prepared by molecular imprinting in nonaqueous medium using a hydrogen-bond donor-acceptor-donor functional monomer (2,6-bis(acrylamido)pyridine), complementary to the imide motif of the template, riboflavin tetra-acetate as template and pentaerythritol triacrylate (PETA) as a hydrophilic cross-linking monomer. The polymer was then packed in columns and used for extraction of riboflavine from beverages. Riboflavine (Rf) was selectively removed from milk and an artificial vitamin mixture but the nonspecific binding was still significant, as judged from the binding of Rf to a control nonimprinted polymer. In order to suppress this nonspecific binding, attempts to hydrolytically hydrophilize the polymer matrix were performed. The preferred approach consisted in a controlled base hydrolysis of pendent unreacted acrylate groups, using hydroxides with differently sized counterions as reagents. This resulted in a decreased binding of Rf to both polymers, but to an equal extent implying a preferential suppression of the nonspecific contribution to the binding. The hydrophilized polymers, when subjected to beer, showed larger imprinting factors at lower phase ratios compared to the nontreated polymers and a maximum removal of 86% compared to 47% for the nonimprinted control polymer.

A Molecular Dynamics Study of the Early Stages of Calcium Carbonate Growth

The precipitation of calcium carbonate in water has been examined using a combination of molecular dynamics and umbrella sampling. During 20 ns molecular dynamics trajectories at elevated calcium carbonate concentrations, amorphous particles are observed to form and appear to be composed of misaligned domains of vaterite and aragonite. The addition of further calcium ions to these clusters is found to be energetically favorable and virtually barrierless. By contrast, there is a large barrier to the addition of calcium to small calcite crystals. Thus, even though calcite nanocrystals are stable in solution, at high supersaturations, particles of amorphous material form because this material grows much faster than ordered calcite nanocrystals.

Liquid densities, heat capacities, refractive index and excess quantities for {protic ionic liquids plus water} binary system

Densities, rho, of aqueous solutions of the room temperature protic ionic liquid (PIL), pyrrolidinium nitrate are determined at the atmospheric pressure over the temperature range from (283.15 to 323.15) K and within the whole composition range. The molar isobaric heat capacities, C(p), and refractive index, n(D), of {PIL + water} binary system are measured at 298.15 K. The excess molar volumes V(E), excess molar isobaric heat capacities C(p)(E), and deviation from ideality of refractive index Delta(phi)n, of pyrrolidinium nitrate aqueous solutions were deduced from the experimental results as well as apparent molar volumes V(phi), partial molar volumes (V) over bar (m,i), and thermal expansion coefficients alpha(p). The V(E) values were found to be positive over the entire composition range at all temperatures studied therein, whereas deviations from ideality were negative for refractive index Delta(phi)n. The volumetric properties of binary mixtures containing water and four other protic ionic liquids, such as pyrrolidinium hydrogen sulfate, pyrrolidinium formiate, collidinium formate, and diisopropyl-ethylammonium formate were also determined at 298.15 K. Results have been then discussed in terms of molecular interactions and molecular structures in these binary mixtures. (C) 2009 Elsevier Ltd. All rights reserved.

Simulations of Biased Agonists in the β2 Adrenergic Receptor with Accelerated Molecular Dynamics

The biased agonism of the G protein-coupled receptors (GPCRs), where in addition to a traditional G protein-signalling pathway a GPCR promotes intracellular signals though ß-arrestin, is a novel paradigm in pharmacology. Biochemical and biophysical studies have suggested that a GPCR forms a distinct ensemble of conformations signalling through the G protein and ß-arrestin. Here we report on the dynamics of the ß2 adrenergic receptor bound to the ß-arrestin and G protein biased agonists and the empty receptor to further characterize the receptor conformational changes caused by biased agonists. We use conventional and accelerated molecular dynamics (aMD) simulations to explore the conformational transitions of the GPCR from the active state to the inactive state. We found that aMD simulations enable monitoring the transition within the nanosecond timescale while capturing the known microscopic characteristics of the inactive states, such as the ionic lock, the inward position of F6.44, and water clusters. Distinct conformational states are shown to be stabilized by each biased agonist. In particular, in simulations of the receptor with the ß-arrestin biased agonist, N-cyclopentylbutanepherine we observe a different pattern of motions in helix 7 when compared to simulations with the G protein biased agonist, Salbutamol that involves perturbations of the network of interactions within the NPxxY motif. Understanding the network of interactions induced by biased ligands and the subsequent receptor conformational shifts will lead to development of more efficient drugs. © 2013 American Chemical Society

