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Bond Lengths (bond + length)
Kinds of Bond Lengths Selected AbstractsOxygen Position, Octahedral Distortion, and Bond-Valence Parameter from Bond Lengths in Ti1,xSnxO2 (0 ,x, 1)JOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 12 2000Toshiya Hirata Based on the virtual crystal approximation (or Vegard's law), the bond lengths of Ti1,xSnxO2 were deduced from those of TiO2 and SnO2, to allow the oxygen position and octahedral distortion to be determined as a function of x. The oxygen positional parameter (u) increased linearly when the Sn4+ cation (which has a larger ionic radius) was substituted for the Ti4+ cation, whereas the octahedral distortion exhibited a nonlinear decay with increasing x in Ti1,xSnxO2. At the same time, the bond-valence parameter, which relates bond valence to bond length, so that the central atom in the octahedron can retain a constant valence of +4.0, exhibited a correlation with u for Ti1,xSnxO2. The present results indicate that the different phonon/physical properties of TiO2 and SnO2 and/or their dependence on x in Ti1,xSnxO2 can be associated with different octahedral distortions. [source] Valence Bond and Molecular Orbital Studies of the A-F Bond Lengths in Some AFn Type Molecules and Their Fluorinated CationsCHEMINFORM, Issue 52 2003Richard D. Harcourt Abstract For Abstract see ChemInform Abstract in Full Text. [source] ChemInform Abstract: The Short N,F Bond in N2F+ and How Pauli Repulsion Influences Bond Lengths.CHEMINFORM, Issue 19 2002NF3X+, NH3X+ (X: F, Theoretical Study of N2X+ Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Geometries and Electronic Structures of Co-Oligomers and Co-Polymers Based on Tricyclic Nonclassical Thiophene: A Theoretical StudyMACROMOLECULAR THEORY AND SIMULATIONS, Issue 7-8 2008Yangwu Fu Abstract The geometries and electronic properties of four copolymers based on tricyclic nonclassical thiophene were studied using DFT at the B3LYP/6-31G(d) level. Bond lengths and their alternation, electron densities at BCPs, NICS, and WBIs were analyzed and correlated with the energy gap. The results show that the degree of conjugation increases upon main chain extension. The energy gap decreased steadily with increasing degree of polymerization. Conjugation is stronger in the central than in the outer section. The results suggest that the narrow HOMO/LUMO separation of tricyclic nonclassical thiophenes can be carried over to their co-polymers by using them as building blocks for the co-polymers. [source] Bond lengths in organic and metal-organic compounds revisited: X,H bond lengths from neutron diffraction dataACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010Frank H. Allen The number of structures in the Cambridge Structural Database (CSD) has increased by an order of magnitude since the preparation of two major compilations of standard bond lengths in mid-1985. It is now of interest to examine whether this huge increase in data availability has implications for the mean bond-length values published in the late 1980s. Those compilations reported mean X,H bond lengths derived from rather sparse information and for rather few chemical environments. During the intervening years, the number of neutron studies has also increased, although only by a factor of around 2.25, permitting a new analysis of X,H bond-length distributions for (a) organic X = C, N, O, B, and (b) a variety of terminal and homometallic bridging transition metal hydrides. New mean values are reported here and are compared with earlier results. These new overall means are also complemented by an analysis of X,H distances at lower temperatures (T, 140,K), which indicates the general level of librational effects in X,H systems. The study also extends the range of chemical environments for which statistically acceptable mean X,H bond lengths can be obtained, although values from individual structures are also collated to further extend the chemical range of this compilation. Updated default `neutron-normalization' distances for use in hydrogen-bond and deformation-density studies are also proposed for C,H, N,H and O,H, and the low-temperature analysis provides specific values for certain chemical environments and hybridization states of X. [source] 2-Amino-5-(3,4-dimethoxybenzylidene)-1-methylimidazol-4(5H)-one N,N -dimethylformamide monosolvateACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2010Laura M. Tvedte The crystal structure of the title compound, C13H15N3O3·C3H7NO, was determined as part of a larger project focusing on creatinine derivatives as potential pharmaceuticals. The molecule is essentially planar, in part because of intramolecular hydrogen bonding. Inversion-related pairs of molecules result from intermolecular hydrogen bonding. The , systems of 2-amino-5-(3,4-dimethoxybenzylidene)-1-methylimidazol-4(5H)-one and an inversion-related molecule overlap slightly, indicating a small amount of ,,, stacking. Bond