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Electron Density (electron + density)
Kinds of Electron Density Terms modified by Electron Density Selected AbstractsTopological Analysis of Electron Densities: Is the Presence of an Atomic Interaction Line in an Equilibrium Geometry a Sufficient Condition for the Existence of a Chemical Bond?CHEMISTRY - A EUROPEAN JOURNAL, Issue 18 2004Arne Haaland Prof. Abstract The structure, energetics, and electron density in the inclusion complex of He in adamantane, C10H16, have been studied by density functional theory calculations at the B3LYP6-311++G(2p,2d) level. Topological analysis of the electron density shows that the He atom is connected to the four tertiary tC atoms in the cage by atomic interaction lines with (3,,1) critical points. The calculated dissociation energy of the complex He@adamantane(g)=adamantane(g) + He(g) of ,E=,645 kJ,mol,1 nevertheless shows that the He,tC interactions are antibonding. [source] Quantum Crystallography: Electron Density and Bonding, a MicrosymposiumACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2004Seppo Manninen First page of article [source] Semilocalized approach to investigation of chemical reactivityINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2003V. GineityteArticle first published online: 21 JUL 200 Abstract Application of the power series for the one-electron density matrix Gineityte, V., J Mol Struct Theochem 1995, 343, 183 to the case of two interacting molecules is shown to yield a semilocalized approach to investigate chemical reactivity, which is characterized by the following distinctive features: (1) Electron density (ED) redistributions embracing orbitals of the reaction centers of both molecules and of their neighboring fragments are studied instead of the total intermolecular interaction energy; (2) the ED redistributions are expressed directly in the basis of fragmental orbitals (FOs) without passing to the basis of delocalized molecular orbitals (MOs) of initial molecules; (3) terms describing the ED redistributions due to an intermolecular contact arise as additive corrections to the purely monomolecular terms and thereby may be analyzed independently; (4) local ED redistributions only between orbitals of the reaction centers of both molecules are described by lower-order ter s of the power series, whereas those embracing both the reaction centers and their neighborhoods are represented by higher-order terms. As opposed to the standard perturbative methods based on invoking the delocalized (canonical) MOs of isolated molecules, the results of the approach suggested are in-line with the well-known intuition-based concepts of the classic chemistry concerning reactivity, namely, with the assumption about different roles of the reaction center and of its neighborhood in a chemical process, with the expectation about extinction of the indirect influence of a certain fragment (substituent) when its distance from the reaction center grows, etc. Such a parallelism yields quantum chemical analogs for the classic concepts and thereby gives an additional insight into their nature. The scope of validity of these concepts also is discussed. Applicability of the approach suggested to specific chemical problems is illustrated by a brief consideration of the SN2 and AdE2 reactions. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 302,316, 2003 [source] Electron density and energy density view on the atomic interactions in SrTiO3ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2002Elizabeth A. Zhurova The results of topological analysis of the electron density in an SrTiO3 crystal based on the experimental (at 145,K) and theoretical data are presented and discussed. The features of the electron density lead to the conclusion that the Ti,O interaction is of the partly polar covalent (or intermediate) type. Complicated atomic shapes defined by the zero-flux surfaces in the electron density are revealed. It is found that, in general, they are far from spherical and have very slight asphericity in the close-packed layers. The topological coordination numbers of Sr and Ti are the same as the geometrical numbers, whereas the topological coordination for the O atom (6) differs from the geometrical value (12). The latter results from the specific shape of the Ti-atom basin, which prevents bond-path formation between the O atoms. The analysis of the kinetic and potential energy densities derived from the electron density using the density functional theory formulae revealed the stabilizing crystal-forming role of the O atoms in SrTiO3. Structural homeomorphism between the experimental electron density and the potential and kinetic energy densities is observed. [source] Structure of the