Compositional-Dependent Structural Parameters and Energetics of Hibonite: Quantum-Chemical Investigation.

One of the first minerals to condense from the early solar nebula was hibonite (CaAl12O19), demonstrating a hexagonal crystal structure. There are five unique aluminum cation sites (M1-M5) in hibonite. Although hibonite contains aluminum, it can also have 3d transitional metals that substitute at aluminum cation sites, such as titanium, and other metals such as magnesium. Titanium can occur in multiple oxidation states, linking to redox conditions. A single substitution occurs when a single aluminum atom is replaced by a single titanium atom, causing the Ti to take on a 3+ oxidation state. On the other hand, Ti achieves an oxidation state of 4+ during a double substitution when a pair of aluminum atoms is replaced by a titanium and a magnesium atom. A density functional theory-based calculation is used to explore the relationship between the number of substitutions and the lattice parameters of the hibonite crystal. The calculated results reveal that the lengths of both unit cells (a and c) increase with an increasing number of single or double substitutions. The rate of increment per substitution depends on the cation sites, M1-M5, and substitution types. Along with the expansion of the unit cell of the hibonite due to the substitution, the substituted unit cell gains energy (and in turn stability) compared to the substituted unit cell without expansion, dependent on the lattice site and substitutions.

Quantum Chemical Investigation of Snow-Mercury Interactions and Their Implication of Mercury Deposition in the Arctic.

Elemental gaseous Hg is emitted into the atmosphere through various anthropogenic and natural processes. Mercury's different species and respective transport ranges, atmospheric physical and chemical transformations, and interaction with the earth's surfaces all contribute to the global cycling of toxic mercury. Under sunlight, halogens, ozone, and nitro species oxidize the emitted elemental Hg to gaseous Hg (II) molecules, which deposit onto the snow and ice surfaces in the Arctic. To investigate the fate of deposited mercury, a quantum chemical investigation was conducted using first-principles density functional theory (DFT) to analyze the interaction between various mercury molecules and snow clusters of differing sizes. Results show that all oxidized mercury molecules: XHgY, BrHgOX, BrHgXO XHgOH, XHgO2H, and XHgNO2, with X, Y = Cl, Br, and I atoms have thermodynamically stable interactions with snow clusters. Further, the adsorption energy of all mercury molecules increases with increasing size of snow clusters. Additionally, the orientations of deposited mercury molecules on the cluster surface also influence the mercury-snow interactions.

Environmental Mercury Chemistry - In Silico.

Mercury (Hg) is a global environmental contaminant. Major anthropogenic sources of Hg emission include gold mining and the burning of fossil fuels. Once deposited in aquatic environments, Hg can undergo redox reactions, form complexes with ligands, and adsorb onto particles. It can also be methylated by microorganisms. Mercury, especially its methylated form methylmercury, can be taken up by organisms, where it bioaccumulates and biomagnifies in the food chain, leading to detrimental effects on ecosystem and human health. In support of the recently enforced Minamata Convention on Mercury, a legally binding international convention aimed at reducing the anthropogenic emission of-and human exposure to-Hg, its global biogeochemical cycle must be understood. Thus, a detailed understanding of the molecular-level interactions of Hg is crucial. The ongoing rapid development of hardware and methods has brought computational chemistry to a point that it can usefully inform environmental science. This is particularly true for Hg, which is difficult to handle experimentally due to its ultratrace concentrations in the environment and its toxicity. The current account provides a synopsis of the application of computational chemistry to filling several major knowledge gaps in environmental Hg chemistry that have not been adequately addressed experimentally. Environmental Hg chemistry requires defining the factors that determine the relative affinities of different ligands for Hg species, as they are critical for understanding its speciation, transformation and bioaccumulation in the environment. Formation constants and the nature of bonding have been determined computationally for environmentally relevant Hg(II) complexes such as chlorides, hydroxides, sulfides and selenides, in various physical phases. Quantum chemistry has been used to determine the driving forces behind the speciation of Hg with hydrochalcogenide and halide ligands. Of particular importance is the detailed characterization of solvation effects. Indeed, the aqueous phase reverses trends in affinities found computationally in the gas phase. Computation has also been used to investigate complexes of methylmercury with (seleno)amino acids, providing a molecular-level understanding of the toxicological antagonism between Hg and selenium (Se). Furthermore, evidence is emerging that ice surfaces play an important role in Hg transport and transformation in polar and alpine regions. Therefore, the diffusion of Hg and its ions through an idealized ice surface has been characterized. Microorganisms are major players in environmental mercury cycling. Some methylate inorganic Hg species, whereas others demethylate methylmercury. Quantum chemistry has been used to investigate catalytic mechanisms of enzymatic Hg methylation and demethylation. The complex interplay between the myriad chemical reactions and transport properties both in and outside microbial cells determines net biogeochemical cycling. Prospects for scaling up molecular work to obtain a mechanistic understanding of Hg cycling with comprehensive multiscale biogeochemical modeling are also discussed.

