Differences In Bond Lengths Research Articles

Anisotropic ideal strengths of superhard monoclinic and tetragonal carbon and their electronic origin

The mechanical and electronic properties, and the atomic deformation mechanism of recently reported monoclinic ($C$2/$m$) and body-centered-tetragonal ($I$4/mmm) carbon polymorphs are studied by first-principles methods. The calculated elastic moduli and ideal strengths suggest that both polymorphs have low compressibility and are superhard, but their relatively lower ideal strength as compared with diamond indicates that they are intrinsically weaker because of differences in bond lengths and concomitant fluctuation of valence charge density. Analyses of electronic structure and atomic deformation mechanism demonstrate that the polarity of the bonds, which results from the fluctuations, is responsible for the lower strength.

Phase diagram, structure, and electronic properties of (Ga1−xZnx)(N1−xOx) solid solutions from DFT-based simulations

We construct an accurate cluster expansion for the (Ga${}_{1\ensuremath{-}x}$Zn${}_{x}$)(N${}_{1\ensuremath{-}x}$O${}_{x}$) solid solution, based on density functional theory (DFT). The subsequent Monte Carlo simulation reveals a phase diagram which has a wide miscibility gap and an $x=0.5$ ordered compound. The disordered phase displays strong short-range order (SRO) at synthesis temperatures. To study the influences of SRO on the lattice and electronic properties, we conduct DFT calculations on snapshots from the Monte Carlo simulation. Consistent with previous theoretical and experimental findings, lattice parameters were found to deviate from Vegard's law with small upward bowing. Bond lengths depend strongly on local environment, with a variation much larger than the difference of bond length between ZnO and GaN. The downward band gap bowing deviates from parabolic by having a more rapid onset of bowing at low and high concentrations. An overall bowing parameter of 3.3 eV is predicted from a quadratic fit to the compositional dependence of the calculated band gap. Our results indicate that SRO has significant influence over both structural and electronic properties.

Microwave Spectra and Structures of 1,2-(ortho)- and 1,7-(meta)-Carborane, C2B10H12

The microwave spectra of 1,2- and 1,7-dicarba-closo-dodecaborane(12), C(2)B(10)H(12) (ortho- and meta-carborane), have been recorded for the first time at room temperature in the 32-88 and 24-80 GHz spectral ranges, respectively. The spectra of the parent species (1,2-C(2)(11)B(10)H(12) and 1,7-C(2)(11)B(10)H(12)) have been assigned, together with those of four monosubstituted ((10)B) 1,2-C(2)(10)B(11)B(9)H(12) and 1,7-C(2)(10)B(11)B(9)H(12) isotopologues. The microwave spectra confirm that the structures of each of these two molecules are slightly distorted icosahedrons of C(2v) symmetry. A previous determination of the gaseous structures of these two carboranes by the gas electron-diffraction method was based on several assumptions about the B-B bond length differences. All B-B bond lengths have now been redetermined using the substitution (r(s)) method, which is independent of such restraints. Although several of the r(s) and electron-diffraction bond lengths are in good agreement, there are also differences of up to 0.026 Å. Quantum chemical calculations at the B3LYP/6-311++G(3df,3pd) level of theory have also been performed.

Valence electron structure and hydrogen storage properties analysis of Mg2Ni

The valence electron structure and theoretical cohesive energy of Mg2Ni were calculated by means of bond length difference method (BLD) in the Empirical Electron Theory of Solids and Molecules (EET). Ionicity of chemical bonds in Mg2Ni was given by EET together with PVL valence bond theory. Results show that, the theoretical cohesive energy of Mg2Ni is 746.5 kJ/mol, in good agreement with the experimental value. In Mg2Ni, the interactions between atoms along c-axis are stronger than those along a-axis and b-axis, taking on obvious anisotropy, so that the pulverization easily occurs after repeated absorption and desorption of hydrogen. In the alloy, the interaction between Ni-Mg atoms dominates and tetrahedral clusters made of Ni-Mg atoms provide hydrogen proper interstices. Chemical bonds of Mg2Ni are so complicated that there are not only covalent components but also metallic one as well as ionic ones. The ionicity of Mg2Ni is very small with the value of only 0.04.