Water-hydrophobic compound interactions with the microbial cell

The structural interactions of biological macromolecules, their biochemical activities and, ultimately, the metabolic function of cellular systems are dependent upon weak inter- and intra-molecular forces such as hydrogen bonds, Van der Waals forces, and the hydrophobic effect. Water molecules, and those of hydrophobic substances such as hydrocarbons, can take part in and/or modify these interactions and thereby determine the operational and structural stability of the microbial cell and its macromolecular systems. We explain how the cytosol, plasma membrane and the extracellular solution form a material and energetic continuum; and discuss the behavior of hydrophobic substances of extracellular origin as they migrate into the plasma membrane and into the cell's interior. The adverse effects of substances with a log P octanol-water =2, that partition into the hydrophobic domains of biological macromolecules, are discussed in relation to microbial cell function; and we speculate whether the cellular stress that they induce is symmetrical or asymmetrical in nature. In the context of the microbial environment, we take a situational-functional approach to consider how hydrophobic stressors interact with the microbial cell, and what types of evasion tactics microbes can employ to minimize their inhibitory activities. Finally, we discuss the ecological implications of hydrocarbon-induced cellular stress for microbial systems.

Influence of chloride, water, and organic solvents on the physical properties of ionic liquids

We report here the first systematic study of the effect of impurities and additives (e.g., water, chloride, and cosolvents) on the physical properties of room-temperature ionic liquids. Remarkably, it was discovered that the viscosity of mixtures was dependent mainly on the mole fraction of added molecular solvents and only to a lesser extent upon their identity, allowing viscosity changes during the course of a reaction to be entirely predictable. While the addition of such molecular solvents decreases the viscosity and density, chloride impurities, arising from the preparation of the ionic liquids, increase viscosity dramatically. The commonly used methods of preparation were validated with respect to chloride impurity.

Flux of ionic dyes across microneedle-treated skin:effect of molecular characteristics

Drug flux across microneedle (MN)-treated skin is influenced by the characteristics of the MN array, formed microconduits and physicochemical properties of the drug molecules in addition to the overall diffusional resistance of microconduits and viable tissue. Relative implication of these factors has not been fully explored. In the present study, the in vitro permeation of a series of six structurally related ionic xanthene dyes with different molecular weights (MW) and chemical substituents, across polymer MN-pretreated porcine skin was investigated in relation of their molecular characteristics. Dyes equilibrium solubility, partition coefficient in both n-octanol or porcine skin/aqueous system, and dissociation constants were determined. Results indicated that for rhodamine dyes, skin permeation of the zwitterionic form which predominates at physiological pH, was significantly reduced by an increase in MW, the skin thickness and by the presence of the chemically reactive isothiocyanate substituent. These factors were generally shown to override the aqueous solubility, an important determinant of drug diffusion in an aqueous milieu. The data obtained provided more insight into the mechanism of drug permeation across MN-treated skin, which is of importance to both the design of MN-based transdermal drug delivery systems and of relevance to skin permeation research.

The Role of Water and Adsorbed Hydroxyls on Ethanol Electrochemistry on Pd: New Mechanism, Active Centers and Energetics for Direct Ethanol Fuel Cell Running in Alkaline Medium

First principles calculations with molecular dynamics are
utilized to simulate a simplified electrical double layer formed in the
active electric potential region during the electrocatalytic oxidation of
ethanol on Pd electrodes running in an alkaline electrolyte. Our
simulations provide an atomic level insight into how ethanol oxidation
occurs in fuel cells: New mechanisms in the presence of the simplified
electrical double layer are found to be different from the traditional
ones; through concerted-like dehydrogenation paths, both acetaldehyde
and acetate are produced in such a way as to avoid a variety of
intermediates, which is consistent with the experimental data obtained
from in situ FTIR spectroscopy. Our work shows that adsorbed OH on
the Pd electrode rather than Pd atoms is the active center for the
reactions; the dissociation of the C−H bond is facilitated by the
adsorption of an OH− anion on the surface, resulting in the formation
of water. Our calculations demonstrate that water dissociation rather than H desorption is the main channel through which
electrical current is generated on the Pd electrode. The effects of the inner Helmholtz layer and the outer Helmholtz layer are
decoupled, with only the inner Helmholtz layer being found to have a significant impact on the mechanistics of the reaction. Our
results provide atomic level insight into the significance of the simplified electrical double layer in electrocatalysis, which may be
of general importance.