major carrot allergen Dau,c,1ACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2009-Housley, Zora Markovi Dau,c,1 is a major allergen of carrot (Daucus carota) which displays IgE cross-reactivity with the homologous major birch-pollen allergen Bet,v,1. The crystal structure of Dau,c,1 has been determined to a resolution of 2.7,Å, revealing tight dimers. The structure of Dau,c,1 is similar to those of the major allergens from celery, Api,g,1, and birch pollen, Bet,v,1. Electron density has been observed in the hydrophobic cavity of each monomer and has been modelled with polyethylene glycol oligomers of varying length. Comparison of the surface topology and physicochemical properties of Dau,c,1 and Bet,v,1 revealed that they may have some, but not all, epitopes in common. This is in agreement with the observation that the majority of carrot-allergic patients have Bet,v,1 cross-reactive IgE antibodies, whereas others have Dau,c,1-specific IgE antibodies which do not recognize Bet,v,1. [source] X-ray structure of the NO-bound CuB in bovine cytochrome c oxidaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2010Kazuhiro Ohta The X-ray crystallographic structure of nitric oxide-treated bovine heart cytochrome c oxidase (CcO) in the fully reduced state has been determined at 50,K under light illumination. In this structure, nitric oxide (NO) is bound to the CcO oxygen-reduction site, which consists of haem and a Cu atom (the haem a3,CuB site). Electron density for the NO molecule was observed close to CuB. The refined structure indicates that NO is bound to CuB in a side-on manner. [source] Photochromic Properties of Perhydro- and Perfluorodithienylcyclopentene Molecular SwitchesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2003Jaap J. D. de Jong Abstract Various substituted phenylthienyl perhydro- and perfluorocyclopentenes have been synthesized in order to compare their spectroscopic and photochromic properties. The difference in the electron densities of the central cyclopentene moieties in the perhydrocyclopentene and perfluorocyclopentene molecular switches has only a small effect on the absorption maxima of the electronic spectra, but causes some subtle changes in substituent and solvatochromic effects. The photochromic behaviour is remarkably similar, and both type of switches combine excellent quantum yields (0.6) with high degrees of photoconversion (> 0.85). The main difference is the lower photochemical and thermal stability of the perhydrocyclopentene molecular switches. It is concluded that in most studies the perhydrocyclopentenes are an excellent alternative for the perfluorocyclopentenes, while the perfluorocyclopentenes might be better suited for applications such as data storage, which depend critically on fatigue resistance and thermal stability. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] DPPH (=,2,2-Diphenyl-1-picrylhydrazyl,=,2,2-Diphenyl-1-(2,4,6-trinitrophenyl)hydrazyl) Radical-Scavenging Reaction of Protocatechuic Acid Esters (=,3,4-Dihydroxybenzoates) in Alcohols: Formation of Bis-alcohol AdductHELVETICA CHIMICA ACTA, Issue 4 2006Shizuka Saito Abstract Protocatechuic acid esters (=,3,4-dihydroxybenzoates) scavenge ca. 5,equiv. of radical in alcoholic solvents, whereas they consume only 2,equiv. of radical in nonalcoholic solvents. While the high radical-scavenging activity of protocatechuic acid esters in alcoholic solvents as compared to that in nonalcoholic solvents is due to a nucleophilic addition of an alcohol molecule at C(2) of an intermediate o -quinone structure, thus regenerating a catechol (=,benzene-1,2-diol) structure, it is still unclear why protocatechuic acid esters scavenge more than 4,equiv. of radical (C(2) refers to the protocatechuic acid numbering). Therefore, to elucidate the oxidation mechanism beyond the formation of the C(2) alcohol adduct, 3,4-dihydroxy-2-methoxybenzoic acid methyl ester (4), the C(2) MeOH adduct, which is an oxidation product of methyl protocatechuate (1) in MeOH, was oxidized by the DPPH radical (=,2,2-diphenyl-1-picrylhydrazyl) or o -chloranil (=,3,4,5,6-tetrachlorocyclohexa-3,5-diene-1,2-dione) in CD3OD/(D6)acetone 3,:,1). The oxidation mixtures were directly analyzed by NMR. Oxidation with both the DPPH radical and o -chloranil produced a C(2),C(6) bis-methanol adduct (7), which could scavenge additional 2,equiv. of radical. Calculations of LUMO electron densities of o -quinones corroborated the regioselective nucleophilic addition of alcohol molecules with o -quinones. Our results strongly suggest that the regeneration of a catechol structure via a nucleophilic addition of an alcohol molecule with a o -quinone is a key reaction for the high radical-scavenging activity of protocatechuic acid esters in