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Bond Distances (bond + distance)
Kinds of Bond Distances Selected AbstractsElectronic structures and chemical bonding in diatomic ScX to ZnX (X = S, Se, Te)JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2007Z. J. Wu Abstract Bond distances, vibrational frequencies, electron affinities, ionization potentials, dissociation energies, and dipole moments of the title molecules in neutral, positively, and negatively charged ions were studied using density functional method. Ground electronic state was assigned for each molecule. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that, besides ionic component, covalent bonds are formed between the metal s, d orbitals, and the p orbital of S, Se, and Te. For neutral and cationic molecules, the covalent character increases from ScX to CrX and from FeX to CuX with an exception of decrease at MnX and ZnX, while for anionic molecules, the trend is not obvious. For both neutral and charged molecules, the sulfides have the shortest bond distance and largest vibrational frequency, while tellurides have the largest bond distance and smallest vibrational frequency. For neutral and anionic molecules, the dissociation energy of sulfides is the largest, that of tellurides is the smallest, while this only remains true for cationic molecules from ScX+ to FeX+. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 703,714, 2007 [source] Electronic structures of 3d -metal mononitridesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2006Zhijian Wu Abstract Bond distances, vibrational frequencies, electron affinities, ionization potentials, and dissociation energies of the title molecules in neutral, positively, and negatively charged ions were studied by use of density functional methods B3LYP, BLYP, BHLYP, BPW91, and B3PW91. The calculated results are compared with experiments and previous theoretical studies. It was found that the calculated properties are highly dependent on the functionals employed, in particular for the dissociation energy and vibrational frequency. For neutral species, pure density functional methods BLYP and BPW91 have relatively good performance in reproducing the experimental bond distance and vibrational frequency. For cations, hybrid exchange functional methods B3LYP and B3PW91 are good in predicting the dissociation energy. For both neutral and charged species, BHLYP tends to give smaller dissociation energy. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 267,276, 2006 [source] (5S)-3-Oxo-4-oxa- endo -tricyclo[5.2.1.02,6]dec-8-en-5-yl acetateACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2000Dianne D. Ellis The molecular structure of C11H12O4, based on a norbornene core, was established to confirm the configuration of an acetoxy side-chain group in addition to the formation of the endo product. The acetoxy side chain lies in an axial position relative to the five-membered fused ring. Bond distances and angles show no unusual features, with all geometric parameters lying within their expected ranges. The overall stereochemistry of the molecule was ascertained from the chiral furanone starting material. [source] A linear three-center four electron bonding identity nucleophilic substitution at carbon, boron, and phosphorus.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 7 2010A theoretical study in combination with van't Hoff modeling Abstract We studied various identity nucleophilic substitution reactions based on an SN2 reaction profile. With calculations and experimental geometries concerning the nature of the various complexes indicated as stable, intermediate, and transition state we were able to show the additional value of van't Hoff 's tetrahedron by changing its geometry via a trigonal pyramid into a trigonal bipyramid. The ratio of the apical and the corresponding tetrahedral bond distance is then 1.333. This value has been used in general as a calibration point for the understanding of the (in)stabilities of the complex formation on the SN2 reaction coordinate. The relevance of this approach has been also proved for enzymatic reactions focused on carbon and phosphorus substrates. Furthermore, it could be established that identity proton-in-line displacements are fully comparable with the relocation of carbon in a nucleophilic substitution reaction as Cl, + CH3Cl. The significance of this information will afford new insight in the dynamics of a linear three-center four-electron complex. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesteraseJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2009Xin Zhang Abstract Combined QM(PM3)/MM molecular dynamics simulations together with QM(DFT)/MM optimizations for key configurations have been performed to elucidate the enzymatic catalysis mechanism on the detoxification of paraoxon by phosphotriesterase (PTE). In the simulations, the PM3 parameters for the phosphorous atom were reoptimized. The equilibrated configuration of the enzyme/substrate complex showed that paraoxon can strongly bind to the more solvent-exposed metal ion Zn,, but the free energy profile along the binding path demonstrated that the binding is thermodynamically unfavorable. This explains why the crystal structures of PTE with substrate analogues often exhibit long distances between the phosphoral oxygen and Zn,. The subsequent SN2 reaction plays the key role in the whole process, but controversies exist over the identity of the nucleophilic species, which could be either a hydroxide ion terminally coordinated to Zn, or the ,-hydroxo bridge between the ,- and ,-metals. Our simulations supported the latter and showed that the rate-limiting step is the distortion of the bound paraoxon to approach the bridging hydroxide. After this preparation step, the bridging hydroxide ion attacks the phosphorous center and replaces the diethyl phosphate with a low barrier. Thus, a plausible way to engineer PTE with enhanced catalytic activity is to stabilize the deformed paraoxon. Conformational analyses indicate that Trp131 is the closest residue to the phosphoryl oxygen, and mutations to Arg or Gln or even Lys, which can shorten the hydrogen bond distance with the phosphoryl oxygen, could potentially lead to a mutant with enhanced activity for the detoxification of organophosphates. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Electronic structures and chemical bonding in diatomic ScX to ZnX (X = S, Se, Te)JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2007Z. J. Wu Abstract Bond distances, vibrational frequencies, electron affinities, ionization potentials, dissociation energies, and dipole moments of the title molecules in neutral, positively, and negatively charged ions were studied using density functional method. Ground electronic state was assigned for each molecule. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that, besides ionic component, covalent bonds are formed between the metal s, d orbitals, and the p orbital of S, Se, and Te. For neutral and cationic molecules, the covalent character increases from ScX to CrX and from FeX to CuX with an exception of decrease at MnX and ZnX, while for anionic molecules, the trend is not obvious. For both neutral and charged molecules, the sulfides have the shortest bond distance and largest vibrational frequency, while tellurides have the largest bond distance and smallest vibrational frequency. For neutral and anionic molecules, the dissociation energy of sulfides is the largest, that of tellurides is the smallest, while this only remains true for cationic molecules from ScX+ to FeX+. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 703,714, 2007 [source] Electronic structures of 3d -metal mononitridesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2006Zhijian Wu Abstract Bond distances, vibrational frequencies, electron affinities, ionization potentials, and dissociation energies of the title molecules in neutral, positively, and negatively charged ions were studied by use of density functional methods B3LYP, BLYP, BHLYP, BPW91, and B3PW91. The calculated results are compared with experiments and previous theoretical studies. It was found that the calculated properties are highly dependent on the functionals employed, in particular for the dissociation energy and vibrational frequency. For neutral species, pure density functional methods BLYP and BPW91 have relatively good performance in reproducing the experimental bond distance and vibrational frequency. For cations, hybrid exchange functional methods B3LYP and B3PW91 are good in predicting the dissociation energy. For both neutral and charged species, BHLYP tends to give smaller dissociation energy. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 267,276, 2006 [source] Deuterated analogues of 4,8-dimethyldecanal, the aggregation pheromone of Tribolium castaneum: synthesis and pheromonal activityJOURNAL OF LABELLED COMPOUNDS AND RADIOPHARMACEUTICALS, Issue 13 2004Junheon Kim Abstract To elucidate the deuterium isotope effect (DIE) in pheromonal activity and to investigate the biosynthetic pathway of 4,8-dimethyldecanal (4,8-DMD; 1), the aggregation pheromone of the red flour beetle (Tribolium castaneum), deuterated analogues of 4,8-DMDs (2, 3, 4, and 5), were synthesized and their pheromonal activities were tested using a two-hole pitfall olfactometer. Although no apparent DIE was observed in their pheromonal activities, 4,8-DMD- 1-d1 (2) was less attractive than other analogues, which suggested that the bond distance between the formyl group of 1 and its receptor was critical in pheromone recognition by T. castaneum. Copyright © 2004 John Wiley & Sons, Ltd. [source] trans -[1,3-Bis(2,4,6-trimethylphenyl)imidazolidin-2-ylidene]dichlorido(triphenylphosphine-,P)palladium(II)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2007Hayati Türkmen The title complex, [PdCl2(C21H26N2)(C18H15P)], shows slightly distorted square-planar coordination around the PdII metal centre. The Pd,C bond distance between the N-heterocyclic ligand and the metal atom is 2.028,(5),Å. The dihedral angle between the two trimethylphenyl ring planes is 36.9,(2)°. [source] Crystallographic report: 2-FurfurylgermatraneAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 4 2004Edmunds Lukevics Abstract The germanium atom is penta-coordinated and adopts a trigonal bipyramidal geometry. The 2-furfuryl group and the nitrogen atom each occupy an apical position with a transannular N,Ge bond distance of 2.173(3) Å. Copyright © 2004 John Wiley & Sons, Ltd. [source] ,-Oxo-bis[(2,3,12,13-tetrabromo-5,10,15,20-tetraphenylporphyrinato)iron(III)] bis(dichloromethane) solvateACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2000Ming Li The precise structure of the title compound, [Fe2O(C44H24Br4N4)2]·2CH2Cl2, is reported. The Fe,N distances are non-equivalent in pairs because of the asymmetric peripheral substitution; the values are 2.098,Å to the brominated rings and 2.041,Å to the other two rings. The Fe,O bond distance is 1.7583,(4),Å. The molecule has required twofold symmetry so that there is one unique porphyrin macrocycle and one Fe,O bond length in contrast to a previous report on the same species. [source] Bis(N,N,-dimethylimidazol-2-ylidene)mercury chlorotriiodomercury dimethyl sulfoxide solvateACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2000Alex M. Clark The double mercury salt [Hg(C5H8N2)2][HgClI3]·C2H6OS was prepared and its structure characterized. The [Hg(C5H8N2)2]2+ cation lies about an inversion centre and the [HgClI3]2, anion lies on a mirror plane. Cations and anions are linked to form a one-dimensional polymer by weak Hg,Cl interactions [Hg,Cl 3.3744,(3),Å]. The mercury,carbene bond distance [2.076,(7),Å] is typical of a dicationic mercury,carbene species. [source] Modeling formation of molecules in the interstellar medium by radical reactions with polycyclic aromatic hydrocarbonsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2010Yenner Bentarcurt Abstract Adsorptions of CH°2, CH°3, NH°2, and OH° radicals and molecule formation on a partially hydrogenated surface of a polycyclic aromatic hydrocarbon (PAH) (C24H27+) were modeled. It was found that radical adsorptions are feasible with important modifications of surface bond strengths and bond distances. Adsorbed hydrogen may diffuse due to adsorbate-surface interactions. Formations of CH4, NH3, H2O, CH3NH2, and CH3OH were studied by Eley-Rideal (ER) and Langmuir-Hishelwood (LH) mechanisms. Potential energetic surfaces were performed for both mechanisms and the ER presents lower reaction energy barriers than the LH one, in all cases. Parametric quantum program (CATIVIC) was employed and comparisons with DFT results were performed. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2560,2572, 2010 [source] Theoretical studies on high-valent manganese porphyrins: Toward a deeper understanding of the energetics, electron distributions, and structural features of the reactive intermediates of enzymatic and synthetic manganese-catalyzed oxidative processesISRAEL JOURNAL OF CHEMISTRY, Issue 1 2000Abhik Ghosh We present here a relatively comprehensive theoretical study, based on nonlocal density functional theory calculations, of the energetics, electron distributions, and structural features of the low-lying electronic states of various high-valent intermediates of manganese porphyrins. Two classes of molecules have been examined: (a) compounds with the general formula [(P)MnX2]0 (P = porphyrin; X = F, Cl, PF6) and (b) high-valent