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Density-functional Theory (density-functional + theory)
Terms modified by Density-functional Theory Selected AbstractsChemInform Abstract: Electronic Structure Calculations for the Ternary Intermetallic Compounds A2MX and AMX2 (A: Li; M: Rh, Pd, Ir, Pt; X: Al, Ga, In) Using Density-Functional Theory.CHEMINFORM, Issue 23 2001Lydia Drews-Nicolai Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Ab-initio simulations of materials using VASP: Density-functional theory and beyondJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2008Jürgen Hafner Abstract During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science,promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many-body effects within density-functional theory (DFT) and the upcoming post-DFT methods. (ii) The implementation of the new functionals and many-body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local-density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, hybrid functional mixing DFT, and exact (Hartree-Fock) exchange] and post-DFT approaches [DFT + U for strong electronic correlations in narrow bands, many-body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic-connection fluctuation-dissipation theorem (AC-FDT)] in the Vienna ab initio simulation package VASP. VASP is a plane-wave all-electron code using the projector-augmented wave method to describe the electron-core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total-energy calculations and structural optimizations for systems with thousands of atoms and ab initio molecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces, interfaces and thin films, chemical reactions, and catalysis) are reviewed. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Dispersion interactions in density-functional theoryJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 12 2009Erin R. Johnson Abstract Density-functional theory (DFT) allows for the calculation of many chemical properties with relative ease, thus making it extremely useful for the physical organic chemistry community to understand and focus on various experiments. However, density-functional techniques have their limitations, including the ability to satisfactorily describe dispersion interactions. Given the ubiquitous nature of dispersion in chemical and biological systems, this is not a trivial matter. Recent advances in the development of DFT methods can treat dispersion. These include dispersion-corrected DFT (using explicit, attractive dispersion terms), parameterized functionals, and dispersion-correcting potentials, all of which can dramatically improve performance for dispersion-bound species. In this perspective, we highlight the achievements made in modeling dispersion using DFT. We hope that this will provide valuable insight to both computational chemists and experimentalists, who aim to study physical processes driven by dispersion interactions. Copyright © 2009 John Wiley & Sons, Ltd. [source] Understanding chemical shielding tensors using group theory, MO analysis, and modern density-functional theoryCONCEPTS IN MAGNETIC RESONANCE, Issue 2 2009Cory M. Widdifield Abstract In this article, the relationships between molecular symmetry, molecular electronic structure, and chemical shielding (CS) tensors are discussed. First, a brief background on the CS interaction and CS tensors is given. Then, the visualization of the three-dimensional nature of CS is described. A simple method for examining the relationship between molecular orbitals (MOs) and CS tensors, using point groups and direct products of irreducible representations of MOs and rotational operators, is outlined. A number of specific examples are discussed, involving CS tensors of different nuclei in molecules of different symmetries, including ethene (D2h), hydrogen fluoride (C,v), trifluorophosphine (C3v), and water (C2v). Finally, we review the application of this method to CS tensors in several interesting cases previously discussed in the literature, including acetylene (D,h), the PtX42, series of compounds (D4h) and the decamethylaluminocenium cation (D5d). © 2009 Wiley Periodicals, Inc. Concepts Magn Reson Part A 34A: 91,123, 2009. [source] Conformational Analysis and CD Calculations of Methyl-Substituted 13-Tridecano-13-lactonesHELVETICA CHIMICA ACTA, Issue 2 2005Elena Voloshina Conformational models covering an energy range of 3,kcal/mol were calculated for (13S)-tetradecano-13-lactone (3), (12S)-12-methyltridecano-13-lactone (4), and (12S,13R)-12-methyltetradecano-13-lactone (8), starting from a semiempirical Monte-Carlo search with AM1 parametrization, and subsequent optimization of the 100 best conformers at the 6-31G*/B3LYP and then the TZVP/B3LYP level of density-functional theory. CD Spectra for these models were calculated by the time-dependent DFT method with the same functional and basis sets as for the ground-state calculations and Boltzmann weighting of the individual conformers. The good correlation of the calculated and experimental spectra substantiates the interpretation of these conformational models for the structure,odor correlation of musks. Furthermore, the application of the quadrant rule in the estimation of the Cotton effect for macrolide conformers is critically discussed. [source] Outlying Charge, Stability, Efficiency, and Algorithmic Enhancements in the Quantum-Mechanical