alcoholic solvents. [source] Hot-electron numerical modelling of short gate length pHEMTs applied to novel field plate structuresINTERNATIONAL JOURNAL OF NUMERICAL MODELLING: ELECTRONIC NETWORKS, DEVICES AND FIELDS, Issue 1 2003Shahzad Hussain Abstract Hot-electron numerical simulations were carried out in order to simulate the DC parameters of pseudomorphic high electron mobility transistors (pHEMTs). The hot-electron effects were studied by simulating several HEMT device structures. Hot-carrier injection in the substrate and the formation of the peak of electric field in the channel were studied in detail. The inclusion of a field-plate contact in a multiple recessed pHEMT structure lowered the peak value of the electric field by 24% compared with the conventional pHEMT. These devices were modelled by solving the two-dimensional Poisson, current continuity and energy transport equations consistently with the time-independent Schrödinger wave equation. Appropriate Ohmic boundaries are discussed here and implemented in the simulations of pHEMT structures. A new integral approximation is used to calculate electron densities and electron energy densities for degenerate approximations. Copyright © 2002 John Wiley & Sons, Ltd. [source] Inequivalent electron densities derived from an approximate correlated ground-state wave function using the Hiller,Sucher,Feinberg identity: Comparisons with quantum Monte Carlo densities for He and Ne atomsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2009Claudio Amovilli Abstract The Hiller,Sucher,Feinberg (HSF) identity is combined with the three-parameter correlated wave function of Chandrasekhar in order to generate an alternative electron density ,(r) for the He atom. This and the conventional "local" operator form of ,(r) are then compared with a diffusion quantum Monte Carlo density. An exact limiting relation is also presented, via HSF identity, between the one-particle density matrix and the pair density in a many-electron atom, which transcends its Hartree,Fock counterpart and has no N -representability difficulties. For the Ne atom, the accuracy of the semiempirical correlated electron density recently obtained by Cordero et al. (Phys. Rev. A 2007, 75, 052502) using fine-tuning of Hartree,Fock theory was assessed by appealing to the ground-state density from diffusion quantum Monte Carlo. The high accuracy of the Cordero et al. density was thereby confirmed. A HSF calculation on neon, with a correlated many-body wave function as starting point, is a worthwhile future aim. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Asymmetric Activation/Deactivation of Racemic Ru Catalysts for Highly Enantioselective Hydrogenation Irrespective of Ketonic Substrates: Molecular Design of Dimethylbinaphthylamine for Enantiomeric Catalysts DiscriminationADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 1-2 2003Koichi Mikami Abstract Asymmetric activation and deactivation of racemic catalysts are two extremes in asymmetric catalysis. In a combination of these two protocols, higher enantioselectivity can be achieved by maximizing the difference in catalytic activity between the enantiomers of racemic catalysts through selective activation and deactivation of enantiomeric catalysts. 3,3,-Dimethyl-2,2,-diamino-1,1,-binaphthyl (DM-DABN) is thus designed as a chiral poison (deactivator) for complete enantiomer resolution of racemic BINAP-Ru(II) catalysts. The catalyst system of DM-DABN, 1,2-diphenylethylenediamine (DPEN), and racemic BINAP-Ru(II) led to great success in highly enantioselective hydrogenation irrespective of the ketonic substrates. The lower catalytic activity of the BINAP-Ru(II)/DM-DABN complex stems from the electron delocalization from the Ru center to the diamine moiety in contrast to the BINAP-Ru(II)/DPEN complex where the highest electron densities are localized on the Ru-N region. The present ,asymmetric activation/deactivation protocol' can provide a guiding principle for the rational design of a molecule for enantiomeric discrimination between racemic catalysts. [source] Quick scheme for evaluation of atomic charges in arbitrary aluminophosphate sieves on the basis of electron densities calculated with DFT methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2007A. V. Larin Abstract It is demonstrated that unique and simple analytical functions are justified for the atomic charge dependences q of the T (T = Al, P) and O atoms of aluminophosphates (AlPOs) using DFT calculations with several basis sets, starting from STO-3G to 3-21G and 6-21G**. Three internal (bonds, angles, ,) coordinates for the charge dependences of the T atoms and four coordinates for the O are sufficient to reach a precision of 1.8% for the fitted q(Al), 1.0% for q(P), and 2.5% for q(O) relatively to the values calculated at any basis set level. The proposed strategy consists in an iterative scheme starting from charge dependences based on the neighbor's positions only. Electrostatic potential values are computed to illustrate the differences between the calculated and fitted charges in the considered AlPO models. