First-Principles Calculations on the Wettability of Li Atoms on the (111) Surfaces of W and Mo Substrates

Comprehension over the interactions between lithium (Li) atoms and tungsten (W) or molybdenum (Mo) are crucial to improve the wettability of the flowing liquid Li, a candidate plasma facing material in fusion devices, on the surfaces of supported substrate metals. In this work, we utilize first-principles density- functional theory calculations to figure out the adsorption and diffusion properties of Li atoms and clusters on the (111) surfaces of W and Mo. It is found that single Li atom in the fcc-hollow site is the most favored configuration. For the multiple Li atoms adsorption on the substrates, the planar construction is more stable than the stacking one. The electronic structure analysis shows that the lateral interaction between Li atoms is very weak and the binding between Li atom and the substrates is strong; therefore, it can be inferred that the liquid Li is “wetting” intrinsically on the surfaces of the W and Mo substrates. We also investigate the effect of defects (vacancy, H, C, and O) and find that the preexisted vacancy in the substrates has little effect on the wettability; however, the impurities (especially O atom) will hinder the movement of Li atoms on the metal substrates.     

A three dimensional visualisation approach to protein heavy-atom structure reconstruction

Background

A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central α-carbon coordinates.

Results

We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the C_α coordinates. Each heavy atom is visualised on the surfaces of a different two-sphere, that is centered at another heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters, that display a clear and strong dependence on the underlying backbone secondary structure.

Conclusions

We demonstrate that there is a clear interdependence between rotameric states and secondary structure. Our method easily detects those atoms in a crystallographic protein structure which are either outliers or have been likely misplaced, possibly due to radiation damage. Our approach forms a basis for the development of a new generation, visualization based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy.

     

Occluded molecular surface: Analysis of protein packing

We describe a novel method to calculate the packing interactions in protein structural models. The method calculates the interatomic occluded surface areas for each atom in the protein model. The identification of, and degree of interaction with, neighboring atoms is accomplished by extending surface normal from a dot surface of each atom to the point of intersection with neighboring atoms. The combined occluded and non-occluded surface areas may be normalized for the amino acid composition of the protein providing a single parameter, the normalized protein surface ratio, which is diagnostic for native-like Structures. Individual residues in the model which are in infrequent occluded surface environments may be identified. The method provides a means to explicitly describe packing densities and packing environments of individual atoms in a protein model. Finally, the method allows estimation of the complementarity between any interacting molecules, for example a ligand binding to a receptor.     

Protein surface matching by combining local and global geometric information

Comparison of the binding sites of proteins is an effective means for predicting protein functions based on their structure information. Despite the importance of this problem and much research in the past, it is still very challenging to predict the binding ligands from the atomic structures of protein binding sites. Here, we designed a new algorithm, TIPSA (Triangulation-based Iterative-closest-point for Protein Surface Alignment), based on the iterative closest point (ICP) algorithm. TIPSA aims to find the maximum number of atoms that can be superposed between two protein binding sites, where any pair of superposed atoms has a distance smaller than a given threshold. The search starts from similar tetrahedra between two binding sites obtained from 3D Delaunay triangulation and uses the Hungarian algorithm to find additional matched atoms. We found that, due to the plasticity of protein binding sites, matching the rigid body of point clouds of protein binding sites is not adequate for satisfactory binding ligand prediction. We further incorporated global geometric information, the radius of gyration of binding site atoms, and used nearest neighbor classification for binding site prediction. Tested on benchmark data, our method achieved a performance comparable to the best methods in the literature, while simultaneously providing the common atom set and atom correspondences.     

Quantification of protein surfaces,volumes and atom-atom contacts using a constrained Voronoi procedure

MOTIVATION: Geometric representations of proteins and ligands, including atom volumes, atom-atom contacts and solvent accessible surfaces, can be used to characterize interactions between and within proteins, ligands and solvent. Voronoi algorithms permit quantification of these properties by dividing structures into cells with a one-to-one correspondence with constituent atoms. As there is no generally accepted measure of atom-atom contacts, a continuous analytical representation of inter-atomic contacts will be useful. Improved geometric algorithms will also be helpful in increasing the speed and accuracy of iterative modeling algorithms. RESULTS: We present computational methods based on the Voronoi procedure that provide rapid and exact solutions to solvent accessible surfaces, volumes, and atom contacts within macromolecules. Furthermore, we define a measure of atom-atom contact that is consistent with the calculation of solvent accessible surfaces, allowing the integration of solvent accessibility and inter-atomic contacts into a continuous measure. The speed and accuracy of the algorithm is compared to existing methods for calculating solvent accessible surfaces and volumes. The presented algorithm has a reduced execution time and greater accuracy compared to numerical and approximate analytical surface calculation algorithms, and a reduced execution time and similar accuracy to existing Voronoi procedures for calculating atomic surfaces and volumes.     