manganese-oxo species. For [(P)Mn(PF6)2]0, the calculations reveal a number of nearly equienergetic quartet and sextet states as the lowest states, consistent with experimental results on a comparable species, [(TMP)Mn(ClO4)2]0 (TMP = tetramesitylporphyrin). In contrast, [(P)MnCl2]0 and [(P)MnF2]0 have a single well-defined S = 3/2 Mn(IV) ground state, again in agreement with experiment, with the three unpaired spins largely concentrated (>90%) on the manganese atom. Manganese(IV)-oxo porphyrins have an S = 3/2 ground state, with the three unpaired spins distributed approximately 2.3:0.7 between the manganese and oxygen atoms. The metal-to-oxygen spin delocalization, as measured by the oxygen spin population, for MnIV = O porphyrins is less than, but still qualitatively similar to, that in analogous iron(IV)-oxo intermediates, indicating that the MnIV = O bond is significantly weaker than the FeIV = O bond in an analogous molecule. Thus, the optimized metal,oxygen bond distances are 1.654 and 1.674 Å for (P)FeIV(O)(Py) and (P)MnIV(O)(Py), respectively (Py = pyridine). This is consistent with the experimental observation that MnIV = O stretching frequencies are over 10% lower than FeIV = O stretching frequencies for analogous compounds. For [(P)Mn(O)(PF6)]0, [(P)Mn(O)(Py)]+, and [(P)Mn(O)(F)]0, the ground states clearly correspond to a (dxy)2 Mn(V) configuration and the short Mn,O distances of 1.541, 1.546, and 1.561 Å for the three compounds, respectively, reflect the formal triple bond character of the Mn,O interaction. Interestingly, the corresponding Mn(IV)-oxo porphyrin cation radical states are calculated to be a few tenths of an electrovolt higher than the Mn(V) ground states, suggesting that the Mn(IV)-oxo porphyrin cation radicals are not likely to exist as ground-state species. [source] Multilevel structure of reinforcing silica and carbonJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-1 2000D.W. Schaefer Using small-angle x-ray (SAXS), neutron (SANS), x-ray diffraction and light scattering, we study the structure of colloidal silica and carbon on length scales from 4 Å < q,1 < 107 Å where q is the magnitude of the scattering vector. These materials consist of primary particles of the order of 100 Å, aggregated into micron-sized aggregates that in turn are agglomerated into 100 µ agglomerates. The diffraction data show that the primary particles in precipitated silica are composed of highly defective amorphous silica with little intermediate-range order (order on the scale of several bond distances). On the next level of morphology, primary particles arise by a complex nucleation process in which primordial nuclei briefly aggregate into rough particles that subsequently smooth out to become the seeds for the primaries. The primaries aggregate to strongly bonded clusters by a complex process involving kinetic growth, mechanical disintegration and restructuring. Finally, the small-angle scattering (SAS) data lead us to postulate that the aggregates cluster into porous, rough-surfaced, non-mass-fractal agglomerates that can be broken down to the more strongly bonded aggregates by application of shear. We find similar structure in pelletized carbon blacks. In this case we show a linear scaling relation between the primary and aggregate sizes. We attribute the scaling to mechanical processing that deforms the fractal aggregates down to the maximum size able to withstand the compaction stress. Finally, we rationalize the observed structure based on empirical optimization by filler suppliers and some recent theoretical ideas due to Witten, Rubenstein and Colby. [source] Reduced basis set for the gold atom in cluster complexesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2004Harold Basch Abstract To extend the metal cluster size used in interfacing between bulk metals and molecules in ab initio studies of molecular electronics and chemisorption, a reduced size atomic orbital basis set for the gold atom has been generated. Based on the SKBJ relativistic effective core potential set, the three component 5d Gaussian orbital basis set is completely contracted. Comparisons between the full and reduced basis set in Au atom clusters and cluster complexes for geometry, bond distances, dipole moments, atomic charges, spin, bond dissociation energies, lowest energy harmonic frequencies, electron affinities, ionization energies, and density of states distributions show the contracted set to be a viable replacement for the full basis set. This result is obtained using both the B3LYP and BPW91 exchange-correlation potentials in density functional theory. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 899,906, 2004 [source] Improved intermolecular force field for molecules containing H, C, N, and O atoms, with application to nucleoside and peptide crystalsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2001Donald E. Williams Abstract A new intermolecular force field for nitrogen atoms in organic molecules was derived from a training dataset of 76 observed azahydrocarbon crystal structures and 11 observed heats of sublimation. The previously published W99 force field for hydrogen, carbon, and oxygen was thus extended to include nitrogen atoms. Nitrogen atoms were divided into four classes: N(1) for triply bonded nitrogen, N(2) for nitrogen with no bonded hydrogen (except the triple bonded case), N(3) for nitrogen with one bonded hydrogen, and N(4) for nitrogen with two or more bonded hydrogens. H(4) designated hydrogen bonded to nitrogen. Wavefunctions of 6-31g** quality were calculated for each molecule and the molecular electric potential (MEP) was modeled with net atomic and supplementary site charges. Lone pair electron charge sites were included for nitrogen atoms where appropriate, and methylene bisector charges were used for CH2 and CH3 groups when fitting the MEP. XH bond distances were set to standard values for the wave function calculation and then foreshortened by 0.1 Å for the MEP and force field fitting. Using the force field optimized to the training dataset, each azahydrocarbon crystal structure was relaxed by intermolecular energy minimization. Predicted maximum changes in unit cell edge lengths for each crystal were 3% or less. The complete force field for H, C, N, and O atoms was tested by intermolecular energy relaxation of nucleoside and peptide molecular crystals. Even though these molecules were not included in any of the training datasets for the force field, agreement with their observed crystal structures was very good, with predicted unit cell edge shifts usually less than 2%. These tests included crystal structures of representatives of all eight common nucleosides found in DNA and RNA, 15 dipeptides, four tripeptides, two tetrapeptides, and a pentapeptide with two molecules in the asymmetric unit. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1154,1166, 2001 [source] Computational studies of the cone and 1,2,3 alternate calix[6]arene bis-crown-4 isomers: structures, NMR shifts, atomic charges, and steric compressionJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 12 2009Meghan N. Lawson Abstract The cone and 1,2,3 alternate isomers of calix[6]arene bis-crown-4 were investigated computationally. Structural optimizations, energies, bond distances, and Mulliken charges were calculated by the application of the B3LYP/6-31g(d) method/basis, followed by NMR calculations via both B3LYP/6-31g(d) and HF/6-31g(d). Calculations were completed at three different levels of imposed symmetry, and two calculations investigated the chloroform solvent effects. Better NMR results were obtained from HF/6-31g(d) calculations that did not impose molecular symmetry constraints. Consideration of solvent effects improved ground state energies, but other improvements were minimal and not significant enough to justify the added computational expense of solvent calculations. Overall results are consistent with known experimental assignments and were valuable for assigning previously unknown NMR peaks. Net charges, electrostatic forces, and local dipoles , but not bond lengths , are strongly correlated to spectroscopic manifestations of steric compression. Copyright © 2009 John Wiley & Sons, Ltd. [source] Vibrational spectroscopic and force field studies of copper(II) chloride and bromide compounds, and crystal structure of KCuBr3JOURNAL OF RAMAN SPECTROSCOPY, Issue 1 2008Liubov V. Stepakova Abstract Vibrational spectroscopic and force field studies have been performed of 15 related copper(II) chloride and copper(II) bromide compounds, including hydrated salts crystallizing in ternary aqueous systems with alkali and ammonium halides. For halocuprates with distorted octahedral coordination characteristic stretching Raman wavenumbers, corresponding to symmetric stretching CuIIX modes in the equatorial plane, were found in the ranges 247,288 cm,1 for X = Cl, and 173,189 cm,1 for X = Br, while the low-wavenumber stretching modes for the weaker axial CuX interactions varied considerably. The