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Electric field-derived point charges to mimic the electrostatics in molecular crystalsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2006Andrew E. Whitten Abstract Because of the way the electrostatic potential is defined in a crystal, it is not possible to determine potential-derived charges for atoms in a crystal. To overcome this limitation, we present a novel method for determining atomic charges for a molecule in a crystal based on a fit to the electric field at points on a surface around the molecule. Examples of fits to the electric field at points on a Hirshfeld surface, using crystal Hartree,Fock electron densities computed with a DZP basis set are presented for several organic molecular crystals. The field-derived charges for common functional groups are transferable, and reflect chemical functionality as well as the subtle effects of intermolecular interactions. The charges also yield an excellent approximation to the electric field surrounding a molecule in a crystal for use in cluster calculations on molecules in solids. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1063,1070, 2006 [source] Starting SCF calculations by superposition of atomic densitiesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2006J. H. Van Lenthe Abstract We describe the procedure to start an SCF calculation of the general type from a sum of atomic electron densities, as implemented in GAMESS-UK. Although the procedure is well known for closed-shell calculations and was already suggested when the Direct SCF procedure was proposed, the general procedure is less obvious. For instance, there is no need to converge the corresponding closed-shell Hartree,Fock calculation when dealing with an open-shell species. We describe the various choices and illustrate them with test calculations, showing that the procedure is easier, and on average better, than starting from a converged minimal basis calculation and much better than using a bare nucleus Hamiltonian. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 926,932, 2006 [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] The ionization of the emission-line gas in young radio galaxiesMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2009J. Holt ABSTRACT This paper is the second in a series in which we present intermediate-resolution, wide-wavelength coverage spectra for a complete sample of 14 compact radio sources, taken with the aim of investigating the impact of the nuclear activity on the circumnuclear interstellar medium (ISM) in the early stages of radio source evolution. In the first paper (Holt, Tadhunter & Morganti), we presented the kinematic results from the nuclear emission-line modelling and reported fast outflows in the circumnuclear gas. In this paper, we use the line fluxes to investigate the physical conditions and dominant ionization mechanisms of the emission-line gas. We find evidence for large electron densities and high reddening in the nuclear regions, particularly in the broader, blueshifted components. These results are consistent with the idea that the young, recently triggered radio sources still reside in dense and dusty cocoons deposited by the recent activity triggering event (merger/interaction). In addition, we find that the quiescent nuclear and extended narrow components are consistent with active galactic nucleus (AGN) photoionization, split between simple-slab AGN photoionization and mixed-medium photoionization models. For the nuclear broader and shifted components, the results are less clear. Whilst there are suggestions that the broader components may be closer to shock plus precursor models on the diagnostic diagrams, and that the electron temperatures and densities are high, we are unable to unambiguously distinguish the dominant ionization mechanism using the optical emission-line ratios. This is surprising given the strong evidence for jet,cloud interactions (broad emission lines, large outflow velocities and strong radio-optical alignments), which favours the idea that the warm gas has been accelerated in shocks driven by the radio lobes expanding through a dense cocoon of gas deposited during the triggering event. [source] Density gradients in Galactic planetary nebulaeMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 1 2007J. P. Phillips ABSTRACT Certain hydrodynamic models of planetary