Adsorption and spin state properties of Cr,Ni, Mo,and Pt deposited on Li+ and Na+ monovalent cation impurities of MgO (001) surface: DFT calculations

We have analyzed, by means of density functional theory calculations and the embedded cluster model, the adsorption and spin-state properties of Cr, Ni, Mo, and Pt deposited on a MgO crystal. We considered deposition at the Mg²⁺ site of a defect-free surface and at Li⁺ and Na⁺ sites of impurity-containing surfaces. To avoid artificial polarization effects, clusters of moderate sizes with no border anions were embedded in simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces. The interaction between a transition metal atom and a surface results from a competition between Hund's rule for the adsorbed atom and the formation of a chemical bond at the interface. We found that the adsorption energies of the metal atoms are significantly enhanced by the cation impurities, and the adsorption energies of the low-spin states of spin-quenched complexes are always more favorable than those of the high-spin states. Spin polarization effects tend to preserve the spin states of the adsorbed atoms relative to those of the isolated atoms. The metal–support interactions stabilize the low-spin states of the adsorbed metals with respect to the isolated metals, but the effect is not always enough to quench the spin. Spin quenching occurs for Cr and Mo complexes at the Mg²⁺ site of the pure surface and at Li⁺ and Na⁺ sites of the impurity-containing surfaces. Variations of the spin-state properties of free metals and of the adsorption and spin-state properties of metal complexes are correlated with the energies of the frontier orbitals. The electrostatic potential energy curves provide further understanding of the nature of the examined properties.     

A DFT study of the effect of NNN Al atom on strength of Brönsted acid sites of HY zeolite

A density functional theory study has been employed to investigate the effect of next-nearest-neighbours aluminium (NNN Al) atom on the acid strength of Brönsted acid site in Y zeolite. Additionally, the distribution of NNN Al atom was also studied. The obtained results show that thermodynamically, the favourable sites for location of NNN Al atom are the diagonal sites of the four-membered ring and meta-position of hexagon I. Furthermore, the increase of NNN Al atoms causes the nonlinear reduction of the strength of Brönsted acid sites. When the number of NNN Al atoms is greater than two, the increasing extent of acid strength is not obvious with the reduction in the number of NNN Al atoms. But the acid strength will increase linearly with the further reduce of the number of NNN Al atoms. Compared with deprotonation energy (E_D), ammonia adsorption energy (E_ads) could give a more reasonable measuring result for the acid strength.     

Molecular dynamics simulation of solvated azurin: correlation between surface solvent accessibility and water residence times

A system containing the globular protein azurin and 3,658 water molecules has been simulated to investigate the influence on water dynamics exerted by a protein surface. Evaluation of water mean residence time for elements having different secondary structure did not show any correlation. Identically, comparison of solvent residence time for atoms having different charge and polarity did not show any clear trend. The main factor influencing water residence time in proximity to a specific site was found to be its solvent accessibility. In detail for atoms belonging to lateral chains and having solvent-accessible surface lower than approximately 16 A(2)a relation is found for which charged and polar atoms are surrounded by water molecules characterized by residence times longer than the non polar ones. The involvement of the low accessible protein atom in an intraprotein hydrogen bond further modulates the length of the water residence time. On the other hand for surfaces having high solvent accessibility, all atoms, independently of their character, are surrounded by water molecules which rapidly exchange with the bulk solvent. Proteins 2000;39:56-67.     

