Trifurcated (Four-Center) Hydrogen Bond in Solid State Crystal Structure of 5′-Amino-5′-deoxyadenosine p-Toluenesulfonate

Abstract

The crystal structure of 5′-amino-5′-deoxyadenosine (5′-Am.dA) p-toluenesulfonate has been determined by X-ray crystallographic methods. It belongs to the orthorhombic space group P2₁2₁2₁ with a=7.754(3)Å, b=8.065(l)Å and c=32.481(2)Å. This nucleoside shows a syn conformation about the glycosyl bond and C2′-endo-C3′-exo puckering for the ribose sugar. The orientation of N5′ atom is gauche-trans about the exocyclic C4′-C5′ bond. The amino nitrogen N5′ forms a trifurcated hydrogen bond with N3, O9T and 04′ atoms. Adenine bases form A.A.A triplets through hydrogen bonding between N6, N7 and N1 atoms of symmetry related nucleoside molecules.     

Fluorination of BC3 nanotubes: DFT studies

We have studied the adsorption of atomic and molecular fluorines on a BC₃ nanotube by using density functional calculations. It was found that the adsorption of atomic fluorine on a C atom of the tube surface is energetically more favorable than that on a B atom by about 0.97 eV. The adsorption of atomic fluorine on both C and B atoms significantly affects the electronic properties of the BC₃ tube. The HOMO-LUMO energy gap is considerably reduced from 2.37 to 1.50 and 1.14 eV upon atomic F adsorption on B and C atoms, respectively. Molecular fluorine energetically tends to be dissociated on B atoms of the tube surface. The associative and dissociative adsorption energies of F₂ were calculated to be about ?0.42 and ?4.79 eV, respectively. Electron emission density from BC₃ nanotube surface will be increased upon both atomic and molecular fluorine adsorptions due to work function decrement.     

Density functional study of H<Subscript>2</Subscript>O molecule adsorption on α-U(001) surface

Periodic density functional theory (DFT) calculations were performed to investigate the adsorption of H₂O on U(001) surface. The metallic nature of uranium atom and different adsorption sites of U(001) surface play key roles in the H₂O molecular dissociate reaction. The long-bridge site is the most favorable site of H₂O-U(001) adsorption configuration. The triangle-center site of the H atom is the most favorable site of HOH-U(001) adsorption configuration. The interaction between H₂O and U surface is more evident on the first layer than that on any other two sub-layers. The dissociation energy of one hydrogen atom from H₂O is ?1.994 to ?2.215 eV on U(001) surface, while the dissociating energy decreases to ?3.351 to ?3.394 eV with two hydrogen atoms dissociating from H₂O. These phenomena also indicate that the O_ads can promote the dehydrogenation of H₂O. A significant charge transfer from the first layer of the uranium surface to the H and O atoms is also found to occur, making the bonding partly ionic.     

Applications of Genetic Algorithms in Cluster Optimisation

Abstract

Applications of Genetic Algorithms for optimisation of atomic clusters are reported. It is shown that the genetic algorithms are very useful tools for determining the minimum energy structures of clusters of atoms described by interatomic potential functions containing up to a few hundred atoms. The algorithm generally outperforms other optimisation methods for this task. A number of applications are given including covalent carbon and silicon clusters, close-packed structures such as argon and silver and the two-component C—H system.     

NH3 on a BC3 nanotube: effect of doping and decoration of aluminum

The adsorption of the NH₃ molecule was investigated on pristine, Al-doped and Al-decorated BC₃ nanotubes (BC₃NT) using density functional theory calculations. It was found that NH₃ prefers to be adsorbed on a B atom of the tube wall, releasing energy of 1.02 eV. Al-doping increases the acidity of the tube surface and, therefore, its reactivity toward NH₃ so that the released energy in this case is about 1.62 eV, while decorating the BC₃NT with Al atom decreases the acidity and reactivity. Although Al-doping has no significant effect on the electronic properties of the BC₃NT, Al-decoration significantly reduces its HOMO/LUMO energy gap from 2.37 to 1.16 eV so that the tube becomes an n-type semiconductor. However, we believe that the acidity of the BC₃NTs may be controlled by doping or decoration of Al atoms.     