tetrahedral coordination for Cs2CuCl4 and Cs2CuBr4 leads to somewhat lower CuX symmetric stretching wavenumbers, 295 and 173 cm,1, respectively. The assignments of the copper,ligand stretching vibrations were performed with the aid of normal coordinate calculations. Correlations between force constants, averaged CuX stretching wavenumbers and bond distances have been evaluated considering the following aspects: (1) Jahn,Teller tetragonal distortion (axial elongation) of the octahedral copper(II) coordination environment, (2) differences between terminal and bridging halide ligands (3) effects of coordinated water and the influence of outer-sphere cations. Force constant ratios for terminal and bridging metal,halide bonds reveal characteristic differences between planar and tetrahedrally coordinated M2X6 species. In the hydrated copper(II) halide complexes, the halide ligands are more strongly bound than coordinated water molecules. The crystal structure of KCuBr3 (K2Cu2Br6), which was determined to provide structural information for the force field analyses, contains stacks of planar dimeric [Cu2Br6]2, complexes held together by weak axial CuBr interactions. Copyright © 2007 John Wiley & Sons, Ltd. [source] Vibrational spectroscopic analysis of 3-hydroxy-1,5-diazacyclooctane and its copper(II) complexJOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2001Lian He The changes in the vibrational spectra between 3-hydroxy-1,5-diazacyclooctane and its copper(II) complex were studied by Fourier transform Raman and infrared spectroscopy for the first time. The vibrational bands near 472 and 204 cm,1 were assigned to the Cu,N and Cu,O stretching vibrations in the copper(II) complex, respectively. CNDO/2M and AM1 methods were used to calculate Mulliken orders and bond distances on the basis of the copper(II) complex's crystal structure. The mechanism of the changes in the vibrational spectra is discussed. Copyright © 2001 John Wiley & Sons, Ltd. [source] Ultrahigh-resolution crystallography and related electron density and electrostatic properties in proteinsJOURNAL OF SYNCHROTRON RADIATION, Issue 3 2008Claude Lecomte With an increasing number of biological macromolecular crystal structures measured at ultrahigh resolution (1,Å or better), it is necessary to extend to large systems the experimental valence electron density modelling that is applied to small molecules. A database of average multipole populations has been built, describing the electron density of chemical groups in all 20 amino acids found in proteins. It allows calculation of atomic aspherical scattering factors, which are the starting point for refinement of the protein electron density, using the MoPro software. It is shown that the use of non-spherical scattering factors has a major impact on crystallographic statistics and results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. It is also possible to obtain a realistic valence electron density model, which is used in the calculation of the electrostatic potential and energetic properties of proteins. [source] X-ray diffraction study of amorphous phase of BaSi2 under high pressurePHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 1 2007T. Nishii Abstract A high-pressure synchrotron X-ray diffraction study of zintl phase BaSi2 semiconductor has been performed up to 45 GPa. The pressure-induced amorphization occurred at 13 GPa. In the amorphous phase, the Ba,Si bond distance decreased with increasing pressure, while the Ba,Ba bond distances were almost unchanged. The Rietveld refinement revealed that these distances in the crystal phase decreased with increasing pressure. By combining these results, the Ba,Si bond compressibility in both phases is almost identical. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] On the application of an experimental multipolar pseudo-atom library for accurate refinement of small-molecule and protein crystal structuresACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2007Bartosz Zarychta With an increasing number of biomacromolecular crystal structures being measured to ultra-high resolution, it has become possible to extend to large systems experimental charge-density methods that are usually applied to small molecules. A library has been built of average multipole populations describing the electron density of chemical groups in all 20 amino acids found in proteins. The library uses the Hansen & Coppens multipolar pseudo-atom model to derive molecular electron density and electrostatic