lengths, angles and torsion angles are consistent with similar structures, except in the imidazolone ring near the doubly bonded C atom, where significant differences occur. [source] Crystal structure of N-[(1Z)-1-(3-methyl-3-phenylcyclobutyl)-2-thiomorpholin-4-ylethylidene] thioureaCRYSTAL RESEARCH AND TECHNOLOGY, Issue 7 2005U. Sar Abstract The crystal structure of N-[(1Z)-1-(3-methyl-3-phenylcyclobutyl)-2-thiomorpholin-4-ylethylidene] thiourea (C18H26N4S2) has been determined by X-ray crystallographic techniques. The compound crystallizes in the orthorhombic space group Pbca, with unit cell parameters: a = 15.692(3), b = 20.803(8), c = 11.979(6)Å, Z = 8, V = 3911(7)Å3. The crystal structure was solved by direct methods and refined by full-matrix least squares to a final R-value of 0.084 for 1447 observed reflections [I > 2, ( I ) ]. In the thiosemicarbazide moiety, the S = C bond length is 1.656(6), N-C-N angle is 115.6(5)°. The crystal structure is stabilized by the intermolecular N-H...S hydrogen bonds. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Preparation and investigation of (CuInSe2)x(2ZnSe)1-x and (CuInTe2)x(2ZnTe)1-x solid solution crystalsCRYSTAL RESEARCH AND TECHNOLOGY, Issue 4 2004I. V. Bodnar Abstract The (CuInSe2)x(2ZnSe)1-x and (CuInTe2)x(2ZnTe)1-x solid solution crystals prepared by Bridgman method and chemical vapor transport have been studied. The nature of the crystalline phases, the local structure homogeneity and composition of these materials have been investigated by X-ray diffraction (XRD) and Electron Probe Microanalysis (EPMA) methods. The analysis revealed the presence of chalcopyrite-sphalerite phase transition between 0.6 , X , 0.7. Lattice constants, value of , position parameter and bond length between atoms were also calculated. It was found that the lattice parameters exhibit a linear dependence versus composition. The transmission spectra of solid solution crystals in the region of the main absorption edge were studied. It was established that the optical band gap of these materials changes non-linearly with the X composition. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Molecular mechanics in the context of the finite element methodINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 7 2009Jens Wackerfuß Abstract In molecular mechanics, the formalism of the finite element method can be exploited in order to analyze the behavior of atomic structures in a computationally efficient way. Based on the atom-related consideration of the atomic interactions, a direct correlation between the type of the underlying interatomic potential and the design of the related finite element is established. Each type of potential is represented by a specific finite element. A general formulation that unifies the various finite elements is proposed. Arbitrary diagonal- and cross-terms dependent on bond length, valence angle, dihedral angle, improper dihedral angle and inversion angle can also be considered. The finite elements are formulated in a geometrically exact setting; the related formulas are stated in detail. The mesh generation can be performed using well-known procedures typically used in molecular dynamics. Although adjacent elements overlap, a double counting of the element contributions (as a result of the assembly process) cannot occur a priori. As a consequence, the assembly process can be performed efficiently line by line. The presented formulation can easily be implemented in standard finite element codes; thus, already existing features (e.g. equation solver, visualization of the numerical results) can be employed. The formulation is applied to various interatomic potentials that are frequently used to describe the mechanical behavior of carbon nanotubes. The effectiveness and robustness of this method are demonstrated by means of several numerical examples. Copyright © 2008 John Wiley & Sons, Ltd. [source] Thermal dehydration kinetics of a rare earth hydroxide, Gd(OH)3INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 2 2007Chengkang Chang This paper reports the synthesis, characterization, and dehydration kinetics of a rare earth hydroxide, Gd(OH)3. Uniform rod-like Gd(OH)3 powder was prepared by a colloidal hydrothermal method. The powder thus obtained dehydrated into its oxide form in a two-step process, where crystalline GdOOH was obtained as the intermediate phase. Crystal structure study revealed a monoclinic structure for GdOOH, with space group P2/1m and lattice parameters a = 6.0633, b = 3.7107, c = 4.3266, and , = 108.669. The first-step dehydration follows the F2 mechanism, while the second step follows the F1 model, indicating that both the steps are controlled by nucleation/growth mechanism. The activation energy Ea and frequency factor A are 231±12 kJ/mol and 2.08 × 1018 s,1 for the first step and 496 ± 32 kJ/mol and 7.88 × 1033 s,1 for the second step, respectively. Such high activation energy calculated from the experimental data can be ascribed to the high bonding energy of GdO bond, and the difference in activation energy for the two steps is due to the change in the bond length of hexagonal Gd(OH)3 and monoclinic GdOOH. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 39: 75,81, 2007 [source] Comparative study on the nonadditivity of methyl group in lithium bonding and hydrogen bondingINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2009Qingzhong Li Abstract Quantum chemical calculations at the second-order Moeller,Plesset (MP2) level with 6-311++G(d,p) basis set have been performed on the lithium-bonded and hydrogen-bonded systems. The interaction energy, binding distance, bond length, and stretch frequency in these systems have been analyzed to study the nonadditivity of methyl group in the lithium bonding and hydrogen bonding. In the complexes involving with NH3, the introduction of one methyl group into NH3 molecule results in an increase of the strength of lithium bonding and hydrogen bonding. The insertion of two methyl groups into NH3 molecule also leads to an increase of the hydrogen bonding strength but a decrease of the lithium bonding strength relative to that of the first methyl group. The addition of three methyl groups into NH3 molecule causes the strongest hydrogen bonding and the weakest lithium bonding. Although the presence of methyl group has a different influence on the lithium bonding and hydrogen bonding, a negative nonadditivity of methyl group is found in both interactions. The effect of methyl group on the lithium bonding and hydrogen bonding has also been investigated with the natural bond orbital and atoms in molecule analyses. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Blue-shifted H-bond in aromatic sulfines: An ab initio calculationINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 7 2007H. Roohi Abstract The intramolecular CH···OS H-bond in the aromatic sulfines, HRCSO, was analyzed by NBO and QTAIM methods. The results of QTAIM analysis at the MP2/aug-cc-pVDZ level of theory show that the CH···OS H-bond meets all the characteristics of an improper, blue shift hydrogen bond. NBO analysis at the MP2/6,31++G(d,p)//MP2/aug-cc-pVDZ level predicts a normal relationship between change of bond length and CH rehybridization. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Endohedral carbon chains in chiral single-wall carbon nanotubesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 11 2006Ravi K. Vadapalli Abstract Using a first-principles, local density functional approach, we report the bond length optimization of endohedral linear carbon chains. In these calculations, all-carbon nanowire structures were constructed by inserting cumulenic linear carbon chains inside the semiconducting (7,3) and metallic (7,4) single-wall carbon nanotubes with radii of ,0.35 nm. Our calculations show that the total energy results for the endohedral chains inside both (7,3) and (7,4) nanotubes are well described with a common total energy curve having an equilibrium bond length of ,0.129 nm. The electronic band structures of the carbon nanowires are described in terms of a rigid-band model, with the Fermi level for the carbon nanowire effectively pinned near the top of bands originating from the valence band of the single-wall nanotube. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Bond length features of linear carbon chains of finite to infinite size: Visual interpretation from Pauling bond ordersINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2003Zexing Cao Abstract Schemes for Kekulé structure counting of linear carbon chains are suggested. Mathematical formulas, which calculate the Pauling bond order P(k, N) of a chemical bond numbered by k, are given for the carbon chain with N carbon atoms. By use of the least-squares fitting of a linearity, relationships between Pauling bond orders and bond lengths are obtained, and such correlation of the Pauling bond order,bond length can be qualitatively extended to the excited states. The relative magnitudes of Pauling bond orders in unsaturated carbon chains dominate C,C bond lengths a well as the bond length feature with the chain size increasing. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 144,149, 2003 [source] Pressure Dependence of Exchange Parameters and Neel Temperature in La2CuO4ISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 2007Anatolii Ya. Microscopic mechanisms responsible for the observed pressure dependencies of the Neel temperature TN and parameters of isotropic and anisotropic exchange interaction in the orthorhombic antiferromagnet La2CuO4 are investigated. Within the framework of the Anderson microscopic theory of superexchange interaction, the expressions establishing interrelation between parameters of isotropic and anisotropic (both symmetric and antisymmetric) exchange interactions and by the structural parameters describing the Cu-O-Cu bonding angle and the Cu-O bond length in La2CuO4 are obtained. Experimentally determined