Chlorotriphenyl(quinolinium-2-carboxylato)tin(IV) monohydrate

The crystal structure of chlorotriphenyl(quinolinium-2-carboxylato)tin(IV) monohydrate is reported. The crystals are monoclinic, space group C2/c with cell parameters a = 20.048(3) Å, b = 11.724(1) Å, c = 23.291(3) Å, ]gb = 113.42(1), Z = 8, refined to R_F = 0.034 on 3331 observed reflections. The tin(IV) atom is five-coordinate, being found to three phenyl groups, the chlorine atom and an oxygen from the quinaldic acid. The geometry around the tin atom is trigonal bipyramidal, with the three phenyl groups occupying the equatorial positions, and the chlorine and quinaldic acid oxygen, the apical ones. The acidic proton of quinaldic acid has shifted position in the complex, and is bound to the heterocyclic nitrogen atom.The acid is thus coordinated in the form of a zwitterion. These trigonal bipyramidal units are linked together as dimers by pairs of water molecules, each of which hydrogen-bonds to the non-coordinated carboxylate oxygen atoms of both quinaldic acid molecules, plus the heterocyclic nitrogen atom of one quinaldic acid molecule. For complex formation with the protonated acid, the heterocyclic nitrogen should be alpha to the carboxylic acid group.     

Coupling of Penetrant and Polymer Motions During Small-Molecule Diffusion In a Glassy Polymer

Abstract

Multidimensional transition-state theory was used to simulate methane jump motions in glassy atactic polypropylene at 233 K in the limit of small methane concentrations. Transition states were found with respect to both penetrant and polymer degrees of freedom, using all generalized coordinates associated with atoms interacting with the methane penetrant. Animations followed the multidimensional reaction coordinate for three different jumps.

The jump mechanism involved polymer atoms retracting to form a channel, followed by penetrant motion through the channel. Methyl groups within 4 Å of the penetrant transition state location were displaced by 0.9 Å on average, while carbon atoms and methyl groups further than 9 Å from the penetrant transition state location were displaced by less than 0.2 Å.

The energy profiles along the diffusion path differed considerably among all jumps simulated, and the jump rate did not correlate simply with changes in particular types of degrees of freedom. Jumps for which the penetrant transition state location was within 5 Å of a chain start or end had average rates of order 60 μs^?1, while jumps further from a chain start or end were an order of magnitude slower.     

RNA double-helical fragments at atomic resolution: II. The crystal structure of sodium guanylyl-3′,5′-cytidine nonahydrate

The crystal structure of sodium guanylyl-3′,5′-cytidine (GpC) nonahydrate has been determined by X-ray diffraction procedures and refined to an R value of 0.054. GpC crystallizes with four molecules per monoclinic unit cell, space group C2, with cell dimensions: $\text{a = 21.460, b = 16.297, c = 9.332}\text{A}\text{?}\text{and}\text{β = 90.54 °}$. Two molecules of GpC related by the 2-fold axis of the crystal form a small segment of right-handed, anti-parallel double-helical RNA in the crystal. Guanine is paired to cytosine through three hydrogen bonds of lengths 2.91, 2.95 and 2.86 Å. The bases along each strand are heavily stacked at a distance of about 3.4 Å. The fragments form skewed flattened rods within the lattice by the inter-molecular stacking of guanines with each other and the stacking of cytosine with the guanosine Ol′atom. The sodium cations are bound only to the ionized phosphate groups in this structure and exhibit face-sharing octahedral co-ordination. The sodium cations serve to bridge the rods of GpC fragments and organize them into sheets within the crystal. There are 18 water molecules per double-helical fragment which are all part of the first co-ordination shell of nitrogen, oxygen or sodium atoms.     