What causes iron-sulphur bonds in active sites of one-iron superoxide reductase and two-iron superoxide reductase to differ?

AbstractThe electronic and vibrational properties of [Fe(NHis)4(SCys)] sites responsible for the catalysis of superoxide reduction in two types of superoxide reductase (SOR), one-iron superoxide reductase (1Fe-SOR) and two-iron superoxide reductase (2Fe-SOR), were compared previously (Clay et al., 2003); the differences between these two classes of SOR, examined by UV-VIS and NIR absorption, VTMCD, and vibrational spectroscopy techniques, were interpreted as being indicative of weaker Fe-S bonds in 2Fe-SOR in comparison with 1Fe-SOR. Here, we report on density functional (DFT) and semi-empirical (ZINDO/S-CI) calculations exploring the extent of this difference in bonding between the two classes of SOR. The differences observed experimentally between the electronic spectra of the two SORs are shown to probably arise either from different degrees of torsion between the Fe—ligand bonds or from differences in length of the Fe—carboxylate bond, but are shown to be incompatible with any significant differences in Fe—S bond lengths. The differences observed in the vibrational spectra between the two SORs are shown to correlate with differences in the Fe-S bond length of no more than 0.01 Å, which in turn arise from slight differences in the polarity of the medium surrounding the iron active site in the two proteins.

Ab Initio Coupled Cluster Determination of the Equilibrium Structures of cis- and trans-1,2-Difluoroethylene and 1,1-Difluoroethylene

The equilibrium structures of cis- and trans-1,2-difluoroethylene and 1,1-difluoroethylene, C(2)H(2)F(2), have been determined with high-level coupled cluster techniques combined with large basis sets, explicit consideration of core/valence, and scalar relativistic and higher order correlation effects. Excellent agreement was found with new semiexperimental structures, increasing the level of confidence in both approaches. Differences in bond lengths among ethylene and the fluoroethylenes are discussed.

Hardness estimation for covalent crystals using empirical electron theory

Covalent electrons substantially determine the intrinsic hardness of inorganic crystals. A hardness model is presented on the basis of the Empirical Electron Theory generated from Pauling’s covalent bond length equation and the bond length difference method. The calculated hardness values of inorganic crystals are in good agreement with experimental and other theoretical values. Covalent bond energy with polarity correction can be used as an intrinsic indicator linking microscopic electronic structure to macroscopic hardness. A simple mathematical processing of bond energy is performed to extend the model to multi-bonding or multi-component systems. It is also found that spatial distribution of covalent bonds has a great influence on the hardness of inorganic crystals.

N-Butyldichlorido(2-{(1E)-1-[2-(pyridin-2-yl)hydrazin-1-ylidene]ethyl}phenolato)tin(IV)

Two independent mol­ecules comprise the asymmetric unit of the title compound, [Sn(C4H9)(C13H12N3O)Cl2]. The Sn atom in each is coordinated by the tridentate ligand via the phenoxide O, hydrazine N and pyridyl N atoms, forming five- and six-membered chelate rings. The approximately octa­hedral coordination geometry is completed by the α-C atom of the n-butyl group (which is trans to the hydrazine N atom) and two mutually trans Cl atoms. Differences between the mol­ecules are evident in the relative planarity of the chelate rings and in the conformations of the n-butyl groups [C—C—C—C = 177.2 (5) and −64.4 (11)°]. Significant differences in the Sn—Cl bond lengths are related to the formation of N—H⋯Cl hydrogen bonds, which link the mol­ecules comprising the asymmetric unit into dimeric aggregates. These are consolidated in the crystal packing by C—H⋯Cl contacts. The structure was refined as an inversion twin; the minor twin component is 37 (3)%.