pressure dependencies of structural parameters by H. Takahashi et al., allow one to present pressure dependencies of exchange parameters and TN in an apparent form. [source] A novel semi-empirical topological descriptor Nt and the application to study on QSPR/QSARJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2007Congyi Zhou Abstract A novel semi-empirical topological descriptor Nt was proposed by revising the traditional distance matrix based on the equilibrium electronegativity and the relative bond length. Nt can not only efficiently distinguish structures of organic compounds containing multiple bonds and/or heteroatoms, but also possess good applications of QSPR/QSAR (quantitative structure-property/activity relationships) to a large diverse set of compounds, which are alkanes, alkenes, alkynes, aldehydes, ketones, thiols, and alkoxy silicon chlorides with all the correlation coefficients of the models over 0.99. The LOO CV (leave-one-out cross-validation) method was used to testify the stability and predictive ability of the models. The validation results verify the good stability and predictive ability of the models employing the cross-validation parameters: RCV, SEPCV and SCV, which demonstrate the wide potential of the Nt descriptor for applications to QSPR/ QSAR. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Atom,atom partitioning of total (super)molecular energy: The hidden terms of classical force fieldsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2007M. Rafat Abstract Classical force fields describe the interaction between atoms that are bonded or nonbonded via simple potential energy expressions. Their parameters are often determined by fitting to ab initio energies and electrostatic potentials. A direct quantum chemical guide to constructing a force field would be the atom,atom partitioning of the energy of molecules and van der Waals complexes relevant to the force field. The authors used the theory of quantum chemical topology to partition the energy of five systems [H2, CO, H2O, (H2O)2, and (HF)2] in terms of kinetic, Coulomb, and exchange intra-atomic and interatomic contributions. The authors monitored the variation of these contributions with changing bond length or angle. Current force fields focus only on interatomic interaction energies and assume that these purely potential energy terms are the only ones that govern structure and dynamics in atomistic simulations. Here the authors highlight the importance of self-energy terms (kinetic and intra-atomic Coulomb and exchange). © 2006 Wiley Periodicals, Inc. J Comput Chem 2007 [source] Raman spectroscopic study of the uranyl selenite mineral marthozite Cu[(UO2)3(SeO3)2O2]·8H2OJOURNAL OF RAMAN SPECTROSCOPY, Issue 10 2008Ray L. Frost Abstract The mineral marthozite, a uranyl selenite, has been characterised by Raman spectroscopy at 298 K. The bands at 812 and 797 cm,1 were assigned to the symmetric stretching modes of the (UO2)2+ and (SeO3)2, units, respectively. These values gave the calculated UO bond lengths in uranyl of 1.799 and/or 1.814 Å. Average UO bond length in uranyl is 1.795 Å, inferred from the X-ray single crystal structure analysis of marthozite by Cooper and Hawthorne. The broad band at 869 cm,1 was assigned to the ,3 antisymmetric stretching mode of the (UO2)2+ (calculated UO bond length 1.808 Å). The band at 739 cm,1 was attributed to the ,3 antisymmetric stretching vibration of the (SeO3)2, units. The ,4 and the ,2 vibrational modes of the (SeO3)2, units were observed at 424 and 473 cm,1. Bands observed at 257, and 199 and 139 cm,1 were assigned to OUO bending vibrations and lattice vibrations, respectively. OH···O hydrogen bond lengths were inferred using Libowiztky's empirical relation. The infrared spectrum of marthozite was studied for complementation. Copyright © 2008 John Wiley & Sons, Ltd. [source] A Raman spectroscopic study of the uranyl selenite mineral haynesiteJOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2006Ray L. Frost Abstract The mineral haynesite, a uranyl selenite, has been characterised by Raman spectroscopy at 298 and 77 K. Two bands at 811.5 and 800.2 cm,1 are assigned to the symmetric stretching modes of the (UO2)2+ and (SeO3)2, units respectively. These values give calculated UO bond lengths of 1.799 and/or 1.801 Å. The broad band at 861.8 cm,1 is assigned to the ,3 antisymmetric stretching mode of the (UO2)2+ (calculated UO bond length 1.813 Å). Additional bands are observed in the 77 K spectrum. In the spectroscopy of selenite compounds, the position of the antisymmetric stretching vibration occurs at lower wavenumbers than the symmetric stretching mode and thus the band at 740.5 cm,1 is attributed to the ,3 antisymmetric stretching vibration of the (SeO3)2, units. The ,4 and the ,2 vibrational modes of the (SeO3)2, units are observed at 418.5 and 472.1 cm,1. Bands observed at 278.3, 257.3 and 218.8 cm,1 are assigned to OUO bending vibrations. Copyright © 2006 John Wiley & Sons, Ltd. [source] Film Growth and Surface Roughness with Effective Fluctuating Covalent Bonds in Evaporating Aqueous Solution of Reactive Hydrophobic and Polar Groups: A Computer Simulation ModelMACROMOLECULAR THEORY AND SIMULATIONS, Issue 3 2006Shihai Yang Abstract Summary: A computer simulation model is proposed to study film growth and surface roughness in aqueous (A) solution of hydrophobic (H) and hydrophilic (P) groups on a simple three dimensional lattice of size with an adsorbing substrate. Each group is represented by a particle with appropriate characteristics occupying a unit cube (i.e., eight sites). The Metropolis algorithm is used to move each particle stochastically. The aqueous constituents are allowed to evaporate while the concentration of H and P is constant. Reactions proceed from the substrate and bonded particles can hop within a fluctuating bond length. The film thickness () and its interface width () are examined for hardcore and interacting particles for a range of temperature (). Simulation data show a rapid increase in and followed by its non-monotonic growth and decay before reaching steady-state and near equilibrium () in asymptotic time step limit. The growth can be described by power laws, e.g., with a typical value of in initial time regime followed by at . For hardcore system, the equilibrium film thickness () and surface roughness () seem to scale linearly with the temperature, i.e., at low and at higher . For interacting functional groups in contrast, the long time (unsaturated) film thickness and surface roughness, and decay rapidly followed by a slow increase on raising the temperature. Growth of the average film thickness at a temperature . [source] Sub-5-fs Real-time Spectroscopy of Transition States in Bacteriorhodopsin During Retinal Isomerization,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 2 2007Takayoshi Kobayashi By using a sub-5-fs visible laser pulse, we have made the first observation of the vibrational spectra of the transition state during trans-cis isomerization in the retinal chromophore of bacteriorhodopsin (bRS68). No instant isomerization of the retinal occurs in spite of electron promotion from the bonding ,-orbital to the anti-bonding ,*-orbital. The difference between the in-plane and out-of-plane vibrational frequencies (about 1150,1250 and 900,1000 cm,1, respectively) is reduced during the first time period. The vibrational spectra after this period became very broad and weak and are ascribed to a "silent state." The silent state lasts for 700,900 fs until the chromophore isomerizes to the cis -C13=C14 conformation. The frequency of the C=C stretching mode was modulated by the torsion mode of the C13=C14 double bond with a period of 200 fs. The modulation was clearly observed for four to five periods. Using the empirical equation for the relation between bond length and stretching frequency, we determined the transitional C=C bond length with about 0.01 Å accuracy during the torsion motion around the double bond with 1-fs time resolution. [source] The local structure of ,-FeSi2 under high pressurePHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 3 2009Yoshihisa Mori Abstract We report the results of the high-pressure X-ray diffraction study and the high-pressure extended X-ray absorption fine structure study for ,-FeSi2 using the synchrotron radiation sources. The bond lengths of Fe,Fe, Si,Si, and Fe,Si under pressure were refined by the Rietveld method and the EXAFS analysis. It is interesting that the bond length of Si,Si is almost unchanged with increasing pressure. The DV-X, molecular orbital calculation was carried out for the crystal structure at 34.9 GPa and shows that the highest occupied molecular orbital consists of only 3d orbital of Fe atom. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Redox-dependent structural changes in archaeal and bacterial Rieske-type [2Fe-2S] clustersPROTEIN SCIENCE, Issue 12 2002Nathaniel J. Cosper Abstract Proteins containing Rieske-type [2Fe-2S] clusters play important roles in many biological electron transfer reactions. Typically, [2Fe-2S] clusters are not directly involved in the catalytic transformation of substrate, but rather supply electrons to the active site. We report herein X-ray absorption spectroscopic (XAS) data that directly demonstrate an average increase in the iron,histidine bond length of at least 0.1 Å upon reduction of two distantly related Rieske-type clusters in archaeal Rieske ferredoxin from Sulfolobus solfataricus strain P-1 and bacterial anthranilate dioxygenases from Acinetobacter sp. strain ADP1. This localized redox-dependent structural change may fine tune the protein,protein interaction (in the case of ARF) or the interdomain interaction (in AntDO) to facilitate rapid electron transfer between a lower potential Rieske-type cluster and its redox partners, thereby regulating overall oxygenase reactions in the cells. [source] Modeling of loops in protein structuresPROTEIN