Heterogeneous Single Atom Electrocatalysis,Where “Singles” Are “Married”

There is an intensive search for heterogeneous single atom catalysts (SACs) of high activity, efficiency, durability, and selectivity for a wide variety of electrocatalytic conversion and chemical reactions, such as the hydrogen evolution reaction (HER), oxygen evolution/reduction reaction (OER and ORR), CO₂ reduction reaction (CO₂ RR), and nitrogen reduction reaction (NRR). With the downsizing from nanoparticles and clusters to single atoms, there are steady changes in the bond and coordination environment for each and every atom involved. Indeed, the single atoms in these electrocatalysts are not “singles”; they are “married” to the supporting surfaces, and their performance is controlled by the bonding and coordination with the substrate surfaces. Herein, an overview is presented on the brief history leading to the rapid development of SACs and their current status, by focusing on their synthesis, control of composition, strategies to realize single atoms with the desired bonds and coordination, and targeted performance in selected reactions. Their applications in the selected spectrum of energy conversion and chemical reactions are discussed, in relation to their structures at varying length scales down to the atomic level. A particular emphasis is placed on on‐going research activities, together with the future perspectives and particular challenges for SACs.     

Quantum chemical modeling study of adsorption of benzoic acid on anatase TiO2 nanoparticles

The semi-empirical MSINDO method has been used to investigate the mode of adsorption of benzoic acid on the nano anatase TiO(2) (100) surface. The (100) surface is modeled with a Ti(36)O(90)H(36) cluster. Molecular dynamics simulations for the adsorption behavior of benzoic acid indicate it is linked to the TiO(2) surface through interactions from the oxygen atoms of the carboxylic acid moiety with surface titanium atoms. The benzoic acid may be positioned with its aromatic ring either parallel or perpendicular relative to the surface, however the perpendicular adsorption mode is more stable. The calculated substrate-surface interaction energy is influenced by the number of linkages between the substrate and the surface as well as the degree of hydrogen bonding between the acid hydrogen and lattice oxygen atom. The greater stability of the perpendicular adsorption orientation is ascribed to the higher number of linkages between the substrate and the surface. It is concluded that the simplified model is sufficiently detailed to elucidate surface interactions.     

Coarse‐ and fine‐grained models for proteins: Evaluation by decoy discrimination

Coarse‐grained models for protein structure are increasingly used in simulations and structural bioinformatics. In this study, we evaluated the effectiveness of three granularities of protein representation based on their ability to discriminate between correctly folded native structures and incorrectly folded decoy structures. The three levels of representation used one bead per amino acid (coarse), two beads per amino acid (medium), and all atoms (fine). Multiple structure features were compared at each representation level including two‐body interactions, three‐body interactions, solvent exposure, contact numbers, and angle bending. In most cases, the all‐atom level was most successful at discriminating decoys, but the two‐bead level provided a good compromise between the number of model parameters which must be estimated and the accuracy achieved. The most effective feature type appeared to be two‐body interactions. Considering three‐body interactions increased accuracy only marginally when all atoms were used and not at all in medium and coarse representations. Though two‐body interactions were most effective for the coarse representations, the accuracy loss for using only solvent exposure or contact number was proportionally less at these levels than in the all‐atom representation. We propose an optimization method capable of selecting bead types of different granularities to create a mixed representation of the protein. We illustrate its behavior on decoy discrimination and discuss implications for data‐driven protein model selection. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

sGAL: a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking

sGAL is a computer program designed to find pairs of sites suitable for introducing chemical cross-links into proteins. sGAL takes a protein structure file in PDB format as input, truncates each residue sequentially to its gamma side chain atom to mimic mutation to Cys, and calculates the exposed surface area of the gamma atom. The user then inputs the minimum and maximum lengths of the cross-linker. sGAL provides as output pairs of residues that would have exposed gamma atom separations that fall within this range. Furthermore, if a line joining the pair of gamma atoms contacts more than a given number of buried atoms, that pair is discarded. In this way, sites for which the protein would sterically interfere with cross-linking are avoided. AVAILABILITY: http://www.chem.utoronto.ca/staff/GAW/links.html; (Surface Racer is also required see: http://monte.biochem.wisc.edu/~tsodikov/surface.html).     

