Density functional studies of closed-shell attractions of S(AuPH3)2 and HS(AuPH3)2 + and their dimers

With the help of quantum chemical calculations, S(AuPH₃)₂, [HS(AuPH₃)₂]⁺ and their dimers have been examined by using scalar-relativistic theory. In agreement with experimental data, [HS(AuPH₃)₂ ⁺]₂ is a C_2h structure. However, [S(AuPH₃)₂]₂ is predicted to favor a D_2d structure. Experimental structure parameters of the title compounds were reproduced at the Xα level. The electronic structure and HOMO–LUMO gaps were investigated. When two monomers formed a dimer, the electronic structure of the dimer changed only slightly, but the chemical stability decreased. The intermolecular aurophilic interaction energy is decomposed and analyzed.     

Decarbonylation of As2Co2(CO)6, a binuclear cobalt carbonyl derivative of diarsenic

The structures and relative energies of the As₂Co₂(CO)_n (n = 6, 5, 4) derivatives are predicted by density functional theory to be analogous to those of the corresponding H₂C₂Co₂(CO)_n derivatives. Thus As₂Co₂(CO)₆ is predicted to have three carbonyls on one cobalt atom eclipsed relative to the three carbonyls on the other cobalt atom. The corresponding As₂Co₂(CO)₆ structure with a staggered rather than eclipsed arrangement of the Co(CO)₃ units is a transition state rather than a genuine minimum. For As₂Co₂(CO)₅ the structure in which an equatorial group is removed from the As₂Co₂(CO)₆ structure and a singly bridged As₂Co₂(CO)₄(μ-CO) structure are predicted to have essentially the same energies, within <2 kcal/mol. A higher energy As₂Co₂(CO)₅ structure by 9 ± 2 kcal/mol is derived from the As₂Co₂(CO)₆ structure by removal of an axial carbonyl group. The two unbridged As₂Co₂(CO)₅ structures correspond to those observed experimentally in the photolysis of As₂Co₂(CO)₆ in Nujol matrices at low temperatures. In such photolysis experiments the higher energy isomer is produced initially and then converted to the lower energy isomer upon annealing. A singly bridged structure was found for As₂Co₂(CO)₄. The analogous structure was not observed in the previous work with H₂C₂Co₂(CO)₄. However, such a H₂C₂Co(CO)₃(μ-CO) structure is found here for the acetylene complex. This singly bridged structure is predicted to lie 1.9 kcal/mol below the H₂C₂Co₂(CO)₄4-1S structure by the BP86 method but 3.5 kcal/mol above the latter by the B3LYP method. In addition to the singly bridged As₂Co₂(CO)₄ structure, the same six unbridged structures were located for As₂Co₂(CO)₄ that were previously found for H₂C₂Co₂(CO)₆.     

First-principles investigation of the novel structure,elastic and thermodynamic properties of IrAl3 coating

IrAl₃ coating is a promising advanced functional material. However, the crystal structure and relevant properties of IrAl₃ remain controversy. Here, we apply the first-principles calculations to investigate the crystal structure, elastic and thermodynamic properties of IrAl₃. The phonon dispersion curves and phonon density of states of IrAl₃ are calculated. We find that the reported hexagonal structure (P63/mmc) is dynamically instable. However, three new phases: tetragonal (P4/mbm) and cubic (Pm-3n and Pm-3?m) structures are predicted. In particular, IrTi₃-type structure is a derivative cubic structure because Al atom occurs migration from (0, 0.50, 0.50) site to (0, 0.25, 0.50) site. IrTi₃-type derivative cubic structure shows high shear deformation resistance and high elastic stiffness in comparison to other three structures. The strong shear deformation resistance and high elastic stiffness are attributed to the symmetrical Ir–Al bond. However, AuCu₃-type structure shows the high Debye temperature and low heat capacity in comparison to other structures.     

The structure of triple-stranded G-2C polynucleotide helices.

