Bond Angle Distortion Research Articles

A copper(i)-catalysed template synthesis of aryl-arsonium and -stibonium systems. Solvatochromic tetraaryl-arsonium and -stibonium iminophenolate betaines

A series of aryl-arsonium and -stibonium salts bearing an imino substituent in the ortho position to the cationic centre has been prepared by the reactions of ortho-halogenoarylimines with triaryl-arsines and -stibines in the presence of copper(I) iodide in acetonitrile. X-Ray crystal structural studies reveal the existence of intramolecular coordination from the imino nitrogen to arsenic and antimony, with consequent distortion of bond angles about the group 15 element, which adopts a trigonal bipyramidal structure. Deprotonation of arsonium and stibonium salts derived from ortho-halogenoaryliminophenols gives a series of highly coloured aryl-arsonium and -stibonium iminophenolate betaines, which have been shown to exhibit a significant degree of negative solvatochromism, similarly to their previously reported arylphosphonium analogues. The visible absorption properties and solvatochromism are largely independent of the nature of the group 15 element, implying little d-orbital contribution to bonding in either ground or excited states.

The penultimate rotamer library

All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those with B-factors >/=40 or van der Waals overlaps >/=0.4 A) greatly improves the clustering of rotamer populations. Asn, Gln, or His side chains additionally benefit from flipping of their planar terminal groups when required by atomic overlaps or H-bonding. Sensitivity to skew and to the boundaries of chi angle bins is avoided by using modes rather than traditional mean values. Rotamer definitions are listed both as the modal values and in a preferred version that maximizes common atoms between related rotamers. The resulting library shows significant differences from previous ones, differences validated by considering the likelihood of systematic misfitting of models to electron density maps and by plotting changes in rotamer frequency with B-factor. Few rotamers now show atomic overlaps in ideal geometry; those overlaps are relatively small and can be understood in terms of bond angle distortions compensated by favorable interactions. The new library covers 94.5% of examples in the highest quality protein data with 153 rotamers and can make a significant contribution to improving the accuracy of new structures. Proteins 2000;40:389-408.

Correlation between bond distortion and the band-tail electronic density of states in amorphous silicon: a tight-binding recursion study

We study the spatial structure of the electronic states in amorphous silicon using a tight-binding Hamiltonian and the recursion method. A realistic cluster consisting of 4096 atoms in a periodic cubic supercell, obtained using reverse Monte–Carlo methods, is used as a model of amorphous silicon [B.R. Djordjevic, M.F. Thorpe, F. Wooten, Phys. Rev. B 52 (1995) 5685]. The local density of states for each of the 16 384 orbitals is computed. Our aim is to provide some insight into the nature of the band tail states and we particularly address the following issues. We examine the relative contributions of the p-orbitals and the s-orbitals to the density of states in the region of the band tail and gap. We investigate the geometric nature of these states. Finally, we study the correlation between the structural distortions in the amorphous silicon cluster and the spatial distribution of the band tail and gap states. Our results show that the p-orbitals contribute a large fraction of the density of states in the valence band tail. This fraction decreases as the energy increases across the gap into the conduction band. We observe the expected change from extended states deep in the valence and conduction band to localized states in the band gap. An attempt was made to characterize this change in terms of the fraction of the total density of states required for a percolating nearest-neighbor path in the cluster as a function of the energy. No abrupt change was observed in this quantity for energies in the region of the band tails. Although there are 4096 atoms in the cluster, 90% of the density of states in the band tail and gap is localized on only 416 atoms, that is, we find a backbone of atoms in the cluster responsible for a large fraction of the states in this energy range. We also find a strong correlation between atoms contributing a high density of states in the band tail and gap region and atoms with a large bond angle distortion.