potential distributions. The library values are obtained from several small peptide or amino acid crystal structures refined against ultra-high-resolution X-ray diffraction data. The library transfer is applied automatically in the MoPro software suite to peptide and protein structures measured at atomic resolution. The transferred multipolar parameters are kept fixed while the positional and thermal parameters are refined. This enables a proper deconvolution of thermal motion and valence-electron-density redistributions, even when the diffraction data do not extend to subatomic resolution. The use of the experimental library multipolar atom model (ELMAM) also has a major impact on crystallographic structure modelling in the case of small-molecule crystals at atomic resolution. Compared to a spherical-atom model, the library transfer results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. Upon transfer, crystallographic statistics of fit are improved, particularly free R factors, and residual electron-density maps are cleaner. [source] Concomitant polymorphic behavior of di-,-thiocyanato-,2N:S;,2S:N -bis[bis(tri- p -fluorophenylphosphine-,P)silver(I)]ACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2010Bernard Omondi The structures of two polymorphs, both monoclinic P21/n [polymorph (I)] and P21/c [polymorph (II)], of di-,-thiocyanato-,2N:S;,2S:N -bis[bis(tri- p -fluorophenylphosphine-,P)silver(I)] complexes have been determined at 100,K. In both polymorphs the complex has a dinuclear structure where the silver(I) coordinates to two phosphine ligands and two bridging thiocyanate anions to form complexes with distorted tetrahedral geometry. Polymorph (I) has just one half of the [Ag2(SCN)2{P(4-FC6H4)3}4] molecule at (0, ½, 0) from the origin in the asymmetric unit. Polymorph (II) has one and a half molecules of [Ag2(SCN)2{P(4-FC6H4)3}4] in the asymmetric unit; the half molecule is situated at (0, 1, ½), while the full molecule is located at (1/3, ½, 1/3) from the origin. The Ag,P bond distances range from 2.4437,(4) to 2.4956,(7),Å in both polymorphs. The Ag,S distances are 2.5773,(7),Å in (I) and 2.5457,(5), 2.5576,(5) and 2.5576,(5),Å in (II). The full molecule in polymorph (II) has slightly shorter Ag,N bond distances [2.375,(1) and 2.367,(2),Å] compared with the half molecules in both polymorphs [2.409,(2),Å in (II) and 2.395,(2),Å in (I)]. The two polymorphs are compared using r.m.s. overlay calculations as well as half-normal probability plot analysis. [source] Molecular and crystalline structures of three (S)-4-alkoxycarbonyl-2-azetidinones containing long alkyl side chains from synchrotron X-ray powder diffraction dataACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2009Luis E. Seijas The (S)-4-alkoxo-2-azetidinecarboxylic acids are optically active ,-lactam derivatives of aspartic acid, which are used as precursors of carbapenem-type antibiotics and poly-,-aspartates. The crystal structures of three (S)-4-alkoxo-2-azetidinecarboxylic acids with alkyl chains with 10, 12 and 16 C atoms were solved using parallel tempering and refined against the X-ray powder diffraction data using the Rietveld method. The azetidinone rings in the three compounds display a pattern of asymmetrical bond distances and an almost planar conformation; these characteristics are compared with periodic solid-state, gas-phase density-functional theory (DFT) calculations and MOGUL average bond distances and angles from the CSD. The compounds pack along [001] as corrugated sheets separated by approximately 4.40,Å and connected by hydrogen bonds of the type N,H...O. [source] Following an isosymmetric phase transition by changes in bond lengths and anisotropic displacement parameters: the case of meta -carboxyphenylammonium phosphiteACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2009El-Eulmi Bendeif Crystal structure studies in the 100,345,K temperature range were performed to relate the molecular structure changes of meta -carboxyphenylammonium phosphite (m -CPAMP) to its first-order phase transition at Tc = 246,(2),K. Thermal displacement parameters and most bond distances show an abrupt jump at the transition. Such a structural change is related to collective effects leading to competition between intra- and intermolecular interactions. [source] Structural stability and formability of ABO3 -type perovskite compoundsACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2007Huan Zhang On the basis of the bond-valence model (BVM) and structure-map