The thermal stability of a new polynucleotide complex has been used to establish the hydrogen-bonding structure of three-stranded C-G·CH⁺ helices. In the Hoogsteen structure, the 8NH₂ group of 8NH₂GMP can form a third hydrogen bond to the CH⁺ strand, but in the alternative structure, the 8NH₂ group can form no interbase hydrogen bonds. For the new complex, 8NH₂GMP·2 poly(C), a transition temperature of 80°C is observed under conditions in which the corresponding complex formed with 5′-GMP has a T_m of 20°C. We conclude from this 60° elevation of transition temperature that a third hydrogen bond is formed by the 8NH₂ group and that the structure must have Hoogsteen bonding. In order to be compatible with this structure in regular helices formed by U,C copolymers, A·2U bonding would also have to have a Hoogsteen structure.     

Solution Structure of the HIV Protease Inhibitor Acetyl-pepstatin as Determined by NMR and Molecular Modeling

Abstract

The structure of acetyl-pepstatin has been investigated in solution by two-dimensional NMR spectroscopy and molecular modeling. The analysis of DQFCOSY, TOCSY and NOESY spectra lead to a full assignment of the NMR signals both in DMSO-d₆ and in TFE-d₃:H₂O 1:1. Interproton distances, dihedral angles and exchange regimes of NH or OH protons were derived from ROESY connectivities, coupling constants and temperature dependences of the chemical shifts, respectively. Molecular modeling using the NMR distance and dihedral angle constraints obtained in DMSO-d₆ yielded a model showing a well-defined structure for the N-terminal segment Ac-1 to Sta-4, but a flexible structure for the C-terminal segment. The structure was less defined in TFE-d₃:H₂O 1:1 and ¹³C T₁ measurements are indicative of higher mobility. Comparison of the NMR-determined solution structure of acetyl-pepstatin with its crystal structure when bound to HIV-1 protease shows that the conformation is more extended in the complex as a result of intermolecular interactions.     

The crystal structure of a nonalkenic,cyclic trimer of levoglucosenone

A single-crystal, X-ray diffraction study was performed on a nonalkenic, cyclic trimer (C₁₈H₁₈O₉, 4) of levoglucosenone, in order to confirm its chemical structure. Crystals of 4 are orthorhombic, with unit-cell parameters of a = 792.20, b = 1874.35, c = 2383.02 pm, space group P2₁2₁2₁, and z = 8. The structure was solved by direct methods, and refined by least-squares to R = 0.032, based on 2990 unique reflections. Each asymmetrical unit contains two symmetry-independent molecules of 4 and one of acetone. The previously assigned chemical structure and stereochemistry of 4 were found to be correct.     

Structure of deoxyhaemoglobin Yakima: a high-affinity mutant form exhibiting oxy-like 1 2 subunit interactions

Crystals of deoxyhaemoglobin Yakima (Asp Gl(99)β → His) are isomorphous with those of deoxyhaemoglobin A, even though the mutation produces disturbances in both the tertiary structure of the subunits and the quaternary structure of the tetramer. Asp Gl(99)β₂ lies at the α₁β₂ subunit interface, and in deoxyhaemoglobin A forms a crucial hydrogen bond with Tyr C7(42) α₁. The histidine residue that replaces the aspartate results in the removal of this single important intersubunit bond, and it further acts as a wedge between the α₁ and β₂ subunits, so that they are pushed apart and displaced part of the way towards the oxy structure. These disturbances are accompanied by the formation of a new intersubunit hydrogen bond, which is usually only observed in the oxy quaternary structure of haemoglobin. The disturbances at the α₁β₂ contact affect the stereochemistry of the entire molecule and are transmitted to the α and β haems. The X-ray structure of deoxy Yakima therefore provides a stereochemical explanation for its abnormal function; this being an abnormally high affinity for oxygen and vastly diminished haem-haem interactions.     