Influence of Micro-Addition Chromium on the Valence Electron Structure and Toughness of Fe<sub>2</sub>B Phase

Fe2B is a kind of typical intermetallic compound, which has good corrosion resistance in molten zinc. However, the fatal intrinsic brittleness limits its further application in the Hot-Dip Galvanizing Industry. Therefore, it is worthwhile to improve the toughness of Fe2B phase. In this study, the fracture toughness property of Fe2B phase with and without micro-addition chromium is investigated. In comparison with pure Fe2B phase, the intrinsic brittleness of Fe2B phase with chromium is lower. In addition, the valence electron structure of Fe2B containing various chromium content is calculated by the method of bond length difference (BLD). The results show that, in the (Fe1-x Crx)2B phase, the number of covalent electron pairs and the weaker bond energy are increased by the substituting atom-Cr. The calculated results are in good agreement with experimental observations.

A Comparison of Cocrystal Structure Solutions from Powder and Single Crystal Techniques

We demonstrate the effectiveness and accuracy of high resolution powder diffraction for determination of cocrystal structures through a double-blind study. Structures of 10 cocrystals of varying complexity were determined independently using single crystal and powder techniques. The two methodologies give identical molecular packing and hydrogen bond topology, and an rms difference in covalent bond lengths of 0.035 A. Powder techniques are clearly sufficient to establish a complete characterization of cocrystal geometry.

ChemInform Abstract: Gas-Phase Structures of Ethynyl and Vinyl Pentafluorosulfur Derivatives: An Electron Diffraction and Microwave Spectroscopy Study

Abstract The gas-phase structures of ethynyl- and vinyl sulfur pentafluoride were determined by joint analyses of electron diffraction and microwave spectroscopic data. The following skeletal geometric parameters ( r z values with 3σ uncertainties) were obtained. SF 5 CCH: (SF) mean = 1.574 (1) A, ΔSF=(SF e SF a )=0.018 (14) A, SC=1.736 (6) A, CC=1.200 (7) A, F e SF a =88.9 (2)°; SF 5 CHCH 2 : (SF) mean 1.581 (1) A, ΔSF=0.020 (16) A, SC=1.787 (9) A, CC=1.337 (17) A, F e SF a =88.4 (3)° SCC=124.5 (15)°. In both compounds the equatorial SF bonds are longer than the axial ones, in accordance with the predicted “cis influence” in octahedral main group element compounds. The actual values for the bond length differences ΔSF, however, are poorly determined. The variation of the (SF) mean bond lengths between the ethynyl and vinyl derivatives can be rationalized by the different group electronegativities of these two substituents. The variation of the SC bond lengths reflects the different covalent radii of sp and sp 2 hybridized carbon atoms.

Calculation of crystal cohesive energy of ZrB2 compound

The valence electron structure (VES) of ZrB2 was set up with the bond length difference (BLD) method based on empirical electron theory (EET) of solids and molecules, and there were 43 potential hybridization combinations. Based on the calculation result of the melting point, the 16th hybridization step of Zr atom and fifth hybridization step of B atom are ascertained as the final hybridization combination. Therefore, the covalent electron number and the bonding energy of the strongest bond (the B-B bonds), the theoretical melting point, and the crystal cohesive energy of the ZrB2 compound can be figured out.

A biophysical elucidation for less toxicity of Agglutinin than Abrin-a from the Seeds of Abrus Precatorius in consequence of crystal structure

X-ray crystal structure determination of agglutinin from abrus precatorius in Taiwan is presented. The crystal structure of agglutinin, a type II ribosome-inactivating protein (RIP) from the seeds of Abrus precatorius in Taiwan, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of abrin-a as the template. The structure has space group P41212 with Z = 8, and been refined at 2.6 Å to R-factor of 20.4%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.009 Å and 1.3°. Primary, secondary, tertiary and quaternary structures of agglutinin have been described and compared with those of abrin-a to a certain extent. In subsequent docking research, we found that Asn200 of abrin-a may form a critical hydrogen bond with G4323 of 28SRNA, while corresponding Pro199 of agglutinin is a kink hydrophobic residue bound with the cleft in a more compact complementary relationship. This may explain the lower toxicity of agglutinin than abrin-a, despite of similarity in secondary structure and the activity cleft of two RIPs.