Effect of Ligand Adsorption on the Electronic Properties of the PbS(100) Surface.

A first-principles density functional theory calculation was carried out to study the adsorption of acetic acid, methyl amine, methanethiol, and hydrogen iodide on the (100) surface of PbS. All four ligands are common capping agents used in colloidal PbS quantum dot-based photovoltaics. Interestingly, among the considered adsorbates, dissociative adsorption was energetically preferred for hydrogen iodide, while associative adsorption was favorable for the rest. Associative adsorption was driven by strong interactions between the electronegative elements (Y) in the respective ligands and the Pb surface atoms via Pb 6p-Y np bond hybridization (n represents the valence quantum number of the respective electronegative elements). Importantly, the adsorption of ligands altered the work function of PbS, with contrasting trends for associative (decrease in the work function) versus dissociative (increase in the work function) adsorption. The changes in the work function correlates well with a corresponding shift in the 5d level of surface Pb atoms. Other important observations include variations in the work function that linearly change with increasing the surface coverage of adsorbed ligands as well as with the strength of the adsorption of ligands.

A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders.

In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

Machine Learning Approaches for Skin Neoplasm Diagnosis.

Approaches for skin neoplasm diagnosis include physical exam, skin biopsy, lab tests of biopsy samples, and image analyses. These approaches often involve error-prone and time-consuming processes. Recent studies show that machine learning shows promise in effectively classifying skin images into different categories such as melanoma and melanocytic nevi. In this work, we investigate machine learning approaches to enhance the performance of computer-aided diagnosis (CADx) systems to diagnose skin diseases. In the proposed CADx system, generative adversarial network (GAN) discriminator is used to identify (and remove) fake images. Exploratory data analysis (EDA) is applied to normalize the original data set for preventing model overfitting. Synthetic minority oversampling technique (SMOTE) is employed to rectify class imbalances in the original data set. To accurately classify skin images, the following machine learning models are utilized: linear discriminant analysis (LDA), support vector machine (SVM), convolutional neural network (CNN), and an ensemble CNN-SVM. Experimental results using the HAM10000 data set demonstrate the ability of the machine learning models to improve CADx performance in treating skin neoplasm. Initially, the LDA, SVM, CNN, and ensemble CNN-SVM show 49%, 72%, 77%, and 79% accuracy, respectively. After applying GAN (discriminator) and SMOTE, the LDA, SVM, CNN, and ensemble CNN-SVM show 76%, 83%, 87%, and 94% accuracy, respectively. We plan to explore other machine learning models and data sets in our next endeavor.

Size-dependent permittivity and intrinsic optical anisotropy of nanometric gold thin films: a density functional theory study.

Physical properties of materials are known to be different from the bulk at the nanometer scale. In this context, the dependence of optical properties of nanometric gold thin films with respect to film thickness is studied using density functional theory (DFT). We find that the in-plane plasma frequency of the gold thin film decreases with decreasing thickness and that the optical permittivity tensor is highly anisotropic as well as thickness dependent. Quantitative knowledge of planar metal film permittivity's thickness dependence can improve the accuracy and reliability of the designs of plasmonic devices and electromagnetic metamaterials. The strong anisotropy observed may become an alternative method of realizing indefinite media.

Relationship between dye-iodine binding and cell voltage in dye-sensitized solar cells: a quantum-mechanical look.

It has been proposed that iodine binding to dyes may actually decrease the cell efficiency of a dye-sensitized solar cell. A previous experimental study showed that a two-atom change from oxygen to sulfur increased recombination of iodine with injected electrons by a factor of approximately 2. Here, it is shown that iodine binding is a plausible explanation for this effect. The steric and conjugation effects are quantified separately using a set of model compounds. Quantum-chemical calculations show that elongation of the hydrocarbon chain has only an insignificant effect on the iodine and bromine binding to the chalcogen atoms (O, S, Se). The conjugation, however, significantly disfavors the iodine and bromine interaction. Iodine and bromine binding to the dye and model compounds containing sulfur is significantly more favorable than to their oxygen containing counterparts. Bromine binding to dyes is shown to be stronger than that of iodine. Accordingly, bromine binding to dyes may contribute significantly to the observed lower efficiencies in cells using Br(3)(-)/Br(-) as the redox couple.