Crystal structures of wild-type and mutant plastocyanins from a higher plant, Silene

Plastocyanin functions as an electron carrier between the cytochrome b6f complex and photosystem I. The crystal structures of the wild-type and E43K/D44K double mutant from the higher plant, Silene, have been determined at 2.0 and 1.75 A resolution, respectively. The wild-type plastocyanin comprises two monomers per asymmetric unit, one of which shows the unusually great distance between the copper ion and the Ndelta1 atom of H87 because of the hydrogen bond network formation between H87 and symmetry-related G10. The root mean square deviation for Ca atoms between the wild-type and mutant plastocyanins is 0.44 A, however, the electrostatic potential maps of their molecular surfaces are remarkably different. The low electron-transfer rate in the E43K/D44K mutant results from the hindrance of electrostatic interactions, not from the structural change due to the mutation.     

Coordination between manganese and nitrogen within the ligands in the manganese complexes facilitates the reconstitution of the water-oxidizing complex in manganese-depleted photosystem II preparations

The water-oxidizing complex (WOC) within photosystem II (PSII) can be reconstituted with synthetic manganese complexes by a process called photoactivation; however, the key factors affecting the efficiency of synthetic manganese complexes in reconstitution of electron transport and oxygen evolution activity in manganese-depleted PSII remain unclear. In the present study, four complexes with different manganese coordination environments were used to reconstitute the WOC, and an interesting relationship was found between the coordination environment of the manganese atom in the complexes and their efficiency in restoring electron transport and oxygen evolution. If Mn(II) is coordinated to nitrogen atoms within the ligand, it can restore significant rates of electron transport and oxygen evolution; however, if the manganese atom is coordinated only to oxygen atoms instead of nitrogen atoms, it has no capability to restore electron transport and oxygen evolution. So, our results demonstrate that the capability of manganese complexes to reconstitute the WOC is mainly determined by the coordination between nitrogen atoms from ligands and the manganese atom. It is suggested from our results that the ligation between the nitrogen atom and the manganese atom within the manganese complex facilitates the photoligation of the manganese atom to histidyl residues on the apo-protein in manganese-depleted PSII during photoactivation.     

Characterization and crystal structure of cadmium(II) halide complexes with amino acids and their derivatives: VII. Crystal structures of aquadibromo(3-aminopropanoic acid)cadmium(II), dichloro(4-aminobutanoic acid)cadmium(II), diaquabis(aminohexanoic acid)cadmium(II) tetrachlorocadmium(II), and dibromo(azetidine-3-carboxylic acid)cadmium(II)

Seven cadmium complexes: [CdX2(Hapro)(H2O)n] (X: Cl(1), Br(2)), [CdX2(Hgaba)] (X: Cl(3), Br(4)), [Cd(Hahex)2(H2O)2][CdCl4] (5), and [CdX2(Haze-3)](H2O)n (X: Cl(6), Br(7)) have been prepared and investigated by means of IR and FT Raman spectra. The crystal and molecular structures of 2, 3, 5 and 7 were determined by a single-crystal X-ray diffraction method. In complex 2, the cadmium atom is in a distorted octahedral geometry, ligated by two carboxyl oxygen atoms of Hapro, a water molecule, and three bromine atoms; one is terminal and each of the other two is bridging two cadmium atoms to make a polymer. The structure of 3 consists of one-dimensional polymers bridged by two chlorine atoms and a carboxyl group. The carboxyl oxygen atoms of Hgaba coordinate forkedly to two cadmium atoms. The cadmium atom of [Cd(Hahex)2(H2O)2]2+ in complex 5 is in a distorted octahedral geometry, ligated by four carboxyl oxygen atoms of two molecules of Hahex and by two water molecules. [Cd(Hahex)2(H2O)2]2+ exists between two layers which are formed of infinite [CdCl4]2- chains. The carboxyl oxygen atoms of Hahex coordinate to the same cadmium atom. In complex 7, the cadmium atom is ligated by two carboxyl oxygen atoms and four bridging bromine atoms to make a polymer.     

Volume occupation, environment and accessibility in proteins. The problem of the protein surface.

The volumes occupied by atoms or groups of atoms in ribonuclease S are calculated, using a new treatment of the surface, and considering buried and exposed atoms separately. The volumes occupied by particular atom types fall within a narrow range, with standard deviations between 10% and 15% of the mean. Summation of volumes over main and side-chain groups removes inaccuracies in the single atom data, and results in even narrower distributions. Comparison of the volume spreads with those found in model glasses suggests that the remaining variation is unlikely to be much reduced by improving further either the space-subdivision method or the surface treatment. These improved volume distributions might be used as more stringent criteria against which to test trial tertiary structures.The computer program used produces additional information that could be used to investigate quantitatively the possible freedom of movement in different parts of the molecule. It also provides complementary data on environment and surface exposure.     