SCIENCE, Issue 9 2000András Fiser Abstract Comparative protein structure prediction is limited mostly by the errors in alignment and loop modeling. We describe here a new automated modeling technique that significantly improves the accuracy of loop predictions in protein structures. The positions of all nonhydrogen atoms of the loop are optimized in a fixed environment with respect to a pseudo energy function. The energy is a sum of many spatial restraints that include the bond length, bond angle, and improper dihedral angle terms from the CHARMM-22 force field, statistical preferences for the main-chain and side-chain dihedral angles, and statistical preferences for nonbonded atomic contacts that depend on the two atom types, their distance through space, and separation in sequence. The energy function is optimized with the method of conjugate gradients combined with molecular dynamics and simulated annealing. Typically, the predicted loop conformation corresponds to the lowest energy conformation among 500 independent optimizations. Predictions were made for 40 loops of known structure at each length from 1 to 14 residues. The accuracy of loop predictions is evaluated as a function of thoroughness of conformational sampling, loop length, and structural properties of native loops. When accuracy is measured by local superposition of the model on the native loop, 100, 90, and 30% of 4,, 8,, and 12,residue loop predictions, respectively, had <2 Å RMSD error for the mainchain N, Ca, C, and O atoms; the average accuracies were 0.59 6 0.05, 1.16 6 0.10, and 2.61 6 0.16 Å, respectively. To simulate real comparative modeling problems, the method was also evaluated by predicting loops of known structure in only approximately correct environments with errors typical of comparative modeling without misalignment. When the RMSD distortion of the main-chain stem atoms is 2.5 Å, the average loop prediction error increased by 180, 25, and 3% for 4,, 8,, and 12,residue loops, respectively. The accuracy of the lowest energy prediction for a given loop can be estimated from the structural variability among a number of low energy predictions. The relative value of the present method is gauged by (1) comparing it with one of the most successful previously described methods, and (2) describing its accuracy in recent blind predictions of protein structure. Finally, it is shown that the average accuracy of prediction is limited primarily by the accuracy of the energy function rather than by the extent of conformational sampling. [source] Topological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM)ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2009Jeanette Netzel Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T, 20,K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (lmax = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C,C, C,N and C,O bonds, and for hydrogen bonds together with covalent C,H and N,H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H...O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997). An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead to the correct characterization of chemical bonding. Our results do not confirm suggestions in the literature that the promolecule density might be sufficient for a characterization of hydrogen bonds. [source] Structural analysis of perovskite LaCr1,,,xNixO3 by Rietveld refinement of X-ray powder diffraction dataACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2008J. Yang The crystal structure of perovskite LaCr1,,,xNixO3 (0 ,x, 1.0) has been systematically investigated by analyzing X-ray powder-diffraction data taken at room temperature. Rietveld refinement has confirmed the structural evolution from the orthorhombic phase (Pbnm, Z = 4) to the two-phase (the orthorhombic and the rhombohedral phases) region around x = 0.7, then to the rhombohedral (, Z = 2) phase for 0.8 ,x, 1.0. The lattice parameters are also obtained in the refinement process. The results are discussed in terms of reduced Cr/Ni,O bond length with increasing Ni-doping level, leading to an increased tolerance factor caused by the substitution of smaller Ni3+ ( = 0.60,Å, six-coordinate) ions for larger Cr3+ ( = 0.615,Å, six-coordinate) ions. [source] Quantitative description of the tilt of distorted octahedra in ABX3 structuresACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2007Rafael Tamazyan A description of the tilt of octahedra in ABX3 perovskite-related structures is proposed that can be used to extract the unique values for the tilt parameters ,, , and , of ABX3 structures with regular and distorted octahedra up to the point symmetry , from atomic coordinates and lattice parameters. The geometry of the BX6 octahedron is described by three B,X bond lengths (r1, r2, r3) and three X,B,X bond angles (,12, ,13 and ,23) or alternatively by a local strain tensor together with an average B,X bond length. Connections between the proposed method and Glazer's tilt system are discussed. The