Adsorption of uranyl species onto the rutile (110) surface: a periodic DFT study.

To model the structures of dissolved uranium contaminants adsorbed on mineral surfaces and further understand their interaction with geological surfaces in nature, we have performed periodic density funtional theory (DFT) calculations on the sorption of uranyl species onto the TiO(2) rutile (110) surface. Two kinds of surfaces, an ideal dry surface and a partially hydrated surface, were considered in this study. The uranyl dication was simulated as penta- or hexa-coordinated in the equatorial plane. Two bonds are contributed by surface bridging oxygen atoms and the remaining equatorial coordination is satisfied by H(2)O, OH(-), and CO(3)(2-) ligands; this is known to be the most stable sorption structure. Experimental structural parameters of the surface-[UO(2)(H(2)O)(3)](2+) system were well reproduced by our calculations. With respect to adsorbates, [UO(2)(L1)(x)(L2)(y)(L3)(z)](n) (L1=H(2)O, L2=OH(-), L3=CO(3)(2-), x≤3, y≤3, z≤2, x+y+2z≤4), on the ideal surface, the variation of ligands from H(2)O to OH(-) and CO(3)(2-) lengthens the U-O(surf) and U-Ti distances. As a result, the uranyl-surface interaction decreases, as is evident from the calculated sorption energies. Our calculations support the experimental observation that the sorptive capacity of TiO(2) decreases in the presence of carbonate ions. The stronger equatorial hydroxide and carbonate ligands around uranyl also result in U=O distances that are longer than those of aquouranyl species by 0.1-0.3 Å. Compared with the ideal surface, the hydrated surface introduces greater hydrogen bonding. This results in longer U=O bond lengths, shorter uranyl-surface separations in most cases, and stronger sorption interactions.

Hardware Acceleration of the STRIKE String Kernel Algorithm for Estimating Protein to Protein Interactions.

Protein-protein interaction (PPI) is an important field in bioinformatics which helps in understanding diseases and devising therapy. PPI aims at estimating the similarity of protein sequences and their common regions. STRIKE was introduced as a PPI algorithm which was able to achieve reasonable improvement over existing PPI prediction methods. Although it consumes a lower execution time than most of other state-of the-art PPI prediction methods, its compute-intensive nature and the large volume of protein sequences in protein databases necessitate further time acceleration. In this paper, we develop hardware accelerator designs for the STRIKE algorithm. Results indicate that the weighted STRIKE accelerator execution times are about 10x longer than the unweighted STRIKE accelerator execution times. To further accelerate the performance of the weighted STRIKE, a parallel module accelerator organization duplicating the weighted STRIKE modules is introduced, achieving near linear speedups for long sequences of 100 or more characters. As demonstrated by Verilog simulations and FPGA runs, the weighted STRIKE module accelerator exhibits three orders of magnitude speed improvement over multi-core and cluster computers. Much higher speedups are possible with the parallel module accelerator.

Discovery of a Redox-Activatable Chemical Probe for Detection of Cyclooxygenase-2 in Cells and Animals.

Cyclooxygenase-2 (COX-2) expression is up-regulated in inflammatory tissues and many premalignant and malignant tumors. Assessment of COX-2 protein in vivo, therefore, promises to be a powerful strategy to distinguish pathologic cells from normal cells in a complex disease setting. Herein, we report the first redox-activatable COX-2 probe, fluorocoxib Q (FQ), for in vivo molecular imaging of pathogenesis. FQ inhibits COX-2 selectively in purified enzyme and cell-based assays. FQ exhibits extremely low fluorescence and displays time- and concentration-dependent fluorescence enhancement upon exposure to a redox environment. FQ enters the cells freely and binds to the COX-2 enzyme. FQ exhibits high circulation half-life and metabolic stability sufficient for target site accumulation and demonstrates COX-2-targeted uptake and retention in cancer cells and pathologic tissues. Once taken up, it undergoes redox-mediated transformation into a fluorescent compound fluorocoxib Q-H that results in high signal-to-noise contrast and differentiates pathologic tissues from non-pathologic tissues for real-time in vivo imaging.

Degradation mechanism of methyl mercury selenoamino acid complexes: a computational study.