Crystal and molecular structure of poly(thioether-ketone) from single crystal oligomer data and diffraction-modelling: 1. Polymer crystallised by orientation

The aromatic poly(thioether-ketone) [ArSArCO]n (Ar = 1,4-phenylene) is known to exist in two different crystalline forms, one produced by orientation of the amorphous polymer and the other by heat treatment or crystallisation from the melt. In the present work, single crystal X-ray data for the oligomer [ArCOArSArCOAr] reveal that bond angles at the thioether and carbonyl linkages are substantially different, at 108° and 121° respectively, and that the linear chain-conformation required for polymer crystallisation is achieved by a series of bond-angle distortions elsewhere in the molecule—in particular by pyramidalisation of the carbon atoms adjacent to the thioether bridge. Crystal and molecular simulation of orientation-crystallised poly(thioether-ketone) shows that the unit cell is analogous to the “Form II” cell known for poly(etherketone)s. The polymer crystal structure thus has orthorhombic symmetry (two chains per cell), space group Pb2n, a = 4.12, b = 11.30, c = 10.44Å, and density 1.45gcm−3. The previously reported monoclinic unit cell is shown to be based on a modification of the present orthorhombic lattice.

Lithium Phosphoranylidene Carbenoids Mes*-P(E)C(X)Li(THF)3 (E = NMes*, C(SiMe3)2; X = Br, Cl, F): Synthesis and Structural Investigations in Solution and Solid State

Phosphoranylidene carbenoids Mes*-P(E)C(X){Li(THF)3} (E = C(SiMe3)2, NMes*; X = F, Cl, Br, 10−13, 15) were synthesized and their molecular structures characterized by low-temperature X-ray diffractometry and multinuclear NMR studies. The experiments confirm the presence of monomeric molecules with THF-solvated metal atoms in both solution and solid state. The solid carbenoids display elongated C−X bonds and distortions of carbon bond angles which represent typical features of carbenoids and suggest an interpretation of the bonding situation as a contact ion pair between a carbanion and a solvated metal cation. This is corroborated by NMR studies which show that the dynamic exchange between the two components in solution can be directly monitored in 2D 6Li,31P shift correlations. While structural and spectroscopic data give no evidence for a continuously increasing stability between F-, Cl-, or Br-substituted carbenoids, they reveal the presence of marked structural differences between the E/Z-isomers 10 a...

2-Salicylideneamino-4,5-bis(2-furyl)furan-3-carbonitrile

There are two independent molecules in the asymmetric unit of the title compound, C 20 H 12 N 2 O 4 . The main difference between the independent molecules is that while one of them is nearly planar, the other has the furyl substituents at 24.1 (1) and 16.1 (1)° to the central furan ring. The near planarity of the molecules introduces steric strain and distortions of the exocyclic bond angles around the central furan ring. Each molecule contains a strong intramolecular O-H...N hydrogen bond.

Electron and phonon states in an ideal continuous random network model ofa−SiO2glass

A previously constructed large continuous random network model of amorphous ${\mathrm{SiO}}_{2} (a\ensuremath{-}{\mathrm{SiO}}_{2})$ glass with 1296 atoms and periodic boundary condition has been relaxed with four different sets of pair potentials under constant pressure. By removing the restriction of the cubic symmetry in the original model, the bond-length and bond-angle distortions can be further reduced, resulting in an ideal fully coordinated random network model for $a\ensuremath{-}{\mathrm{SiO}}_{2}.$ On the basis of the calculated vibrational states, it is concluded that the pair potential of Tsuneyuki et al. [Phys. Rev. Lett. 61, 869, 1988] gives the most realistic results for low-energy excitations. Specific-heat calculations using normal modes of vibration show good agreement with experimental data down to 8 K. Analysis of eigenvector components of the lowest nonzero vibrational mode shows that the low-energy atomic vibration involves the floppy movements of more than ten atoms in a chainlike structure. Thus the low-energy vibration in $a\ensuremath{-}{\mathrm{SiO}}_{2}$ is not associated with localized movement of a few atoms. Implications of this finding for the two-level tunneling model in glasses are then discussed. Using this ideal model structure, a first-principles calculation of electronic and optical properties of $a\ensuremath{-}{\mathrm{SiO}}_{2}$ glass is carried out. The reduction in the bond-length and bond-angle distortions leads to a more uniform distribution of effective charges and a slight reduction in the band gap. It is shown that such a topologically disordered network has sharp valence-band edges in the electronic density of states. The mobility edge at the top of the valence band is estimated to be only 0.06 eV, and there is no evidence for any localization for states at the conduction-band edge. The calculated dielectric function for $a\ensuremath{-}{\mathrm{SiO}}_{2}$ is in reasonable agreement with experimental measurements.