method is used to analyze structural transformations of I2/c, Pbnm and Immm structures. The proposed description allows the analysis of group,subgroup relations for the ABX3 structures with distorted octahedra, in terms of octahedral deformations and tilting. The method might also be of interest in the study of the phase transitions in the family of ABX3 structures. [source] Temperature-dependent crystal structure refinement and 57Fe Mössbauer spectroscopy of Cu2Fe2Ge4O13ACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2007Günther J. Redhammer The germanate compound Cu2Fe2Ge4O13, dicopper diiron germanate, was synthesized by solid-state reaction at 1403,K and ambient pressure. There is no change of space-group symmetry between 10 and 900,K. Between 40,K and room temperature the a lattice parameter shows a negative thermal expansion which can be connected to a decreasing Cu,Cu interatomic distance. Above room temperature all the lattice parameters are positively correlated with temperature. Among the structural parameters several alterations with temperature occur, which are most prominent for the distorted Fe3+ octahedral site. Besides an increase of the average bond length and of the interatomic Fe,Fe distances, distortional parameters also increase with temperature, while the average Cu,O bond length remains almost constant between 100 and 900,K, as do the average Ge,O distances. 57Fe Mössbauer spectroscopy was used to detect long-range magnetic ordering in Cu2Fe2Ge4O13. While around 100,K, which is the temperature at which a broad maximum is observed in the magnetic susceptibility, no magnetic ordering was detected in the Mössbauer spectrum, below 40,K a narrow split sextet is developed which is indicative of a three-dimensional magnetic ordering of the sample. [source] Structural characterization of p -benzosemiquinone radical in a solid state: the radical stabilization by a low-barrier hydrogen bondACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2006imir Mol Semiquinone (p -benzosemiquinone), a transient organic radical, was detected in the solid state by EPR spectroscopy revealing four symmetrically equivalent protons. A variable-temperature X-ray diffraction analysis (293 and 90,K) and EPR data support a dynamical disorder of the proton. A low-barrier O,H···O hydrogen bond stabilizes the radical. The C,O bond length is 1.297,(4),Å, corresponding to a bond order of ca 1.5. The geometry of the radical implies an electron delocalization throughout the benzenoid ring. Two polymorphs of semiquinone, monoclinic and triclinic, were observed and their structures determined. Their crystal packings were compared with those of quinhydrone polymorphs. [source] Single-crystal structure refinement of NaTiSi2O6 clinopyroxene at low temperatures (298,<,T,<,100,K)ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2003Günther J. Redhammer The alkali-metal clinopyroxene NaTi3+Si2O6, one of the rare compounds with trivalent titanium, was synthesized at high temperature/high pressure and subsequently investigated by single-crystal X-ray diffraction methods between 298 and 100,K. One main difference between the high- and the low-temperature form is the sudden appearance of two different Ti3+,Ti3+ interatomic distances within the infinite chain of the TiO6 octahedra just below 197 K. This change can be seen as direct evidence for the formation of Ti,Ti singlet pairs in the low-temperature phase. Mean Ti,O bond lengths smoothly decrease with decreasing temperature and the phase transition is associated with a slight jump in the Ti,O bond length. The break in symmetry, however, causes distinct variations, especially with respect to the two Ti,Oapex bond lengths, but also with respect to the four Ti,O bonds in the equatorial plane of the octahedron. The TiO6 octahedron appears to be stretched in the chain direction with a slightly larger elongation in the P low-temperature phase compared with the C2/c high-temperature phase. Polyhedral distortion parameters such as bond-length distortion and octahedral angle variance suggest the TiO6 octahedron in P to be closer to the geometry of an ideal octahedron than in C2/c. Mean Na,O bond lengths decrease with decreasing temperature and the variations in individual Na,O bond lengths are the result of variations in the geometry of the octahedral site. The tetrahedral site acts as a rigid unit, which does not show pronounced changes upon cooling and through the phase transitions. There are neither large changes in bond lengths and angles nor in polyhedral distortion parameters, for the tetrahedral site, when they are plotted. In contrast with the C2/c,P21/c phase transition, found especially in LiMSi2O6 clinopyroxenes, no very large variations are found for the tetrahedral bridging angle. Thus, it is concluded that the main factor inducing the phase transition and controlling the structural variations is the M1 octahedral site. [source] | ||||||||||||||||||||||||||||||||||||||||