The NMR solution structure of subunit G (G61-101) of the eukaryotic V1VO ATPase from Saccharomyces cerevisiae

Subunit G is an essential stalk subunit of the eukaryotic proton pump V₁V_O ATPase. Previously the structure of the N-terminal region, G_1-59, of the 13 kDa subunit G was solved at higher resolution. Here solution NMR was performed to determine the structure of the recombinant C-terminal region (G_61-101) of subunit G of the Saccharomyces cerevisiae V₁V_O ATPase. The protein forms an extended α-helix between residues 64 and 100, whereby the first five- and the last residues of G_61-101 are flexible. The surface charge distribution of G_61-101 reveals an amphiphilic character at the C-terminus due to positive and negative charge distribution at one side and a hydrophobic surface on the opposite side of the structure. The hydrophobic surface pattern is mainly formed by alanine residues. The alanine residues 72, 74 and 81 were exchanged by a single cysteine in the entire subunit G. Cysteines at positions 72 and 81 showed disulfide formation. In contrast, no crosslink could be formed for the mutant Ala74Cys. Together with the recently determined NMR solution structure of G_1-59, the presented solution structure of G_61-101 enabled us to present a first structural model of the entire subunit G of the S. cerevisiae V₁V_O ATPase.     

The structures and stabilities of small diarsenic-doped silicon clusters

The structures and stabilities of As₂-doped Si_n (n = 1-7) clusters have been investigated at the B3LYP level of theory, incorporating the 6-311+G^∗ basis set. An isosceles triangle is predicted to be the lowest-energy structure of the As₂Si cluster, whereas the global minimum of As₂Si₂ possesses an As-As-butterfly structure. The ground state structures for As₂Si₃, As₂Si₄ and As₂Si₅ are all bipyramids: trigonal, tetragonal and pentagonal, respectively, which could have important applications as building blocks to synthesize silicon nanowires. The most stable isomer of As₂Si₆ possesses a tricapped trigonal bipyramid structure. The lowest energy structure of As₂Si₇ can be viewed as a substitutional structure of the tricapped trigonal prism Si₉ isomer. In the majority of the lowest energy isomers, the two As atoms tend to be separated from each other, in order to maximize the number of Si-As bonds, and therefore locate at the axial vertex or face-capping atomic positions, especially for As₂Si₄-As₂Si₇. According to results of the incremental binding energies, the HOMO-LUMO gaps and the vertical ionization potentials, the As₂Si₃ and As₂Si₆ clusters are relatively stable compared to their neighbors. Natural bond orbital analyses suggest that delocalized electrons and multi-centered bonds play an important role in stabilizing the low-energy As₂Si_n structures.     

The complexation between holothurian triterpene glycosides and Chl as the basis for lipid-saponin carriers of subunit protein antigens

The ability of holothurian triterpene glycosides (cucumarioside A₂-2 from Cucumaria japonica, cucumarioside G₁ from C. fraudatrix, frondoside A from C. frondosa, and holotoxin A₁ from Apostichopus japonicus) to form supramolecular lipid-saponin complexes was studied. TEM demonstrated that all the studied compounds form supramolecular cholesterol-saponin complexes (nanoparticles) in aqueous medium. The complexes formed by cucumarioside A₂-2, holotoxin A₁, and frondoside A had a tubular structure and fundamentally differed in the structure from the particles produced by cucumarioside G₁. The morphology of the nanoparticles formed by cucumarioside A₂-2, holotoxin A₁, and cucumarioside G₁ changed depending on the fraction of cholesterol in the lipid-saponin system; however, this pattern was not observed for frondoside A. At the same molar fraction of cholesterol in the lipid-saponin system, cucumarioside A₂-2 formed the particles with the most pronounced tubular structure; the cholesterol-saponin complexes of holotoxin A₁ had a less pronounced tubular structure, whereas the structure of frondoside A particles was extremely heterogeneous. Comparative analysis of the morphology of the described supramolecular complexes and specific structural features of the glycosides demonstrated that the structure of the corresponding nanoparticles depended on the degree of branching of the carbohydrate moiety in the glycoside molecule and the complexation with cholesterol was determined by the specific features of aglycone structure. Thus, the feasibility of producing new generation antigen carriers using the complexes in question was proved.     