nebulae (PNe) suggest that their shells possess appreciable radial density gradients. However, the observational evidence for such gradients is far from clear. On the one hand, Taylor et al. claim to find evidence for radio spectral indices 0.6 < , < 1.8, a trend which is taken to imply a variation ne,r,2 in most of their sample of PNe. On the other hand, Siódmiak & Tylenda find no evidence for any such variations in density; shell inhomogeneities, where they occur, are primarily attributable to ,blobs or condensations'. It will be suggested that both of these analyses are unreliable, and should be treated with a considerable degree of caution. A new analysis within the log(F(5 GHz)/F(1.4 GHz)),log(TB(5 GHz)) plane will be used to show that at least 10,20 per cent of PNe are associated with strong density gradients. We shall also show that the ratio F(5 GHz)/F(1.4 GHz) varies with nebular radius; an evolution that can be interpreted in terms of varying shell masses, and declining electron densities. [source] Multipole electron-density modelling of synchrotron powder diffraction data: the case of diamondACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2010H. Svendsen Accurate structure factors are extracted from synchrotron powder diffraction data measured on crystalline diamond based on a novel multipole model division of overlapping reflection intensities. The approach limits the spherical-atom bias in structure factors extracted from overlapping powder data using conventional spherical-atom Rietveld refinement. The structure factors are subsequently used for multipole electron-density modelling, and both the structure factors and the derived density are compared with results from ab initio theoretical calculations. Overall, excellent agreement is obtained between experiment and theory, and the study therefore demonstrates that synchrotron powder diffraction can indeed provide accurate structure-factor values based on data measured in minutes with limited sample preparation. Thus, potential systematic errors such as extinction and twinning commonly encountered in single-crystal studies of small-unit-cell inorganic structures can be overcome with synchrotron powder diffraction. It is shown that the standard Hansen,Coppens multipole model is not flexible enough to fit the static theoretical structure factors, whereas fitting of thermally smeared structure factors has much lower residuals. If thermally smeared structure factors (experimental or theoretical) are fitted with a slightly wrong radial model (s2p2 instead of sp3) the radial scaling parameters (`,' parameters) are found to be inadequate and the `error' is absorbed into the atomic displacement parameter. This directly exposes a correlation between electron density and thermal parameters even for a light atom such as carbon, and it also underlines that in organic systems proper deconvolution of thermal motion is important for obtaining correct static electron densities. [source] Many body effects in the optical behavior of quantum well excitonsPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 7 2008V. P. Kochereshko Abstract Modulation-doped CdTe/Cd0.7Mg0.3Te quantum well structures with a two dimensional electron gas of low and moderate density (from ne = 3 × 1010 cm,2 up to ne , 1012 cm,2) have been studied. Photoluminescence spectra taken from the quantum well in magnetic fields from 0 T to 45 T at different electron densities were studied. The observed spectra were analyzed in terms of combined exciton-electron processes. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Optimised Plasma Absorption Probe for the Electron Density Determination in Reactive PlasmasPLASMA PROCESSES AND POLYMERS, Issue 1 2009Christian Scharwitz Abstract The plasma absorption probe (PAP) is a recently developed tool for the efficient determination of electron densities, especially in reactive plasmas. A dielectric cover protects this probe against the influences in reactive plasmas and it withstands conditions where Langmuir probes are easily damageable. The lack of adequate calibration constants and the occurrence of multiple absorption signals were two major drawbacks, which are successfully overcome in this work. Design variations are tested by numerical computation and the model-based achievements are established in experiment. In this work, a redesigned PAP is presented, which is optimised for the easy determination of electron densities. The developed tool works fast and efficiently, in particular in discharges in reactive gases. [source] The interplay between experiment and theory in charge-density analysisACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2004Philip Coppens The comparison of theory and experiment remains a cornerstone