technology, the structural stability and formability of ABO3 -type perovskite compounds were investigated in 376 ABO3 -type compounds. A new criterion of structural stability for ABO3 -type perovskite compounds has been established by the bond-valence calculated tolerance factors, which are in the range 0.822,1.139. All global instability indices for ABO3 -type perovskite compounds are found to be less than 1.2,v.u. (valence units) and increase with a decrease in oxidation state of the B cations (i.e. structural stability in the formation of an ideal cubic perovskite follows the order A+B5+O3 -type > A2+B4+O3 -type > A3+B3+O3 -type). Three new two-dimensional structure maps were constructed based on the ideal A,O and B,O bond distances derived from the BVM. These maps indicate the likelihood of particular perovskite compounds being formed. The present work enables novel perovskite and perovskite-related compounds to be explored by screening all the possible elemental combinations in future crystal engineering. [source] Polymorphism of 4-bromobenzophenoneACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2007Mikhail A. Strzhemechny A combination of single-crystal and powder X-ray diffractometry was used to study the structure of two polymorphs of 4-bromobenzophenone over the temperature range from 100 to 300,K. One of the polymorphs of the title compound was known previously and its structure has been determined at room temperature [Ebbinghaus et al. (1997). Z. Kristallogr.212, 339,340]. Two crystal growth methods were employed, one of which (a modification of the Bridgman,Stockbarger technique) resulted in single crystals of a previously unknown structure. The basic physical properties of the stable polymorph are: growth method, from 2-propanol solutions or gradient sublimation; space group, monoclinic P21/c; melting point, Tm = 355.2,K; X-ray density (at 100,K), Dx = 1.646,g,cm,3. The same properties of the metastable polymorph (triclinic ) are: growth method, modified Bridgman,Stockbarger method; X-ray density (at 100,K), Dx = 1.645,g,cm,3; Tm = 354,K. Thermograms suggest that the melting of the metastable form is accompanied by at least a partial crystallization presumably into the monoclinic form; the transformation is therefore monotropic. Analysis of short distances in both polymorphs shows that numerous weak hydrogen bonds of the C,H,, type ensure additional stabilization within the respective planes normal to the longest dimension of the molecules. The strong temperature dependence of the lattice constants and of the weak bond distances in the monoclinic form suggest that the weak bond interactions might be responsible for both the large thermal expansion within plane bc and the considerable thermal expansion anisotropy. [source] Tris(4-bromophenyl)aminium hexachloridoantimonate (`Magic Blue'): a strong oxidant with low inner-sphere reorganizationACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010Mauricio Quiroz-Guzman Both the radical cation tris(4-bromophenyl)aminium hexachloridoantimonate (`Magic Blue'), (C18H12Br3N)[SbCl6], (I), and neutral tris(4-bromophenyl)amine, C18H12Br3N, (II), show extremely similar three-bladed propeller structures with planar N atoms. Key geometric features, such as the C,N bond distances and the angles between the planes of the aryl groups and the central NC3 plane, are identical within experimental uncertainty in the two structures. This contrasts with the significant structural changes observed on oxidation of more electron-rich triarylamines, where resonance contributes to the stabilization of the radical cation, and suggests that, in general, more strongly oxidizing triarylaminium cations will have lower inner-sphere reorganization energies than their lower-potential analogues. [source] Le phosphate de cobalt et de lithium à valence mixte Li4+xCo2,x(P2O7)2 (x = 0,03): étude structurale et analyse de distribution de chargeACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2010Salah Kouass The title compound, namely lithium cobalt(II/III) bis(diphosphate), Li4.03Co1.97(P2O7)2, is a new mixed-valent lithium/cobalt(II/III) phosphate. Three metal sites out of seven are occupied simultaneously by Li+ and CoII/III ions. This disorder was established both from an analysis of the atomic displacement ellipsoids and Li/Co,O bond distances, and by means of a charge-distribution (CHARDI) model, which provides satisfactory agreement on the computed charges (Q) for all the cations. [source] | ||||||||||||||||||||||||||||