Trichlorido{2-[2-(η5-cyclopentadienyl)-2-methylpropyl]-1-trimethylsilyl-1H-imidazole-κN3}titanium(IV) tetrahydrofuran hemisolvate

The title compound, [Ti(C15H23N2Si)Cl3]·0.5C4H8O, has been prepared from {2-[2-(η5-cyclo­penta­dien­yl)-2-methyl­prop­yl]-1H-imidazolyl-κN 1}bis­(N,N-diethyl­amido-κN)titanium(IV), (C12H14N2)Ti(NEt2)2, by reaction with excess of Me3SiCl in tetra­hydro­furan (THF) at 353 K. The crystal structure contains THF as adduct solvent, disordered around a center of inversion. The presence of THF and the adduct ratio has been independently supported by 1H NMR spectroscopy. The coordination polyhedron of the Ti atom is distorted square-pyramidal, assuming the cyclo­penta­dienyl (Cp) ring occupies one coordination site. The Ti, Si and CH2 group C atoms only deviate slightly from the imidazole ring plane [by 0.021 (4), 0.133 (4) and 0.094 (4) Å, respectively]. Comparison of the principal geometric parameters with those of the few known structurally characterized analogues reveal small differences in bond lengths and angles at the Ti atom. The title complex is only stable in THF-d 8 in the presence of excess Me3SiCl, otherwise it exists in an equilibrium with equimolar amounts of dichlorido{2-[2-(η5-cyclo­penta­dien­yl)-2-methyl­prop­yl]-1H-imidazolyl-κN 3}titanium(IV) and chloro­trimethyl­silane.

Synthesis of α- and β- d-glucopyranosyl triazoles by CuAAC ‘click chemistry’: reactant tolerance, reaction rate, product structure and glucosidase inhibitory properties

Cu I-catalysed azide alkyne 1,3-dipolar cycloaddition (CuAAC) ‘click chemistry’ was used to assemble a library of 21 α- d- and β- d-glucopyranosyl triazoles, which were assessed as potential glycosidase inhibitors. In the course of this work, different reactivities of isomeric α- and β-glucopyranosyl azides under CuAAC conditions were noted. This difference was further investigated using competition reactions and rationalised on the basis of X-ray crystallographic data, which revealed significant differences in bond lengths within the azido groups of the α- and β-anomers. Structural studies also revealed a preference for perpendicular orientation of the sugar and triazole rings in both the α- and β-glucosyl triazoles in the solid state. The triazole library was assayed for inhibition of sweet almond β-glucosidase (GH1) and yeast α-glucosidase (GH13), which led to the identification of a set of glucosidase inhibitors effective in the 100 μM range. The preference for inhibition of one enzyme over the other proved to be dependent on the anomeric configuration of the inhibitor, as expected.

Crystallographic rationalization of the reactivity and spectroscopic properties of (2R)-S-(2,5-dihydroxyphenyl)cysteine

At 150 K, the title compound, C(9)H(11)NO(4)S, crystallizes in the orthorhombic form as a zwitterion and has a low gauche conformation [chi = -46.23 (16) degrees] for an acyclic cysteine derivative. A difference in bond length is observed for the alkyl C-S bond [1.8299 (15) A] and the aryl C-S bond [1.7760 (15) A]. The -NH(3)(+) group is involved in four hydrogen bonds, two of which are intermolecular and two intramolecular. The compound forms an infinite three-dimensional network constructed from four intermolecular hydrogen bonds. Characterization data ((13)C NMR, IR and optical rotation) are reported to supplement the incomplete data disclosed previously in the literature.

Octahedral distortion caused by hydrogen bonding in tris(diethylammonium) hexachloridoantimonate(III)

The factors influencing the distortion of inorganic anions in the structures of chloridoantimonates(III) with organic cations, in spite of numerous structural studies on those compounds, have not been clearly described and separated. The title compound, [(C(2)H(5))(2)NH(2)](3)[SbCl(6)], consisting of isolated distorted [SbCl(6)](3-) octahedra that have C(3) symmetry and [(C(2)H(5))(2)NH(2)](+) cations, unequivocally shows the role played by hydrogen bonding in the geometry variations of inorganic anions. The organic cations, which are linked to the inorganic substructure through N-H...Cl hydrogen bonds, are clearly responsible for the distortion of the octahedral coordination of Sb(III) in terms of differences (Delta) in both Sb-Cl bond lengths [Delta = 0.4667 (6) A] and Cl-Sb-Cl angles [Delta = 9.651 (17) degrees].