Density functional theory (DFT) calculations have been carried out on the possible degradation/demethylation mechanism of methyl mercury (CH(3)Hg(+)) complexes with free cysteine and seleonocysteine. The binding of CH(3)Hg(+) ions with one (seleno)amino acid is thermodynamically favorable. However, the binding with another acid molecule is a highly unfavorable process. The CH(3)Hg-(seleno)cysteinate then degrades to bis(methylmercuric)sulphide (selenide for the Se-containing complex) which in turn forms dimethyl mercury and HgS/HgSe, the latter being precipitated out as nanoparticles. The dimethyl mercury interacts with water molecules and regenerates the CH(3)HgOH precursor. The calculated free energies of formation confirm the thermodynamic feasibility of every intermediate step of the degradation cycle and fully support earlier experimental results. In completing the cycle, one unit of mercury precipitates out from two units of sources, and thereby Se antagonizes the Hg toxicity. The degradation of CH(3)Hg-L-cysteinate is thermodynamically more favorable than the formation of CH(3)Hg-L-cysteinate. The preferred degradation of the CH(3)Hg-L-cysteinate suggests that another mechanism for CH(3)Hg to cross the blood-brain barrier should exist.

Chalcogenophilicity of mercury.

Density-functional theory (DFT) calculations have been carried out to investigate the chalcogenophilicity of mercury (Hg) reported recently [J. Am. Chem. Soc. 2010, 132, 647-655]. Molecules of different sizes have been studied including ME, [M(EH)(4)](n), M(SH)(3)EH (M = Cd, Hg; E = S, Se, Te; n = 0, 2+) and [Tm(Y)]MEZ complexes (Tm = tris(2-mercapto-1-R-imidzolyl)hydroborato; Y = H, Me, Bu(t); M = Zn, Cd, Hg; E = S, Se, Te; Z = H, Ph). The bonding of Cd and Hg in their complexes depends on the oxidation state of the metal and nature of the ligands. More electronegative ligands form bonds of ionic type with Cd and Hg while less electronegative ligands form bonds that are more covalent. The Cd-ligand bond distances are shorter for the ionic type of bonding and longer for the covalent type of bonding than those of the corresponding Hg-ligand bonds. The variation of this Cd/Hg bonding is in accordance with the ionic and covalent radii of Cd and Hg. The experimentally observed (shorter) Hg-Se and Hg-Te bond distances in [Tm(Bu(t))]HgEPh (E = S, Se, Te) are due to the lower electronegativity of Se and Te, crystal packing, and the presence of a very bulky group. The bond dissociation energy (BDE) for Hg is the highest for Hg-S followed by Hg-Se and Hg-Te regardless of complex type.

Interactions of the N3 dye with the iodide redox shuttle: quantum chemical mechanistic studies of the dye regeneration in the dye-sensitized solar cell.

The iodide/triiodide redox couple plays a unique role in the dye-sensitized solar cell (DSSC). It is a necessary and unique part of every highly efficient DSSC published to date; alternative redox couples do not perform nearly as well. Hence, a detailed molecular-level understanding of its function is desirable. A density-functional theory (DFT) study has been carried out on the kinetic and thermodynamic aspects of the dye regeneration mechanism involving the iodide/triiodide redox couple and the prototypical N3 dye in the DSSC. The intermediate complexes between the oxidized dye and iodide have been identified. These are outer-sphere complexes of the general formula [dye(+)···I(-)]. Solvent effects are seen to play a critical role in the thermodynamics, whereas relativistic spin-orbit effects are less important. Both the kinetic and thermodynamic data reveal that the formation of complexes between [dye(+)···I(-)] and I(-) is the rate limiting step for the overall dye regeneration process. The regeneration of the neutral dye proceeds with the liberation of I; processes involving atomic iodine or I(-) are inferior, both from thermodynamic and kinetic considerations. The overall dye regeneration reaction is an exothermic process.

Computational studies of structural, electronic, spectroscopic, and thermodynamic properties of methylmercury-amino acid complexes and their Se analogues.

Quantum chemical calculations have been carried out to study the structural, electronic, spectroscopic, and thermodynamic properties of five methylmercury-amino acid complexes and their selenium analogues. The structural properties of methylmercury-amino acids are very similar to their Se analogues except for those properties that are directly related to the Se atom which has a larger covalent radius. Characteristic stretching frequencies are observed for Hg-S/Se and Hg-C bonds. Electronic properties of both methylmercury-amino acids and their Se analogues are different from each other, with the S complexes showing stronger electrostatic attractions which leads to stronger bonds to mercury. The methylmercury complexes with selenoamino complexes, however, are thermodynamically more favorable (DeltaG of formation from suitable model reactants) than those of the corresponding amino acid complexes. This can be traced to the lower stability of the reactant selenoamino acids. Such different stability and favorability of formation might be responsible for the different physiological activity in biological systems such as the Hg-Se antagonism.

Computational studies on the interactions among redox couples, additives and TiO2: implications for dye-sensitized solar cells.