A molecular mechanical study of netropsin-DNA interactions

We present molecular mechanical calculations on the complexes of netropsin with dA₆·dT₆, d(TATATA)₂, d(CGCGCG)₂, and d(CGCGAATTCGCG)₂. The complexes were model built using computer graphics and then completely energy refined. Our calculations are consistent with the observed AT preference for netropsin and suggest that mixed sugar pucker geometries should be more stable than uniform in netropsin complexes with poly[d(A-T)]·poly[d(A-T)] and poly(dA)·poly(dt). The netropsin·d(TATATA) and netropsin·dA₆·dT₆ complexes are significantly different in structure, leading to a possible reason why the observed thermodynamics of netropsin-association with poly[d(A-T)]·poly[d(A-T)] and with poly(dA)·poly(dT) are so different. We also model built and energy refined a structure of netropsin-d(CGCGAATTCGCG)₂ using as a guide the nmr data of Patel [(1982) Proc. Natl. Acad. Sci. USA, 79 , 6424–6428] and found a three-dimensional structure qualitatively consistent with the NOE enhancements observed by him. After our calculations were completed, we learned of an x-ray structure of a netropsin:d(CGCGAATTCGCG)₂ complex, and we compared the structure found in our calculation with the x-ray structure.     

Crystal structure of A3B3 complex of V‐ATPase from Thermus thermophilus

Vacuolar‐type ATPases (V‐ATPases) exist in various cellular membranes of many organisms to regulate physiological processes by controlling the acidic environment. Here, we have determined the crystal structure of the A₃B₃ subcomplex of V‐ATPase at 2.8 Å resolution. The overall construction of the A₃B₃ subcomplex is significantly different from that of the α₃β₃ sub‐domain in F_oF₁‐ATP synthase, because of the presence of a protruding ‘bulge’ domain feature in the catalytic A subunits. The A₃B₃ subcomplex structure provides the first molecular insight at the catalytic and non‐catalytic interfaces, which was not possible in the structures of the separate subunits alone. Specifically, in the non‐catalytic interface, the B subunit seems to be incapable of binding ATP, which is a marked difference from the situation indicated by the structure of the F_oF₁‐ATP synthase. In the catalytic interface, our mutational analysis, on the basis of the A₃B₃ structure, has highlighted the presence of a cluster composed of key hydrophobic residues, which are essential for ATP hydrolysis by V‐ATPases.     

Hydrothermal synthesis and characterization of a two-dimensional nickel(II) complex containing benzenehexacarboxylic acid (mellitic acid)

The hydrothermal synthesis, single crystal X-ray structure and magnetic properties of a two-dimensional (2-D) coordination polymer, [Ni₄(C₆(COO)₆)(OH)₂(H₂O)₆] (1), is described. Complex 1 consists of dimer motifs of pseudo octahedral NiO₆ linked through μ3-OH to generate one-dimensional (1-D) chains which are further bridged by the mellitate ligands to form non interpenetrated undulating sheet structure. The sheets are further connected by hydrogen bonding interaction to yield a three-dimensional (3-D) structure. The temperature dependence of magnetic susceptibilities revealed the presence of antiferromagnetic interaction between nickel centers.     

Hydrothermal synthesis and structural investigation of silver magnesium complex of benzenehexacarboxylic acid (mellitic acid), Ag2Mg2[C6(COO)6] · 8H2O with two-dimensional layered structure

Crystal and molecular structure of silver magnesium mellitate, Ag₂Mg₂[C₆(COO)₆] · 8H₂O, was synthesized hydrothermally and characterized by X-ray structure analysis. The complex crystallizes in the monoclinic system, space group P2/n, with unit cell dimensions of a=7.4347(2), b=9.9858(2), c=14.4248(3) Å, β=99.2429(5)°, V=1055.01(4) ų, and Z=2. The structure was solved and refined to R=0.036 (R_w=0.045) for 1707 independent reflections [I_o>2σ(I_o)]. The Ag cations are coordinated by six carboxylic oxygen atoms of mellitate anions with composition of [C₆(COO)₆]⁶⁻ on the (1 0 1) plane; each mellitate anion linking three neighboring Ag distorted trigonal prisms produces a two-dimensional layered structure parallel to (1 0 1). The Mg cations, which are coordinated by four water molecules and two carboxylic oxygen atoms, are intercalated between the two-dimensional layer stacks. The carboxylate group coordinated to Mg and Ag cations serve as a tridentate ligand in that structure. The number of water molecules incorporated into the mellitate compound is controlled mainly by ionic radii of metal cation in the structure. Furthermore, the ionic radii of metal cations in the mellitate compound play an essential role in arrangement of mellitate anions in the structure, whether as a one-dimensional infinite chain, a two-dimensional layered structure, or a three-dimensional framework structure.     