Studies on the metal—amide bond. XVIII. The crystal and molecular structure of [N,N′-bis(2′-pyridinecarboxamido)-1,3-propane] nickel(II) monohydrate

[N,N′-bis(2′-pyridinecarboxamido)-1,3-propane] - nickel(II) monohydrate, C₁₅H₁₆N₄O₃Ni is monoclinic, space group P2₁/c, with a = 7.174(4), b = 18.590(3), c = 11.641(5) Å, β = 110.69(2)°, Z = 4. The structure was refined to R = 0.030 for 1826 diffractometer data using full-matrix least-squares methods. The N₄-ligand coordinates to the nickel atom in an irregular square plane [average Ni-N_amide 1.864(4), Ni-N_pyridine 1.912(3) Å and N_amide-Ni-N_amide 96.0(1), N_pyridine-Ni-N_pyridine 98.7(1)°] with a tetrahedral twist of 15.9° at the nickel atom. The two picolinamide units are related by an approximate two-fold axis and the enforced strain in the molecule results in significant non-planar distortions in the amide chelate rings and the pyridyl rings. The plane of the chelate molecule lies approximately perpendicular to [100] and the lattice water molecule hydrogen bonds amide oxygen atoms to form chains parallel to [101]     

Studies on the metalamide bond. XIX. A comparison of molecular distortions in the crystal structures of [N,N′-bis(2′-pyridinecarboxamido)-1,2-benzene] nickel(II) with its 6′-methyl-substituted Analogue

[N,N′-Bis(pyridine-2′-carboxamide)-1,2-benzene]nickel(II) monohydrate, C₁₈H₁₄N₄O₃Ni, crystallizes in the monoclinic space group C2/c with a = 14.240(4), b = 20.071(3), c = 16.275(2) Å,β = 97.25(2)^o, Z = 12 and its crystal structure has been refined to R = 0.033 for 3597 diffractometer data. [N,N′-Bis(6′-methylpyridine-2′-carboxamide)-1,2- benzene]nickel(II) monohydrate, C₂₀H₁₈N₄O₃Ni, crystallizes in the orthorhombic space group Pbca with a = 10.14(2) b = 17.12(2), c= 21.11(5) Å, Z = 8 and its crystal structure has been refined to R = 0.088 for 1979 photographic data. In both structures the nickel atoms are four coordinate with the ligands acting as N₄ tetradentates. For the first mentioned complex the structure consists of two independent molecules one of which is constrained, by space group requirements, to have C₂ (2) symmetry. These two molecules are closely similar and both exhibit nearly planar molecular arrangements with a small tetrahedral twist of up to 4^o at the nickel atoms. In the second complex the methyl substitution at the 6′-pyridyl positions causes severe steric strain in the molecule which gives rise to a 14.9^o tetrahedral twist at the nickel atom and approximately 25% pyramidal distortion at both amide nitrogen atoms. The resulting methyl-methyl separation of 3.26(1) Å is considerably less than the sum of the van der Waals radii for two such groups. This close separation leads to carbon-acid character for the methyl group protons which are shown to exchange for deuterons in NMR studies. A full analysis of the out-of-plane distortions and torsion angles of the two structures and a comparison with the previously reported analogous copper structures are made.     

Reactions of metal complexes with carbohydrates: Synthesis and characterization of novel nickel(II) complexes containing glycosylamines derived from a monosaccharide and a diamine. An X-ray crystallographic study of (ethylenediamine) {N-(2-aminoethyl)-d-fructopyranosylamine} nickel(II) · Cl2 · CH3OH

Tris(ethylenediamine)- or tris(trimethylenediamine)-nickel(II) salts react with d-glucose, d-mannose, or d-fructose to give novel, octahedral, nickel(II) complexes containing glycosylamine(s) derived from the reaction of the monosaccharide with the diamine. The complexes have been characterized by elemental analysis, magnetic susceptibility, and electronic absorption, infrared, and circular dichroism spectra. The complexes from aldoses contain two sugar entities, and those from a ketose have one sugar unit. The X-ray crystal structure was determined of one of the products, in which N-(2-aminoethyl)-d-fructopyranosylamine and ethylenediamine are coordinated to a nickel ion. Crystal data for the compound: a = 12.348(5) Å, b = 18.478(8) Å, c = 8.464(4) Å, Z = 4, space group P2₁2₁2₁, 2348 unique observed reflections [Fo > 3σ(Fo)] used in the structure analysis, R = 0.068, Rw = 0.053. The sugar is coordinated to the nickel ion at three points, through the 1- and 3-hydroxyl groups and the nitrogen atom on C-2.     