Structural Properties of Ruthenium Biimidazole Complexes Determining the Stability of their Supramolecular Aggregates

The results of a detailed investigation of the influence of substituents in a variety of ruthenium biimidazole-type complexes [Ru(R-bpy)2(R´-bi(bz)imH2)]2+ (R = H, tBu; R´ = H,Me; bi(bz)imH2 = 2,2´-bi(benz)imidazole) on selected structural and photophysical properties is reported. The photophysical properties are only marginally influenced by the substituents at the bipyridine and the biimidazole core. All complexes show intense absorptions in the visible range of the spectrum with maxima around 475 nm, and emission from the formed excited state occurs at wavelengths between 650 and 670 nm. The comparison of structural properties determined by X-ray analysis within a series of related complexes shows that the Ru-N bond lengths to the coordinated bipyridines are not significantly influenced by the substituents, but slight differences in the Ru-N bond lengths to the biimidazole-type ligands can be detected. The reactions between ruthenium complexes containing different biimidazole-type ligands with the sulfate dianion, however, show a strong correlation between the substituents at the biimidazole core and the solubility of the product. The bibenzimidazolecontaining complexes precipitate from aqueous solution whereas the ruthenium complex containing unsubstituted biimidazole stays in solution. The solid-state structure of one example of the sulfatecontaining products (2b) shows that strong hydrogen bonds between the secondary amine function of the bibenzimidazole and the oxygen functionalities of the sulfate contribute to this unexpected behavior.

Synthesis and Crystal Structure of [Ni(L)(Phen)(H2O)]·3.75H2O

The title compound, [Ni(L)(Phen)(H2O)]·3.75H2O, where L = (E)-2-(5-formyl-2-oxidobenzylideneamino)ethanesulfonate, was synthesized in aqueous methanol in the presence of Ni(II), Phen and the potassium salt of 2-{[(E)-(2-hydroxy-5{[(2-sulfoethyl)imino]methyl}phenyl)methylidene]amino}-1-ethanesulfonic acid. The complex crystallized in the space group of P-1 with a = 13.751 (2) A, b = 14.797 (2) A, c = 15.543 (2) A, α = 105.86 (1)°, β = 103.51 (1)°, γ = 114.38 (1)°, and Z = 2. In [Ni(L)(Phen)(H2O)], the Ni(II) was six coordinated with two O and one N from L, two N from Phen and one O from coordinated water, forming an octahedral geometry. There are two molecules in the asymmetric unit and concomitant differences in the Ni-ligand bond lengths. The complex of [Ni(L)(Phen)(H2O)]·3.75H2O was synthesized in aqueous methanol and crystallized in the space group of P-1. There are two molecules in the asymmetric unit and concomitant differences in the Ni-ligand bond lengths.

Development of a Polarizable Force Field Using Multiple Fluctuating Charges per Atom.

A polarizable force field (PFF) using multiple fluctuating charges per atom, ABEEMσπ PFF, is presented in this work. The fluctuating partial charges are obtained from the electronegativity equalization principle applied to the decomposition scheme of atom-bond regions into multiple charge sites: atomic, lone-pair electron, and σ and π bond regions. These multiple partial charges per atom should better account for the polarization effect than single atomic charge in other PFFs. To evaluate the PFF, structural and energetic properties for some organic and biochemical systems, including rotational barriers; binding energies of base pairs; a base-base interaction in a B-DNA decamer; and interaction energies of ten stationary conformers of a water dimer, peptides, and bases with water molecules, have been calculated and compared with the experimental data or ab initio MP2 results. Molecular dynamics simulations using the PFF have been performed for crambin and BPTI protein systems. Better performances in modeling root-mean-square deviations of backbone bond lengths, bond angles, key dihedral angles, the coordinate root-mean-square shift of atoms, and the distribution of hydrogen bonds have been observed in comparison with other PFFs. These results indicate that the fluctuating charge force field, ABEEMσπ/MM, is accurate and reliable and can be applied to wide ranges of organic and biomolecular systems.