Influence of carbon dioxide supply on the chloroplast structure of Chlorella pyrenoidosa

Summary Electron microscopic investigations show that the structure of the lamellar system of Chlorella pyrenoidosa depends on the carbon dioxide supply in the culture medium. Chloroplasts of C. pyrenoidosa when grown with 0.03% CO₂, show typical grana structure whereas with 3% CO₂ the chloroplast structure is typical of that of the Chlorophyceae.     

Crystal structure at 87 K of sodium α-l-guluronate dihydrate

X-Ray data collected at 87 K showed crystals of sodium α-l-guluronate dihydrate (C₆H₉O₇Na · 2 H₂O) to be orthorhombic, P2₁2₁2₁ with a = 7.591(2), b = 18.884(5), c = 6.842(2) Å, and Z = 4. The structure was solved by direct methods, and full-matrix least-squares refinement based on 1587 F_o yielded R = 0.043 and R_w = 0.033. The structure analysis indicates partial anomeric disorder with α:β ～90:10. The guluronate ring has the ¹C₄(l) conformation. Sodium binds two translation-equivalent guluronate units and one water molecule in a primary five-fold coordination. The complexing oxygen functions, which include all axial hydroxyl groups and one carboxylate oxygen atom in the guluronate ring, describe a distorted trigonal bipyramid. A prominent feature of the crystal structure is the stacks of sodium atoms and guluronate residues in alternating sequence along the c axis. The stacks are held together by an intricate system of hydrogen bonds involving all oxygen atoms in the structure. The water molecules play an important role in this system both as hydrogen donors and acceptors.     

Crystal structures and spectroscopic behavior of monomeric, dimeric and polymeric copper(II) chloroacetate adducts with isonicotinamide, N-methylnicotinamide and N,N-diethylnicotinamide

Substituted pyridines provide structural rigidity and thus permit the metal coordination geometry to guide the direction of propagation of the hydrogen-bonded links between building blocks. In this paper we present the crystal structures and spectroscopic properties of monomeric, dimeric and polymeric copper(II) chloroacetates with isonicotinamide (INA), N-methylnicotinamide (MNA) and N,N-diethylnicotinamide (DENA). The molecular structure of [Cu(ClCH₂CO₂)₂(INA)₂]₂ (1) consists of a rather interesting dinuclear molecule with copper atoms bridged by anti, anti-O,O′ bridging oxygens of two chloroacetate anions. Each copper atom is octahedrally coordinated thus forming a CuN₂O₄ core with two nitrogens, originating from two different isonicotinamide molecules, in trans positions. This complex is one of a very few examples of this rare type of structure in which both carboxylate oxygen anions are coordinated to two copper metal ions. The crystal structure of 1 revealed an infinite 1-D linear hydrogen-bonded chain formed by discrete molecules [Cu(ClCH₂CO₂)₂(INA)₂]₂ connected by strong hydrogen bonds between two amide groups. This structure is the first example, where two pairs of amide groups are involved in hydrogen bonding connecting two molecules. The X-ray structure of the complex [Cu(CCl₃CO₂)₂(INA)₂]_n (3) revealed a tetragonal bipyramidal environment about the copper(II) atom. This structure represents the first example of copper(II) complex, where isonicotinamide acts as a bridging ligand. Strong intramolecular hydrogen bonds, N-H?O, create two eight-membered metallocycle rings which stabilizes the molecular structure. The crystal structure of 3 consists of 2-D sheets of a metal-organic framework. The coordination environment of the copper(II) atom in [Cu(CCl₃CO₂)₂(MNA)₂(H₂O)₂] · 2H₂O (6 · 2H₂O) is an elongated tetragonal bipyramid. Strong intramolecular hydrogen bond interactions involving an axial coordinated water molecule and a carboxylic oxygen atom stabilize the molecular structure. The crystal structure of [Cu₂(ClCH₂CO₂)₄(DENA)]_n (7) shows that the complex is an extended zigzag coordination chain of alternating binuclear paddle-wheel units of the bridging tetracarboxylate type Cu₂(ClCH₂CO₂)₄ and N,N-diethylnicotinamide molecules. This complex represents the first example of copper(II) carboxylates where N,N-diethylnicotinamide molecule acts as a bidentate bridging ligand connecting binuclear paddle-wheel units. The variation in DENA coordination in the polymeric chain can be described by the following formula: -[Cu₂(ClCH₂CO₂)₄]-(DENA-N,O)- [Cu₂(ClCH₂CO₂)₄]-(DENA-O,N)-. All complexes were characterized by electron paramagnetic resonance (EPR) spectroscopy and IR spectroscopy. The present study shows that the pyridine-carboxyamides are very suitable molecules that can be employed as ligands in the construction of extended arrays of transition metal-containing molecules linked via hydrogen bonds.     