One of the major and unique components of dye-sensitized solar cells (DSSC) is the iodide/triiodide redox couple. Periodic density-functional calculations have been carried out to study the interactions among three different components of the DSSC, i.e. the redox shuttle, the TiO(2) semiconductor surface, and nitrogen containing additives, with a focus on the implications for the performance of the DSSC. Iodide and bromide with alkali metal cations as counter ions are strongly adsorbed on the TiO(2) surface. Small additive molecules also strongly interact with TiO(2). Both interactions induce a negative shift of the Fermi energy of TiO(2). The negative shift of the Fermi energy is related to the performance of the cell by increasing the open voltage of the cell and retarding the injection dynamics (decreasing the short circuit current). Additive molecules, however, have relatively weaker interaction with iodide and triiodide.

Study of hydrophilic electrospun nanofiber membranes for filtration of micro and nanosize suspended particles.

Polymeric nanofiber membranes of polyvinyl chloride (PVC) blended with polyvinylpyrrolidone (PVP) were fabricated using an electrospinning process at different conditions and used for the filtration of three different liquid suspensions to determine the efficiency of the filter membranes. The three liquid suspensions included lake water, abrasive particles from a water jet cutter, and suspended magnetite nanoparticles. The major goal of this research work was to create highly hydrophilic nanofiber membranes and utilize them to filter the suspended liquids at an optimal level of purification (i.e., drinkable level). In order to overcome the fouling/biofouling/blocking problems of the membrane, a coagulation process, which enhances the membrane's efficiency for removing colloidal particles, was used as a pre-treatment process. Two chemical agents, Tanfloc (organic) and Alum (inorganic), were chosen for the flocculation/coagulation process. The removal efficiency of the suspended particles in the liquids was measured in terms of turbidity, pH, and total dissolved solids (TDS). It was observed that the coagulation/filtration experiments were more efficient at removing turbidity, compared to the direct filtration process performed without any coagulation and filter media.

A first-principles characterization of water adsorption on forsterite grains.

Numerical simulations examining chemical interactions of water molecules with forsterite grains have demonstrated the efficacy of nebular gas adsorption as a viable mechanism for water delivery to the terrestrial planets. Nevertheless, a comprehensive picture detailing the water-adsorption mechanisms on forsterite is not yet available. Towards this end, using accurate first-principles density functional theory, we examine the adsorption mechanisms of water on the (001), (100), (010) and (110) surfaces of forsterite. While dissociative adsorption is found to be the most energetically favourable process, two stable associative adsorption configurations are also identified. In dual-site adsorption, the water molecule interacts strongly with surface magnesium and oxygen atoms, whereas single-site adsorption occurs only through the interaction with a surface Mg atom. This results in dual-site adsorption being more stable than single-site adsorption.

Accretion disc origin of the Earth's water.

Earth's water is conventionally believed to be delivered by comets or wet asteroids after the Earth formed. However, their elemental and isotopic properties are inconsistent with those of the Earth. It was thus proposed that water was introduced by adsorption onto grains in the accretion disc prior to planetary growth, with bonding energies so high as to be stable under high-temperature conditions. Here, we show both by laboratory experiments and numerical simulations that water adsorbs dissociatively on the olivine {100} surface at the temperature (approx. 500-1500 K) and water pressure (approx. 10⁻8 bar) expected for the accretion disc, leaving an OH adlayer that is stable at least up to 900 K. This may result in the formation of many Earth oceans, provided that a viable mechanism to produce water from hydroxyl exists. This adsorption process must occur in all disc environments around young stars. The inevitable conclusion is that water should be prevalent on terrestrial planets in the habitable zone around other stars.

Synthesis, characterization and structures of methylmercury complexes with selenoamino acids.

Four new methylmercury-selenoamino acid complexes were synthesized, including methylmercury-L-selenoglutathionate, methylmercury-D,L-selenopenicillaminate, and two methylmercury-L-selenomethioninate complexes (one via a Hg-Se bonding and the other Hg-N bonding). All the complexes were characterized by NMR ((1)H, (13)C, (77)Se and (199)Hg), FT-IR and mass spectra. Their molecular structures were established by single crystal X-ray crystallography (for the Hg-N bonding methylmercury-L-selenomethioninate) and by quantum mechanical calculations using Gaussian-03 with the hybrid functional B3LYP/SDD. All four complexes were found to chemically and structurally resemble their sulfur analogues, with a slightly stronger binding affinity of Hg to Se than to S, suggesting chemical and structural mimicry might play a role in methylmercury-selenium antagonism in biological systems.