Predicting absolute contact numbers of native protein structure from amino acid sequence

The contact number of an amino acid residue in a protein structure is defined by the number of C(beta) atoms around the C(beta) atom of the given residue, a quantity similar to, but different from, solvent accessible surface area. We present a method to predict the contact numbers of a protein from its amino acid sequence. The method is based on a simple linear regression scheme and predicts the absolute values of contact numbers. When single sequences are used for both parameter estimation and cross-validation, the present method predicts the contact numbers with a correlation coefficient of 0.555 on average. When multiple sequence alignments are used, the correlation increases to 0.627, which is a significant improvement over previous methods. In terms of discrete states prediction, the accuracies for 2-, 3-, and 10-state predictions are, respectively, 71.4%, 54.1%, and 18.9% with residue type-dependent unbiased thresholds, and 76.3%, 59.2%, and 21.8% with residue type-independent unbiased thresholds. The difference between accessible surface area and contact number from a prediction viewpoint and the application of contact number prediction to three-dimensional structure prediction are discussed.     

A molecular dynamics study on intermediate structures during transition from amorphous to crystalline state

Molecular dynamics (MD) simulations are carried out for model aluminium with 500, 864, 1372 and 2048 atoms interacting with Sutton-Chen version of embedded atom method (SCEAM) based on many body interactions. The systems equilibrated in an FCC structure have, first, been melted and then solidified with specifically selected single cooling rate which forms unstable amorphous state in the system. The local structures of the system have been analysed by bond orientational order parameters to distinguish the simple structures in the systems. The radial distribution functions (RDF) and atomic coordinates have also been analysed for determining the local structural properties. It has been observed that the phase sequences of the systems, except for those of the 2048 atoms, are FCC → Liquid → Amorphous → Mixed Crystal. Types of the crystals in the mixed state depend on the number of the atoms in the system. The final phase of the system with 2048 atoms is amorphous state.     

Question 9: Quantum Self-Assembly and Photoinduced Electron Tunneling in Photosynthetic Systems of Artificial Minimal Living Cells

Natural and artificial living cells and their substructures are self-assembling, due to electron correlation interactions among biological and water molecules, which lead to attractive dispersion forces and hydrogen bonds. Dispersion forces are weak intermolecular forces that arise from the attractive force between quantum multipoles. A hydrogen bond is a special type of quantum attractive interaction that exists between an electronegative atom and a hydrogen atom bonded to another electronegative atom; and this hydrogen atom exist in two quantum states. The best method to simulate these dispersion forces and hydrogen bonds is to perform quantum mechanical non-local density functional potential calculations of artificial minimal living cells consisting of around 1,000 atoms. The cell systems studied are based on peptide nucleic acid and are 3.0–4.2 nm in diameter. The electron tunneling and associated light absorption of the most intense transitions, as calculated by the time dependent density functional theory method, differs from spectroscopic experiments by only 0.2–0.3 nm, which is within the value of experiment errors. This agreement implies that the quantum mechanically self-assembled structures of artificial minimal living cells very closely approximate realistic ones.     

Anticorrosion mechanism of Cr-doped nickel-base alloy in Br/O environment: a DFT study

ABSTRACT

Density functional theory was used to investigate the anticorrosion mechanism of Cr-doped nickel-base alloy in Br/O environment. The adsorption properties including adsorption energy, bond length and electron structure of Br/O on Ni and Cr-doped Ni surfaces have been investigated. We find that the O atom has bigger adsorption activity than the Br atom. The oxide film can be preferentially formed on the Cr-doped nickel-base alloy surface under the coexistence of Br and O atoms. By exploring the interactions between Br and NiO (111) or Cr₂O₃ (100) surfaces, we demonstrate that oxide films could prevent Br from erosion. Results indicate that Cr₂O₃ has stronger corrosion resistance than NiO. The corrosion resistance mechanism of Cr-doped nickel-base alloy is summarised into two processes, i.e. competitive adsorption and adsorption inhibition.