On the Implementation of Friedman Boundary Conditions in Liquid Water Simulations

Abstract

We have applied the image approximation to the reaction field as suggested by H.L. Friedman [Mol. Phys., 29, 1533 (1975)] by investigating appropriate cavity sizes and system parameters for use in molecular simulations. The energy of and the structure around a central simple point charge (SPC) water molecule in a dielectric cavity was found to be in good agreement with the properties of a liquid sample. To confine the water molecules within the cavity, we introduced a short-range repulsion between a real charge and its image as the Lennard-Jones repulsive potential between oxygen atoms of the SPC potential. For a system of 65 water molecules a cavity radius of 10.45 Å is appropriate; this radius is altered to 12.00 Å for a cavity surrounding 113 molecules. The effect of the boundary is restricted to the outer-most water layer which is in contact with the dielectric continuum.     

Water structure in a protein crystal: rubredoxin at 1.2 A resolution

The model for rubredoxin based on X-ray diffraction data has been extensively refined with a 1.2 Å resolution data set. Water oxygen atoms were deleted from the model if B exceeded 50 Ų and occupancy was less than 0.3 eÅ^?3. The final water model consists of 127 sites with B values ranging from 15 to $\text{6}\text{?}$0 Ų and occupancies from unity down to 0.3, the most tightly bound water oxygen atoms being hydrogen bonded to two or more main-chain nitrogen or oxygen atoms. The water forms extensive hydrogen bond networks bridging the crevices on the molecular surfaces and between adjacent molecules. The minimum distances of the water sites from the protein surface are distributed about two distinct maxima, the major one at 2.5 to 3 Å and a minor one at 4 to 4.5 Å. Beyond $\text{5}\text{?}$ to 6 Å from the protein surface, the discrete water merges into the aqueous continuum.     

Investigating the electronic properties of silicon nanosheets by first-principles calculations

Using first-principles total energy calculations within the density functional theory (DFT), we investigated the electronic and structural properties of graphene-like silicon sheets. Our studies were performed using the LSDA (PWC) and GGS (PBE) approaches. Two configurations were explored: one corresponding to a defect-free layer (h-Si), and the other to a layer with defects (d-Si), both of which were in the armchair geometry. These sheets contained clusters of the C(n)H(m) type. We also investigated the effects of doping with group IV-A elements. Structural stability was studied by only considering positive vibration frequencies. Results showed that both h-Si and d-Si present a corrugated structure with concavity. h-Si sheets were found to be ionic (D.M. = 0.33 Debye) with an energy gap (HOMO-LUMO) of 0.77 eV in the LSDA theory and 0.76 eV in the GGS approach, while d-Si sheets were observed to be covalent (D.M. = 2.78 D), and exhibited semimetallic electronic behavior (HOMO-LUMO gap = 0.32 eV within the LSDA theory and 0.33 eV within the GGS approach). d-Si sheets doped with one carbon or one germanium preserved the polarity of the undoped d-Si sheets, as well as their semimetallic electronic behavior. However, when the sheets were doped with two C or two Ge atoms, or with one of each atom (to give Si(52)CGeH(18)), they retained the semimetallic behavior, but they changed from having ionic character to covalent character.     

Synthesis and crystal and molecular structure of a methyl N,N-diethylcarbamylmethylenephosphonato dysprosium thiocyanate complex