Irradiation of water ice by C+ ions in the cosmic environment

We present a first principles molecular dynamics (FPMD) study of the interaction of low energy, positively charged, carbon (C+) projectiles with amorphous solid water clusters at 30 K. Reactions involving the carbon ion at an initial energy of 11 eV and 1.7 eV with 30-molecule clusters have been investigated. Simulations indicate that the neutral isoformyl radical, COH, and carbon monoxide, CO, are the dominant products of these reactions. All these reactions are accompanied by the transfer of a proton from the reacting water molecule to the ice, where it forms a hydronium ion. We find that COH is formed either via a direct, "knock-out", mechanism following the impact of the C+ projectile upon a water molecule or by creation of a COH_2^+ intermediate. The direct mechanism is more prominent at higher energies. CO is generally produced following the dissociation of COH. More frequent production of the formyl radical, HCO, is observed here than in gas phase calculations. A less commonly occurring product is the dihydroxymethyl, CH(OH)_2, radical. Although a minor result, its existence gives an indication of the increasing chemical complexity which is possible in such heterogeneous environments.

Universal tight binding model for chemical reactions in solution and at surfaces. II. Water

A revised water model intended for use in condensed phase simulations in the framework of the self consistent polarizable ion tight binding theory is constructed. The model is applied to water monomer, dimer, hexamers, ice, and liquid, where it demonstrates good agreement with theoretical results obtained by more accurate methods, such as DFT and CCSD(T), and with experiment. In particular, the temperature dependence of the self diffusion coefficient in liquid water predicted by the model, closely reproduces experimental curves in the temperature interval between 230 K and 350 K. In addition, and in contrast to standard DFT, the model properly orders the relative densities of liquid water and ice. A notable, but inevitable, shortcoming of the model is underestimation of the static dielectric constant by a factor of two. We demonstrate that the description of inter and intramolecular forces embodied in the tight binding approximation in quantum mechanics leads to a number of valuable insights which can be missing from ab initio quantum chemistry and classical force fields. These include a discussion of the origin of the enhanced molecular electric dipole moment in the condensed phases, and a detailed explanation for the increase of coordination number in liquid water as a function of temperature and compared with ice-leading to insights into the anomalous expansion on freezing. The theory holds out the prospect of an understanding of the currently unexplained density maximum of water near the freezing point. 

Universal tight binding model for chemical reactions in solution and at surfaces. III. Stoichiometric and reduced surfaces of titania and the adsorption of water

We demonstrate a model for stoichiometric and reduced titanium dioxide intended for use in molecular dynamics and other atomistic simulations and based in the polarizable ion tight binding theory. This extends the model introduced in two previous papers from molecular and liquid applications into the solid state, thus completing the task of providing a comprehensive and unified scheme for studying chemical reactions, particularly aimed at problems in catalysis and electrochemistry. As before, experimental results are given priority over theoretical ones in selecting targets for model fitting, for which we used crystal parameters and band gaps of titania bulk polymorphs, rutile and anatase. The model is applied to six low index titania surfaces, with and without oxygen vacancies and adsorbed water molecules, both in dissociated and non-dissociated states. Finally, we present the results of molecular dynamics simulation of an anatase cluster with a number of adsorbed water molecules and discuss the role of edge and corner atoms of the cluster. (C) 2014 AIP Publishing LLC.

Water in protoplanetary disks

Infrared water line emission from protoplanetary disks, recently observed by the Spitzer and Herschel space telescopes, is thought to trace the surface layer of the inner to outer regions of the disks. We have modelled the water abundance profile and line emission, especially focusing on the effects of dust size growth and turbulent mixing. Comparison between model calculations and observations suggests a small grain model with turbulent mixing is preferred. Copyright © International Astronomical Union 2014.

Novel photocatalytic reactor development for removal of hydrocarbons from water

Hydrocarbons contamination of the marine environment generated by the offshore oil and gas industry is generated from a number of sources including oil contaminated drill cuttings and produced waters. The removal of hydrocarbons from both these sources is one of the most significant challenges facing this sector as it moves towards zero emissions. The application of a number of techniques which have been used to successfully destroy hydrocarbons in produced water and waste water effluents has previously been reported. This paper reports the application of semiconductor photocatalysis as a final polishing step for the removal of hydrocarbons from two waste effluent sources. Two reactor concepts were considered: a simple flat plate immobilised film unit, and a new rotating drum photocatalytic reactor. Both units proved to be effective in removing residual hydrocarbons from the effluent with the drum reactor reducing the hydrocarbon content by 90% under 10 minutes.