of scientific inquiry. Various levels of such comparison applicable to charge-density analysis are discussed, including static and dynamic electron densities, topological properties, d -orbital occupancies and electrostatic moments. The advantages and drawbacks of the pseudoatom multipole are discussed, as are the experimentally constrained wavefunctions introduced by Jayatilaka and co-workers, which combine energy minimization with the requirement to provide a reasonable fit to the X-ray structure factors. The transferability of atomic densities can be exploited through construction of a pseudoatom databank, which may be based on analysis of ab initio molecular electron densities, and can be used to evaluate a host of physical properties. Partitioning of theoretical energies with the Morokuma,Ziegler energy decomposition scheme allows direct comparison with electrostatic interaction energies obtained from electron densities represented by the pseudoatom formalism. Compared with the Buckingham expression for the interaction between non-overlapping densities, the agreement with theory is much improved when a newly developed hybrid EP/MM (exact potential/multipole model) method is employed. [source] Electron-density studies of molecular magnetic materialsACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2004Sébastien Pillet For more than forty years, the experimental determination and analysis of electron densities have played a fundamental role in advances in the chemical bond concept. The present paper illustrates the application of this approach to the field of molecular magnetism with examples that recently appeared in the literature. Particular attention is attached to several classes of materials, purely organic free radicals, coordination compounds and organometallic complexes, which exhibit specific magnetic behaviors. It is shown to what extent the electron-density analysis can shed light on bonding aspects that are closely related to magnetic couplings. Relations between spin delocalization, spin polarization, superexchange and the characteristics of the electron density are described. The use of the topological theory of `atoms in molecules' allows the possible magnetic interaction pathways to be located and defined, especially through weak intermolecular contacts. The complementarity with polarized neutron diffraction and spin-density modeling techniques is particularly evident from the chosen examples. [source] On the origin of topological differences between experimental and theoretical crystal charge densitiesACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2000Anatoliy Volkov Topological analysis of experimental and theoretical (molecular and crystal) electron densities of p -nitroaniline and p -amino- p,-nitrobiphenyl reveals considerable discrepancies between experiment and theory for the bond critical points properties. Particularly large differences occur for the positive curvature along the bond path (,3). The differences become somewhat smaller when more extended basis sets and correlation effects are introduced in the theoretical calculations. The effect of the crystal matrix on the properties of bond critical points is evaluated for the p -nitroaniline molecule using the 6-21G** and 6-31G** basis sets. The differences between the isolated molecule and the molecule in the crystal are too small to explain the quantitative disagreement between the theoretical and experimental topologies reported in the literature and found in the current study. For most bonds, the observed changes in the properties of the electron density agree well for both basis sets but some discrepancies are found for changes in ,3 for N,H and aromatic C,C bonds. When the theoretical densities are projected into the multipole density functions through refinement of the theoretical structure factors, the topological properties change and differences between theory and experiment are reduced. The main origin of the observed discrepancies is attributed to the nature of the radial functions in the experimental multipole model. [source] Modulation functions of incommensurately modulated Cr2P2O7 studied by the maximum entropy method (MEM)ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2010Liang Li The maximum entropy method (MEM) has been used to determine electron density in superspace of incommensurately modulated chromium pyrophosphate from X-ray diffraction data measured by Palatinus et al. [(2006), Acta Cryst. B62, 556,566]. Chromium pyrophosphate, Cr2P2O7, contains ordered regions (83% of the volume) and regions with disorder. Analysis of the MEM density has allowed the determination of the displacive modulation functions within ordered regions. The disordered regions can be described as