Bis-Methyl N,N-diethylcarbamylmethylenephosphonato dysprosium thiocyanate, Dy[O₂P(OCH₃)CH₂C(O)N(C₂H₅)₂]₂(NCS) was prepared from the combination of ethanolic solutions of Dy(NCS)₃·xH₂O and (CH₃O)₂P(O)CH₂C(O)N(C₂H₅)₂. The complex was characterized by infrared and NMR spectroscopy, and single crystal X-ray diffraction methods. The crystal structure was determined at 25 °C from 3727 independent reflections by using a standard automated diffractometer. The complex was found to crystallize in the monoclinic space group P2₁/c with a = 13.282(4) Å, b = 19.168(5) Å, c = 9.648(2) Å, β = 90.09(2)°, Z = 4, V = 2456.4 ų and ?_cald = 1.72 g cm^?3. The structure was solved by standard heavy atom techniques, and blocked least-squares refinement converged with R_f = 4.7% and R_wF = 4.9%. The Dy atom is seven coordinate and bonded in a bidentate fashion to two anionic phosphonate ligands [O₂P(OCH₃)CH₂C(O)N(C₂H₅)₂^?] through the carbonyl oxygen atoms and one of two phosphonate oxygen atoms. In addition, each Dy atom is coordinated to two phosphonate oxygen atoms from two neighboring complexes and to the nitrogen atom of a thiocyanate ion. This coordination scheme gives rise to a two-dimensional polymeric structure. Some important bond distances include DyNCS 2.433(8) Å, DyO(carbonyl)_avg 2.39(2) Å, DyO(equat. phosphoryl)_avg 2.303(8) Å, DyO(axial phosphoryl)_avg 2.25(2), PO(phosphoryl)_avg 1.493(3) Å and CO(carbonyl)_avg 1.25(1) Å.     

The EXAFS study on the local structure of lanthanum in spinach PSII

The complex of photosystem II (PSII) had been prepared from spinach by treatment with Triton X-100. The PSII, which had been depleted of the extrinsic 17- and 23-kDa polypeptides, was obtained by exposing the solution to a high concentration of NaCl, and the complex of PSII-La³⁺ was prepared by treatment with LaCl₃. The result indicated that La³⁺ could inhibit the oxygen-evolution activity of PSII by replacing the Ca²⁺. The local structural environment of La in PSII has been also studied by using extended X-ray absorption fine structure (EXAFS). The primary result of EXAFS indicated that La coordinated with eight oxygen and/or nitrogen atoms, with the distance of the La-O/N bond being 2.5 Å. In addition, La coordinated with four carbon atoms, with a distance of 3.5 Å in the second shell. In the third shell, La coordinated with two manganese atoms, with the distance of La-Mn bond being 4.49 Å, and it was also found that the La-Mn distance (4.49 Å) was longer than that of Ca-Mn (3.3 Å) (1) in PSII.     

Mechanism of the Atomic Intermixing Process in Crystalline Microclusters

Abstract

The Mechanism of atomic intermixing process in crystalline microclusters is studied by molecular dynamics simulation for a two-dimensional system with the Lennard-Jones potential. Temperature is chosen so that a cluster consists of solid-like core region and the region of surface melting. It is found that atomic intermixing in the solid-like core region is caused by the motion of a dislocation through the cluster as well as the random walk of a vacancy in the cluster. Generation of a dislocation or a vacancy occurs at the interfacial region between the liquid-like surface and the solid-like core regions due to large scale fluctuation of the configuration of atoms in the region of surface melting and the opportune collective motion of atoms in the solid-like core region. The rate per atom of atomic intermixing, the basic quantity of our interest (for the definition see the text), in the solid-like core of the microcluster is three to four orders of magnitude larger than that in the bulk crystal.     

X-ray absorption spectroscopy of dimethylsulfoxide reductase from Rhodobacter capsulatus