Supramolecular architectures of cadmium(II) built of 2,2′-biimmidazole and bifunctional carboxylates: Syntheses, crystal structure and properties

A series of four new supramolecular complexes of cadmium(II), {[CdBr(H₂biim)(PyCO₂)(H₂O)](H₂O)}_∞ (1) (H₂biim = 2,2′-biimidazole, PyCO₂ = isonicotinate), [Cd(H₂biim)₂(HBDC)₂] (2) (H₂BDC = terephthalic acid), [Cd(H₂biim)₂(H₂O)₂](BDC) (3) and [Cd(H₂biim)₂(H₂O)₂](PyCO₂)₂ · 4H₂O (4) have been prepared and characterized by X-ray crystallography, IR, fluorescence spectra and thermogravimetric analysis. Compound 1 exhibits an infinite chain-like structure through bridging isonicotinate. Strong interchain hydrogen bonds between isonicotinate and H₂biim result in the robust 2-D sheet structure, responsible for the insolubility. The similar hydrogen bonds between H₂biim and the coordinated 1,4-bdc and complementary hydrogen bonds between monoprotonated bdc are responsible for the robust 2-D layered structure of 2 that is insoluble in aqueous solution. 1,4-Bdc becomes uncoordinated in the soluble complex 3, although it has hydrogen bonded 2-D structure as well.     

Fine Structure of Bacillus subtilis : I. Fixation

The fine structure of Bacillus subtilis has been studied by observing sections fixed in KMnO₄, OsO₄, or a combination of both. The majority of examinations were made in samples fixed in 2.0 per cent KMnO₄ in tap water. Samples were embedded in butyl methacrylate for sectioning. In general, KMnO₄ fixation appeared to provide much better definition of the boundaries of various structures than did OsO₄. With either type of fixation, however, the surface structure of the cell appeared to consist of two components: cell wall and cytoplasmic membrane. Each of these, in turn, was observed to have a double aspect. The cell wall appeared to be composed of an outer part, broad and light, and an inner part, thin and dense. The cytoplasmic membrane appeared (at times, under KMnO₄ fixation) as two thin lines. In cells fixed first with OsO₄ solution, and then refixed with a mixture of KMnO₄ and OsO₄ solutions, the features revealed were more or less a mixture of those revealed by each fixation alone. A homogeneous, smooth structure, lacking a vacuole-like space, was identified as the nuclear structure in a form relatively free of artifacts. Two unidentified structures were observed in the cytoplasm when B. subtilis was fixed with KMnO₄. One a tortuous, fine filamentous element associated with a narrow light space, was often found near the ends of cells, or attached to one end of the pre-spore. The other showed a special inner structure somewhat similar to cristae mitochondriales.