the alternate occupation of two conformations of the pyrophosphate group and two positions of the chromium atom, with occupational probabilities that depend continuously on the phase of modulation t. A structure model based on the interpretation of the MEM density provides a fit to the diffraction data of the same quality as the model given by Palatinus et al. (2006). The failure to find a model that better fits the data is attributed to the intrinsic inaccuracy of ,,0.01,Å for positions derived from the MEM and to the difficulties in constructing an appropriate model for the anharmonic ADPs and their modulation functions from electron densities. [source] Accurate charge density of the tripeptide Ala-Pro-Ala with the maximum entropy method (MEM): influence of data resolutionACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2007Andreas Hofmann The accurate electron density of Ala-Pro-Ala is determined by the maximum entropy method (MEM), employing the same reflection data measured at 100,K which was used for a multipole refinement by Kalinowski et al. [(2007), Acta Cryst. Accepted for publication]. Properties of the electron density are compared with the corresponding properties of the static electron density from the multipole model and to the dynamic MEM electron density of trialanine at 20,K. It is thus shown that the increased thermal smearing at 100,K leads to lower electron densities in the bond critical points and atomic charges closer to zero for Ala-Pro-Ala than has been obtained for trialanine at 20,K. The influence of the resolution of the data is investigated by a series of MEM calculations. Atomic charges and atomic volumes are found not to depend on the resolution, but the charge density in the BCPs decreases with decreasing resolution of the dataset. The origin of this dependence is found to lie mostly in the more accurate estimate of the atomic displacement parameters (ADPs) for the higher-resolution datasets. If these effects are taken into account, meaningful information on chemical bonding can be obtained with data at a resolution better than dmin = 0.63,Å. Alternatively, low-resolution X-ray diffraction data can be used in accurate electron-density studies by the MEM, if another source of accurate values of the ADPs is available, e.g. from refinements with multipole parameters from a database of transferable multipole parameters. [source] Ethyl[tris(3- tert -butyl-5-methylpyrazol-1-yl)hydridoborato]zinc(II)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2010Mukesh Kumar The X-ray crystal structure of the title compound, [Zn(C2H5)(C24H40BN6)], or TptBu,MeZnEt [TptBu,Me is tris(3- tert -butyl-5-methylpyrazolyl)hydridoborate], reveals a distorted tetrahedral geometry around the Zn atom. The Zn center is coordinated by three N atoms of the borate ligand and by one C atom of the ethyl group. The present structure and other tetrahedral Tp zinc alkyl complexes are compared with similar Ttz ligands (Ttz is 1,2,4-triazolylborate), but no major differences in the structures are noted, and it can be assumed that variation of the substitution pattern of Tp or Ttz ligands has little or no influence on the geometry of alkylzinc complexes. Refinement of the structure is complicated by a combination of metric pseudosymmetry and twinning. The metrics of the structure could also be represented in a double-volume C -centered orthorhombic unit cell, and the structure is twinned by one of the orthorhombic symmetry operators not present in the actual structure. The twinning lies on the borderline between pseudomerohedral and nonmerohedral. The data were refined as being nonmerohedrally twinned, pseudomerohedrally twinned and untwinned. None of the approaches yielded results that were unambiguously better than any of the others: the best fit between structural model and data was observed using the nonmerohedral approach which also yielded the best structure quality indicators, but the data set is less than 80% complete due to rejected data. The pseudomerohedral and the untwinned structures are complete, but relatively large residual electron densities that are not close to the metal center are found with values up to three times higher than in the nonmerohedral approach. [source] Conductance asymmetry of a slot gate Si-MOSFET in a strong parallel magnetic fieldANNALEN DER PHYSIK, Issue 12 2009I. Shlimak Abstract We report measurements on a Si-MOSFET sample with a slot in the upper gate, allowing for different electron densities n1,2 across the slot. The dynamic longitudinal resistance was measured by the standard lock-in technique, while maintaining a large DC current through the source-drain channel. We find that the conductance of the sample in a strong parallel magnetic field is asymmetric