Mo K-edge X-ray absorption spectroscopy (XAS) has been used to probe the environment of Mo in dimethylsulfoxide (DMSO) reductase from Rhodobacter capsulatus in concert with protein crystallographic studies. The oxidised (Mo^VI) protein has been investigated in solution at 77?K; the Mo K-edge position (20006.4?eV) is consistent with the presence of Mo^VI and, in agreement with the protein crystallographic results, the extended X-ray absorption fine structure (EXAFS) is also consistent with a seven-coordinate site. The site is composed of one oxo-group (Mo=O 1.71?Å), four S atoms (considered to arise from the dithiolene groups of the two molybdopterins, two at 2.32?Å and two at 2.47?Å, and two O atoms, one at 1.92?Å (considered to be H-bonded to Trp 116) and one at 2.27?Å (considered to arise from Ser 147). The Mo K-edge XAS recorded for single crystals of oxidised (Mo^VI) DMSO reductase at 77?K showed a close correspondence to the data for the frozen solution but had an inferior signal:noise ratio. The dithionite-reduced form of the enzyme and a unique form of the enzyme produced by the addition of dimethylsulfide (DMS) to the oxidised (Mo^VI) enzyme have essentially identical energies for the Mo K-edge, at 20004.4?eV and 20004.5?eV, respectively; these values, together with the lack of a significant presence of Mo^V in the samples as monitored by EPR spectroscopy, are taken to indicate the presence of Mo^IV. For the dithionite-reduced sample, the Mo K-edge EXAFS indicates a coordination environment for Mo of two O atoms, one at 2.05?Å and one at 2.51?Å, and four S atoms at 2.36?Å. The coordination environment of the Mo in the DMS-reduced form of the enzyme involves three O atoms, one at 1.69?Å, one at 1.91?Å and one at 2.11?Å, plus four S atoms, two at 2.28?Å and two at 2.37?Å. The EXAFS and the protein crystallographic results for the DMS-reduced form of the enzyme are consistent with the formation of the substrate, DMSO, bound to Mo^IV with an Mo-O bond of length 1.92?Å.     

Crystal Structure of Sodium Deoxyinosine Monophosphate

Abstract

The crystal and molecular structure of sodium deoxyinosine monophosphate (5′-dIMP) has been determined by x-ray crystallographic methods. The crystals belong to orthorhombic space group P2₁2₁2₁, with a = 21.079(5) Å, b = 9.206(3) Å and c = 12.770(6) Å. This deoxynucleotide shows common nucleotide features namely anti conformation about the glycosyl bond, C2′ endo pucker for the deoxyribose sugar and gauche-gauche orientation for the phosphate group. The sodium ion is directly coordinated to the O3′ atom, a feature observed in many crystal structures of sodium salts of nucleotides.     

Predicting the Structure of the Flavodoxin from Eschericia coli by Homology Modeling,Distance Geometry and Molecular Dynamics

Abstract

As part of our on-going development of a method, based upon distance geometry calculations, for predicting the structures of proteins from the known structures of their homologues, we have predicted the structure of the 176 residue Flavodoxin from Escherichia coli. This prediction was based upon the crystal structures of the homologous Flavodoxins from Anacystis nidulans, Chondrus crispus, Desulfovibrio vulgaris and Clostridium beijerinckii, whose sequence identities with Escherichia coli were 44%, 33%, 23% and 16%, respectively. A total of 13,043 distance constraints among the alpha-carbons of the Escherichia coli structure were derived from the sequence alignments with the known structures, together with 8,893 distance constraints among backbone and sidechain atoms of adjacent residues, 978 between the alpha-carbons and selected atoms of the flavin mononucleotide cofactor, 116 constraints to enforce conserved hydrogen bonds, and 452 constraints on the torsion angles in conserved residues. An ensemble of ten random Escherichia coli structures was computed from these constraints, with an average root mean square coordinate deviation (RMSD) among the alpha carbons of 0.85 Ångstroms (excluding the first 1 and last 6 residues, which have no corresponding residues in any of the homologues and hence were unconstrained); the corresponding average heavy-atom RMSD was 1.60 Å.

Since the distance geometry calculations were performed without hydrogen atoms, protons were added to the resulting structures and these structures embedded in a 50 × 50 × 40 Å solvent box with periodic boundary conditions. They were then subjected to a 20 picosecond dynamical simulated annealing procedure, starting at 300 K and gradually reduced to 10K, in which all the distance and torsion angle constraints were maintained by means of harmonic restraint functions. This was followed up by 1000 iterations of unrestrained conjugate gradients minimization. The goal of this energy refinement procedure was not to drastically modify the structures in an attempt at a priori prediction, but merely to improve upon the predictions obtained from the geometric constraints, particularly with regard to their local backbone and sidechain conformations and their hydrogen bonds. The resulting structures differed from the respective starting structures by an average of 1.52 Å in their heavy atom RMSD's, while the average RMSD among the heavy atoms of residues 2-170 increased slightly to 1.66 Å. We hope these structures will be good enough to enable the phase problem to be solved for the crystallographic data that is now being collected on this protein.