In situ syntheses of trans-spanned octahedral ruthenium complexes. Crystal structures of trans-[Ru(Cl)(trpy){Ph2PC6H4CH2O(CO)(CH2)4(CO)OCH2C6H4PPh2}][PF6]·0.25C6H5Me·0.5CH2Cl2 and trans-[Ru(Cl)(trpy)(PPh3)2][BF4]·CH2Cl2 †

The formation of stable, undistorted octahedral transition metal complexes which contain a trans-spanning bidentate ligand remains a synthetic challenge. The reported complexes are of the type trans-[Ru(Cl)(trpy){Ph2PC6H4CH2O(CO)Y(CO)OCH2C6H4PPh2}][PF6] [where trpy = 2,2′∶6′,2″-terpyridine and Y = (CH2)3 = C3SPAN, 6; (CH2)4 = C4SPAN, 7; or isophthalate = ISPAN, 8] and represent the first examples of trans-spanned transition metal complexes which display little bond angle distortion from octahedral geometry and also contain a bridging linkage which is stable towards oxidation, reduction and hydrolysis. These complexes were characterized by elemental analyses, cyclic voltammetry, conductivity and UV-VIS spectroscopy. COSY, HETCOR and variable temperature (1H and 13C) NMR spectra of the complexes are consistent with a flexible spanning linkage that does not demonstrate restricted rotation about either the P–Cipso or the Ru–P bonds while the X-ray crystal structure analysis of 7 showed that the spanning linkage is positioned to one side of the meridional chloride.

Competing interactions and the isotope effect in colossal magnetoresistance materials

Abstract The experimentally observed large isotope effect on the ferromagnetic transition temperature in doped manganites R1- x A x MnO3 is shown to be in agreement with a local Jahn-Teller coupling mechanism. With increasing doping towards the insulating antiferromagnetic state the Mn-O-Mn bond substantially distorts, which is taken into account through intersite (Mn-O) interband electron-phonon interactions. It is shown that there is a competition between the local Jahn Teller and intersite interband couplings; depending on the bond angle distortion, the isotope effect can be suppressed substantially and even reverse sign, consistent with recent experimental results.

Core reconstruction of the90°partial dislocation in nonpolar semiconductors

We investigate the energetics of the single-period and double-period core reconstructions of the $90\ifmmode^\circ\else\textdegree\fi{}$ partial dislocation in the homopolar semiconductors C, Si, and Ge. The double-period geometry is found to be lower in energy in all three materials, and the energy difference between the two geometries is shown to follow the same trends as the energy gap and the stiffness. Both structures are fully reconstructed, consisting entirely of fourfold coordinated atoms. They differ primarily in the detail of the local strains introduced by the two reconstructions in the core region. The double-period structure is shown to introduce smaller average bond-length deviations, at the expense of slightly larger average bond-angle bending distortions, with respect to the single-period core. The balance between these two strain components leads to the lower energy of the double-period reconstruction.

Racemic Ethyl 4-(2-Fluorophenyl)-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate

The title compound, C21H24FNO3, has potential calcium modulatory properties. The 1,4-dihydropyridine ring has a shallow boat conformation with the 2-fluorophenyl substituent in an axial synperiplanar orientation. The quinoline ring has a half-chair conformation. Steric interactions between the adjacent methyl and ethoxycarbonyl substituents cause local bond-angle distortions. The molecules are linked into chains by intermolecular N—H⋯O hydrogen bonds.

2-[2-(Hydroxyethyl)phenoxy]benzoic Acid

The three-dimensional structure of the title compound, C 15 H 14 O 4 , has been determined. The molecule assumes a skew conformation, the angle between the two phenyl rings being 84.8 (1)°. The carboxylic acid substituent is essentially coplanar with the ring. The molecules are connected by O...O intermolecular hydrogen bonds ranging from 2.6 to 2.9 A. Distorted bond angles at the substituted phenyl C atoms were observed and they agree with the values reported in the literature for other bridged diphenyls.