with respect to the DC current direction. This asymmetry increases with magnetic field. The results are interpreted in terms of electron spin accumulation or depletion near the slot. [source] Application of general formulas for the correction of a lattice-translocation defect in crystals of a lentiviral integrase in complex with LEDGFACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2009Stephen Hare The symmetry inherent to many biological macromolecular assemblies has been implicated in a range of crystal pathologies, including lattice-translocation defects (LTDs). Crystals suffering from classic LTDs contain two lattices that are shifted with respect to each other but nonetheless remain within the length of coherent interference. LTD introduces an undesirable intensity modulation into diffraction data, resulting in scrambled or partially scrambled electron densities. In this report, LTD theory is extended and a new general method for determining defect fractions is developed based on the heights of the non-origin peaks observed in native Patterson maps. The application of this method to crystals of lentiviral integrase in complex with its cofactor, where the observed translocation vector does not equal a small integral fraction of a unit-cell edge, is reported and its general application to all classic LTD cases is predicted. [source] Dynamic Molecular Tweezers Composed of Dibenzocyclooctatetraene Units: Synthesis, Properties, and Thermochromism in Host,Guest ComplexesCHEMISTRY - A EUROPEAN JOURNAL, Issue 28 2009Tomohiko Nishiuchi Abstract Novel dynamic molecular tweezers (DMTs) 3,a, 3,b, 4,a, 4,b, and 5,b, composed of two tub-shaped dibenzocyclooctatetraene (DBCOT) units, were designed and synthesized. The cyclooctatetraene (COT) rings of these DMTs readily invert in solution, and the molecular structure shows rigid syn and anti forms in an equilibrium mixture in solution. The syn and anti conformers can be observed by NMR. The isomerization barriers of 3,a, 3,b, 4,a, 4,b, and 5,b are in the range of 16.5,21.3,kcal,mol,1, depending on steric repulsion between substituents of the COT rings and protons of the central benzene ring. These DMTs form complexes with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) and 1,2,4,5-tetracyano-benzene (TCNB) in solution and in the solid state. The binding abilities of these DMTs increase with electron-donating substituents on COT, which increase the electron densities of the cavity of the syn form, as supported by theoretical calculations. In addition, elongation of the terminal alkoxy chains of the DMTs was found to cause the enhancement of van,der Waals contact with guest molecules. Therefore, 5,b, which has CH2OMe groups on the COT rings and longer ethoxy groups on the terminal benzene rings, showed the highest electron density of the cavity and hence the highest binding ability with the electron-deficient guest molecules. Interestingly, solutions of 3,b, 4,b, and 5,b show thermochromism in the presence of DDQ. A solution of 3,b or 4,b with DDQ in CHCl3 is green due to charge-transfer interaction at room temperature and the color changes from green to yellow upon heating to 60,°C and from green to blue upon cooling to ,40,°C, whereas the high complexation ability of 5,b with DDQ only shows a change in the shade of blue. [source] Current,Voltage Characteristics of a Homologous Series of Polycyclic Aromatic HydrocarbonsCHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2007Thilo Böhme Dr. Abstract A novel alkyl-substituted polycyclic aromatic hydrocarbon (PAH) with D2h symmetry and 78 carbon atoms in the aromatic core (C78) was synthesized, thereby completing a homologous series of soluble PAH compounds with increasing size of the aromatic , system (42, 60, and 78 carbon atoms). The optical band gaps were determined by UV/Vis and fluorescence spectroscopy in solution. Scanning tunneling microscopy (STM) and spectroscopy (STS) revealed diode-like current versus voltage (I,V) characteristics through individual aromatic cores in monolayers at the interface between the solution and the basal plane of graphite. The asymmetry of the current,voltage (I,V) characteristics increases with the increasing size of the aromatic core, and the concomitantly decreasing HOMO,LUMO gap. This is attributed to resonant tunneling through the HOMO of the adsorbed molecule, and an asymmetric position of the molecular species in the tunnel junction. Consistently, submolecularly resolved STM images at negative substrate bias are in good agreement with the calculated pattern for the electron densities of the HOMOs. The analysis provides the basis for tailoring rectification with a single molecule in an STM junction. [source] | |||||||||||||||||||||||||||||||||||||