Tetragonal-strain-induced local structural modifications inInAsxP1−x/InPsuperlattices: A detailed x-ray-absorption investigation

We report a comprehensive investigation of the local structure around As in thin ${\mathrm{InAs}}_{x}{\mathrm{P}}_{1\ensuremath{-}x}$ strained layers in ${\mathrm{InAs}}_{x}{\mathrm{P}}_{1\ensuremath{-}x}/\mathrm{InP}$ superlattices by fluorescence-detected x-ray-absorption fine structure; seven superlattice samples are studied as a function of composition, and compared to six unstrained, bulk samples of similar composition. Contributions up to the third coordination shell around As are clearly visible in the spectra, and are analyzed taking into account important multiple-scattering contributions. Results show that structural modifications due to tetragonal distortion appear mainly in the second and third coordination shells, while nearest-neighbor bond lengths remain closer to the values in unstrained bulk alloys. This implies that in semiconductor alloys tetragonal strain accommodation is mainly obtained through bond-angle distortions, in analogy to the situation in bulk pseudobinary alloys. A model which combines macroscopic elastic theory and the known local structure in bulk pseudobinary alloys is presented, and is found to fit the data very well.

Crystal Growth in Silicon Chemical Vapor Deposition from Silane: The Role of Hydrogen

Crystal growth mechanisms in chemical vapor deposition (CVD) of silane are studied in some detail. An atomic view reveals that the free energy change upon the formation of a small crystal on the (100) silicon surface in Si‐CVD from is always negative, due to the presence of hydrogen. Therefore, nucleation and step growth are unnecessary, in contrast to crystal growth from melt. Epitaxial growth in this case takes place through iterative adsorption and desorption reactions on the periodic surface sites of the substrate. Slow desorption reactions result in vacancies and distorted bond angles which hinder epitaxial growth. Based on this model, the role of H desorption in low temperature Si epitaxy from is investigated. A thermodynamic analysis implies that H desorption is the limiting factor to low temperature epitaxy in the pressure range of 1 to 760 Torr, and the pressure dependence of minimum epitaxial temperature is derived as . Below 1 Torr, adsorption rate becomes the limiting factor to low temperature epitaxy.

Extended x-ray absorption fine structure study of AlxGa(1−x)N films

Extended x-ray absorption fine structure above the Ga–K edge has been used to study the local structure of AlxGa1−xN films grown by metal organic chemical vapor deposition. With increasing Al content, x, the Ga–N bond length decreases, but much less than the average bond length. On the other hand, the x dependence of the Ga–Ga and Ga–Al distances does follow the variation of the average cation–cation distance. We conclude that bond angle distortions accommodate the differences between the Ga–N and Al–N bond lengths.

Local Structural Distortions in InAsP/InP Strained Layer Superlattices

The local structure around As in thin InAs x P 1-x strained layers in InAs x P 1-x /InP superlattices has been probed by fluorescence detected XAFS as a function of composition, and compared to that found in unstrained, bulk samples of similar composition. Contributions up to the third coordination shell around As were clearly visible in the spectra and were analyzed taking into account the major multiple scattering contributions. Differences in the local structure between the thin strained films and the bulk alloys are expected to arise from tetragonal strain due to epitaxy with the substrate. Results are consistent with a picture in which long range order in the strained layers is mainly achieved via bond angle distortions, as first shell bond distances follow the measured and theoretically predicted values of the bulk alloys. Evidence of the influence of tetragonal distortion on the local structure appears in further coordination shells.

Application of a Novel Differential XAFS Approach for Determination of Coordination Geometries

A novel differential XAFS approach has been developed which allows the determination of small distortions in coordination geometry (distortions in bond lengths and angles) about the absorber. The approach requires taking the difference, Δ X , between the XAFS of the sample and a reference material. The Fourier transform of Δ X directly reveals the average of the altered path lengths between the sample and the reference. More importantly, the amplitude of Δ X directly reflects the magnitude of the changes in the bond lengths or angles. FEFF6 calculations verify this approach, and help to interpret the data. Application of this technique has been made to the zincate ion in an alkaline Zn battery, where small distortions from the Td geometry resulting from ion pair interactions can be determined directly.

Giant magnetoresistance studies on La (0.8− x)R xSr 0.2MnO 3 thin films (R  Pr, Nd, Gd, Ho)

The effect of substituting La by a smaller lanthanide element (R) in La 0.8− x R x Sr 0.2MnO 3 ( x = 0.1; R  Pr, Nd, Gd, Ho) thin films on the resistivity ( ϱ) and giant magnetoresistance (GMR) behaviour was studied. The magnitude of GMR shows a maximum as a function of temperature. The temperature at which the maximum value of GMR is observed was found to shift systematically towards higher temperatures (from 210 to 300 K) as the size of the substitution ion increases from Ho to Pr. ϱ( T) also shows a maximum which shifts to higher temperatures as the size of the substitution ion increases. The zero-field resistivity shows a systematic decrease as the size of R 3+ increases. This result is explained qualitatively by invoking the interrelation between the conduction electron hopping probability and the MnOMn bond angle distortion which, in turn, is governed by the size of the substitution ion. Our results show that the size of the rare earth substitution ion can play an important role in tailoring the resistivity and GMR behaviour of La-R-Sr-Mn-O thin films, particularly for room temperature applications.

Disallowed Ramachandran Conformations of Amino Acid Residues in Protein Structures

An analysis of the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in high resolution protein crystal structures has been carried out. A data set consisting of 110 high resolution, non-homologous, protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 18,708 non-Gly residues, which were characterized on the basis of their backbone dihedral angles (φ, ψ). Residues falling outside the defined “broad allowed limits” on the Ramachandran map were chosen and the reported B-factor value of the α-carbon atom was used to further select well defined disallowed conformations. The conformations of the selected 66 disallowed residues clustered in distinct regions of the Ramachandran map indicating that specific φ, ψ angle distortions are preferred under compulsions imposed by local constraints. The distribution of various amino acid residues in the disallowed residue data set showed a predominance of small polar/charged residues, with bulky hydrophobic residues being infrequent. As a further check, for all the 66 cases non-hydrogen van der Waals short contacts in the protein structures were evaluated and compared with the ideal “Ala-dipeptide” constructed using disallowed dihedral angle (φ, ψ) values. The analysis reveals that short contacts are eliminated in most cases by local distortions of bond angles. An analysis of the conformation of the identified disallowed residues in related protein structures reveals instances of conservation of unusual stereochemistry.

Electron states in a nearly ideal random-network model of amorphous SiO2 glass.

A large continuous random-network model with 1296 atoms and periodic boundary conditions has been constructed for amorphous ${\mathrm{SiO}}_{2}$ glass. The atoms in this model are all fully coordinated with an overall small bond length and bond angle distortions. The calculated pair distribution function is in close agreement with the diffraction data. Based on this model, a first-principles calculation of the electron states is performed and the resulting wave functions are analyzed. Subtle differences in the density of states with the crystalline ${\mathrm{SiO}}_{2}$ are found. The calculated density of states are in good agreement with x-ray emission data and show the importance of Si 3d orbitals. The distributions of effective charges on Si and O atoms are studied in relation to the short-range order in the glass. It is found that O atoms with a Si-O-Si bridging angle of less than 120\ifmmode^\circ\else\textdegree\fi{} have smaller effective charges and can be identified as quasidefective centers that are responsible for the two-level tunneling at low temperature. It is also shown that localized states at the top of the band are induced by the elongation of the Si-O bond and those at the bottom of the band are related to atoms with shortened bonds. A mobility edge of 0.2 eV at the top of the valence band is obtained. A similar mobility edge for the conduction band cannot be located because of the much less localized nature of the states. \textcopyright{} 1996 The American Physical Society.