Solvation Method, COSab-GAMESSHELVETICA CHIMICA ACTA, Issue 12 2003Laura In this work, we present algorithmic modifications and extensions to our quantum-mechanical approach for the inclusion of solvent effects by means of molecule-shaped cavities. The theory of conductor-like screening, modified and extended for quantum-mechanical techniques, serves as the basis for our solvation methodology. The modified method is being referred to as COSab-GAMESS and is available within the GAMESS package. Our previous work has emphasized the implementation of this model by way of a distributed multipole approach for handling the effects of outlying charge. The method has been enabled within the framework of open- and closed-shell RHF and MP2. In the present work, we present a) a second method to handle outlying charge effects, b) algorithmic extensions to open- and closed-shell density-functional theory, second-derivative analysis, and reaction-path following, and c) enhancements to improve performance, convergence, and predictability. The method is now surtable for large molecular systems. New features of the enhanced continuum model are highlighted by means of a set of neutral and charged species. Computations on a series of structures with roughly the same molecular shape and volume provides an evaluation of cavitation effects. [source] Ab Initio Structure/Reactivity Investigations of Illudin-Based Antitumor Agents: A Model for Reaction in vivoHELVETICA CHIMICA ACTA, Issue 12 2003Laura (Hydroxymethyl)acylfulvene (HMAF, irofulven; 4), a third-generation derivative of a natural product extracted from the mushroom Omphalotus illudens, is selectively toxic towards certain forms of malignant tumors. Conversion of HMAF and cognates to stable aromatic derivatives is triggered by thiol attack in vitro and in vivo. Quantum-chemical methods predict well the structure for several functionalized derivatives of irofulven as compared to known X-ray crystallographic structures. Computational reaction profiles for thiol attack and aromatic rearrangement of irofulven and illudin S, a toxin from which irofulven is derived, provide insight into HMAF's selectivity and toxicity. Methods used include hybrid density-functional theory (HDFT), HartreeFock (HF), and MøllerPlesset second-order perturbation theory (MP2). Solvent effects have been explored by means of the new continuum-solvation method, COSab, presented in an accompanying paper. [source] Adjusting magnetic moments of Sc13 and Y13 clusters by doping different X atom (X = Na, Mg, Al, Si, P)INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 8 2010Fu-Yang Tian Abstract We have investigated the structural and magnetic properties of the doped XM12 and charged M13 (X = Na, Mg, Al, Si, P; M = Sc, Y) clusters using the density-functional theory with spin-polarized generalized gradient approximation. It was found that doped atoms can induce significant change of the magnetic moments of Sc13 and Y13 clusters. The total magnetic moments of the NaM12, MgM12, AlM12, SiM12, and PM12 clusters are regular 5, 6 (12), 7, 8, and 9 ,b, respectively (but 19 ,b for Sc13 and Y13, 12 ,b for Y, 18 ,b for Sc, Sc, and Y). The doped atom substituting the surface atom of the plausible icosahedral configuration is viewed as the ground-state structure of the XM12 (X = Na, P; M = Sc, Y) and MgSc12 clusters. While for XM12 (X = Al, Si; M = Sc, Y) and MgY12 clusters, the doped atom occupying the central position of the icosahedral configuration is viewed as the ground-state structure. The doping and the charging both enhance the stability of the Sc13 and Y13 clusters. These findings should have an important impact on the design of the adjustable magnetic moments systems. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Structure and stability of high-spin Aun(n = 2,8) clustersINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2009Zhen-Yi Jiang Abstract The structures and relative stability of the maximum-spin n+1Aun and nAu (n = 2,8) clusters have been determined by density-functional theory. The structure optimizations and vibrational frequency analysis are performed with the gradient-corrections of Perdew along with his 1981 local correlation functional, combined with SBKJC effective core potential, augmented in the valence basis set by a set of f functions. We predicted the existence of a number of previously unknown isomers. The energetic and electronic properties of the small high-spin gold clusters are strongly dependent on sizes. The high-spin clusters tend to holding three-dimensional geometry rather than planar form preferred in low-spin situations. In whole high-spin Aun (n = 2,8) neutral and cationic species, 5Au4, 2Au, and 4Au are predicted to be of high stability, which can be explained by valence bond theory. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] The N -particle wave function as a homogeneous functional of the densityINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 14 2007Tamás Gál Abstract It is shown that requiring consistency with the structure of the equation that determines the wave function associated to a density ,() by density-functional theory, yields the N -particle wave function as a degree-half homogeneous functional of the density, and leads to a separation A[N, ,] of N dependence (with N = ,,() d) of density functionals A[,] = A[,,, ,] for which A[,,, ,,] = , A[,, ,]; as a consequence of the linearity of quantum mechanical operators. This implies that the ground-state value of any quantum mechanical observable arises naturally as a degree-one homogeneous N -particle density functional. This general scheme for the structure of density functionals can be considered as the conceptual generalization of the Weizsäcker functional, which is the exact degree-one homogeneous one-particle kinetic-energy density functional. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Revisiting N -continuous density-functional theory: Chemical reactivity and "Atoms" in "Molecules"ISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 2003Morrel H. Cohen We construct an internally-consistent density-functional theory valid for noninteger electron numbers N by precise definition of a density functional that is continuous in N. In this theory, charge transfer between the atoms of a heteronuclear diatomic molecule, which have been separated adiabatically to infinity, is avoided because the hardness for fractional occupation of a single HOMO spin-orbital is negative. This N -continuous density functional makes possible a variational theory of "atoms" in "molecules" that exactly decomposes the molecular electron density into a sum of contributions from its parts. The parts are treated as though isolated. That theory, in turn, gives a deep foundation to the chemical reactivity theory provided that the hardness of entities with vanishing spin density is positive, as argued to be the case here. This transition from negative to positive hardness closely parallels the transition from the Heitler-London to the Hund-Mulliken picture of molecular bonding. [source] First-principle calculations on CO oxidation catalyzed by a gold nanoparticleJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2010Hsin-Tsung Chen Abstract We have elucidated the mechanism of CO oxidation catalyzed by gold nanoparticles through first-principle density-functional theory (DFT) calculations. Calculations on selected model show that the low-coordinated Au atoms of the Au29 nanoparticle carry slightly negative charges, which enhance the O2 binding energy compared with the corresponding bulk surfaces. Two reaction pathways of the CO oxidation were considered: the Eley,Rideal (ER) and Langmuir,Hinshelwood (LH). The overall LH reaction O2(ads) + CO(gas) , O2(ads) + CO(ads) , OOCO(ads) , O(ads) + CO2(gas) is calculated to be exothermic by 3.72 eV; the potential energies of the two transition states (TSLH1 and TSLH2) are smaller than the reactants, indicating that no net activation energy is required for this process. The CO oxidation via ER reaction Au29 + O2(gas) + CO(gas) , Au29,O2(ads) + CO(gas) , Au29,CO3(ads) , Au29,O(ads) + CO2(gas) requires an overall activation barrier of 0.19 eV, and the formation of Au29,CO3(ads) intermediate possesses high exothermicity of 4.33 eV, indicating that this process may compete with the LH mechanism. Thereafter, a second CO molecule can react with the remaining O atom via the ER mechanism with a very small barrier (0.03 eV). Our calculations suggest that the CO oxidation catalyzed by the Au29 nanoparticle is likely to occur at or even below room temperature. To gain insights into high-catalytic activity of the gold nanoparticles, the interaction nature between adsorbate and substrate is also analyzed by the detailed electronic analysis. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Ab-initio simulations of materials using VASP: Density-functional theory and beyondJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2008Jürgen Hafner Abstract During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science,promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many-body effects within density-functional theory (DFT) and the upcoming post-DFT methods. (ii) The implementation of the new functionals and many-body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local-density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, hybrid functional mixing DFT, and exact (Hartree-Fock) exchange] and post-DFT approaches [DFT + U for strong electronic correlations in narrow bands, many-body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic-connection fluctuation-dissipation theorem (AC-FDT)] in the Vienna ab initio simulation package VASP. VASP is a plane-wave all-electron code using the projector-augmented wave method to describe the electron-core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total-energy calculations and structural optimizations for systems with thousands of atoms and ab initio molecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces, interfaces and thin films, chemical reactions, and catalysis) are reviewed. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] A dual-level state-specific time-dependent density-functional theoryJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2008Seiken Tokura Abstract A highly efficient new algorithm for time-dependent density-functional theory (TDDFT) calculations is presented. In this algorithm, a dual-level approach to speed up DFT calculations (Nakajima and Hirao, J Chem Phys 2006, 124, 184108) is combined with a state-specific (SS) algorithm for TDDFT (Chiba et al., Chem Phys Lett 2006, 420, 391). The dual-level SS-TDDFT algorithm was applied to excitation energy calculations of typical small molecules, the Q bands of the chlorophyll A molecule, the charge-transfer energy of the zincbacteriochlorin,bacteriochlorin model system, and the lowest-lying excitation of the circumcoronene molecule. As a result, it was found that the dual-level SS-TDDFT gave correct excitation energies with errors of 0.2,0.3 eV from the standard TDDFT approach, with much lower CPU times for various types of excitation energies of large-scale molecules. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Modified calculations of hydrocarbon thermodynamic propertiesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2006Min Hsien Liu Abstract A test set of 65 hydrocarbons was examined to elucidate theoretically their thermodynamic properties by performing the density-functional theory (DFT) and ab initio calculations. All the calculated data were modified using a three-parameter calibration equation and the least-squares approach, to determine accurately enthalpies of formation (,Hf), entropies (S), and heat capacities (Cp). Calculation results demonstrated that the atomization energies of all compounds exhibited an average absolute relative error ranging between 0.11, 0.13%, and an ,Hf of formation with a mean absolute absolute error (M.|A.E.|) ranging from only 5.7,6.8 kJ/mol (1.3,1.6 kcal/mol) (i.e., those results correlated with those of Dr. Herndon's 1.1 kcal/mol). Additionally, the entropy ranged from 3.5,4.2 J/mol K (0.8,1.0 cal/mol K) M.|A.E.|; a heat capacity between 2.3,2.9 J/mol K (0.5,0.7 cal/mol K) M.|A.E.| was obtained as well. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 537,544, 2006 [source] Electronic structure, chemical bonding, and finite-temperature magnetic properties of full Heusler alloysJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2006Yasemin Kurtulus Abstract The electronic structure, chemical bonding, and magnetic properties of 15 full Heusler alloys X2MnZ have been studied on the basis of density-functional theory using the TB-LMTO-ASA approach and the local-density (LDA), as well as the generalized-gradient approximation (GGA). Correlations between the chemical bondings derived from crystal orbital Hamilton population (COHP) analysis and magnetic phenomena are obvious, and different mechanisms leading to spin polarization and ferromagnetism are derived. As long as a magnetically active metal atom X is present, antibonding XX and XMn interactions at the Fermi level drive the systems into the ferromagnetic ground state; only if X is nonmagnetic (such as in Cu2MnZ), antibonding MnMn interactions arise, which again lead to ferromagnetism. Finite-temperature effects (Curie temperatures) are analyzed using a mean-field description, and a surprisingly simple (or, trivial) relationship between structural properties (MnMn interatomic distances) and TC is found, being of semiquantitative use for the prediction of the latter. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 90,102, 2006 [source] Simulating cyclohexane millisecond oxidation: Coupled chemistry and fluid dynamicsAICHE JOURNAL, Issue 6 2002R. P. O'Connor Cyclohexane partial oxidation over a 40-mesh Pt,10% Rh single-gauze catalyst can produce ,85% selectivity to oxygenates and olefins at 25% cyclohexane conversion and 100% oxygen conversion, with cyclohexene and 5-hexenal as the dominant products. A detailed 2-D model of the reactor is solved using density-functional theory (with 35 reactions among 25 species) and computational fluid dynamics. Rapid quenching in the wake of the wires allows highly nonequilibrium species to be preserved. The simulations show that the competition between cyclohexyl and cyclohexylperoxy radicals is crucial in determining product selectivities. At high temperatures and low pressures, the cyclohexyl radical is favored, leading to high selectivities to cyclohexene. At lower temperatures or high pressures, cyclohexylperoxy radicals are favored, allowing the formation of parent oxygenates to dominate. Numerical simulations suggest ways to tune reactor operation for desired product distributions and allow the investigation of dangerous or costly operating conditions, such as high pressure. [source] Dispersion interactions in density-functional theoryJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 12 2009Erin R. Johnson Abstract Density-functional theory (DFT) allows for the calculation of many chemical properties with relative ease, thus making it extremely useful for the physical organic chemistry community to understand and focus on various experiments. However, density-functional techniques have their limitations, including the ability to satisfactorily describe dispersion interactions. Given the ubiquitous nature of dispersion in chemical and biological systems, this is not a trivial matter. Recent advances in the development of DFT methods can treat dispersion. These include dispersion-corrected DFT (using explicit, attractive dispersion terms), parameterized functionals, and dispersion-correcting potentials, all of which can dramatically improve performance for dispersion-bound species. In this perspective, we highlight the achievements made in modeling dispersion using DFT. We hope that this will provide valuable insight to both computational chemists and experimentalists, who aim to study physical processes driven by dispersion interactions. Copyright © 2009 John Wiley & Sons, Ltd. [source] First-principles calculations of transition phase and thermodynamic properties of CdOPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 6 2008Liping Yao Abstract The transition phase of CdO from NaCl-type (B 1) structure to CsCl-type (B 2) structure is investigated by ab initio plane-wave pseudopotential density-functional theory, and the thermodynamic properties of the B 1 and B 2 structures under high pressure and temperature are obtained through the quasiharmonic Debye model. The transition phase from B 1 structure to B 2 structure occurs at a pressure of 83.1 GPa, which agrees well with other calculated values. Moreover, the relationship of the relative volume V /V0, and the Debye temperature , and the heat capacity CV with the pressure P and temperature T are also successfully obtained. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Half-metallic ferromagnetism in wurtzite SrCPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 1 2008Chang-wen Zhang Abstract The first-principles full potential linearized augmented plane-wave method within density-functional theory is used to investigate electronic structure and magnetism of wurtzite (WZ) crystal structure SrC. It is shown that the WZ SrC is a true half-metallic ferromagnet with a magnetic moment of 2,B per formula unit. The large HM gaps (0.72 eV) and robustness of half-metallicity with respect to the lattice change make it possible candidate grown epitaxially on appropriate substrates in the form of films thick enough, and therefore should be useful in spintronics and other related applications. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Spin polarization and electronic structure of ferromagnetic Mn5Ge3 epilayersPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 8 2005R. P. Panguluri Abstract Germanium-based alloys hold great promise for future spintronics applications, due to their potential for integration with conventional Si-based electronics. High-quality single phase Mn5Ge3(0001) films, grown by solid-phase epitaxy on Ge(111) and GaAs(111), exhibit strong ferromagnetism up to the Curie temperature TC , 296 K. Point Contact Andreev Reflection (PCAR) measurements on Mn5Ge3 epilayers reveal a spin-polarization P = 42 ± 5% for both substrates. We also calculate the spin polarization of bulk Mn5Ge3 in the diffusive and ballistic regimes using density-functional theory (DFT). The measured spin polarization exceeds the theoretical estimates of PDFT = 35 ± 5% and 10 ± 5% for the diffusive and ballistic limits, respectively. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Persistence of the stereochemical activity of the Bi3+ lone electron pair in Bi2Ga4O9 up to 50,GPa and crystal structure of the high-pressure phaseACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010Alexandra Friedrich The crystal structure of the high-pressure phase of bismuth gallium oxide, Bi2Ga4O9, was determined up to 30.5,(5),GPa from in situ single-crystal in-house and synchrotron X-ray diffraction. Structures were refined at ambient conditions and at pressures of 3.3,(2), 6.2,(3), 8.9,(1) and 14.9,(3),GPa for the low-pressure phase, and at 21.4,(5) and 30.5,(5),GPa for the high-pressure phase. The mode-Grüneisen parameters for the Raman modes of the low-pressure structure and the changes of the modes induced by the phase transition were obtained from Raman spectroscopic measurements. Complementary quantum-mechanical calculations based on density-functional theory were performed between 0 and 50,GPa. The phase transition is driven by a large spontaneous displacement of one O atom from a fully constrained position. The density-functional theory (DFT) model confirmed the persistence of the stereochemical activity of the lone electron pair up to at least 50,GPa in accordance with the crystal structure of the high-pressure phase. While the stereochemcial activity of the lone electron pair of Bi is reduced at increasing pressure, a symmetrization of the bismuth coordination was not observed in this pressure range. This shows an unexpected stability of the localization of the lone electron pair and of its stereochemical activity at high pressure. [source] Polymorphism in the nitrate salt of the [Mn(acetylacetonate)2(H2O)2]+ ionACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010A. R. Biju The crystallization of [Mn(acac)2(H2O)2]+ from solutions containing excess nitrate leads to the formation of four polymorphs. All polymorphs contain two different types of complex ions, one containing essentially coplanar acac ligands and the other in which the two acac ligands together assume a chair conformation. Molecular modelling using DFT (density-functional theory) calculations shows that the coplanar conformation is the electronically stable one. The hydrogen bonding between the trans -water molecules and the nitrate ion produces a one-dimensional chain of 12-membered rings, which are further organized into a two-dimensional network via a lattice water molecule. Lattice-energy calculations have been carried out to compare the stabilities of the four polymorphs. [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] Structure and conformational analysis of a bidentate pro-ligand, C21H34N2S2, from powder synchrotron diffraction data and solid-state DFTB calculationsACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2009Edward E. Ávila The molecular and crystalline structure of ethyl 1,,2,,3,,4,,4a,,5,,6,,7,-octahydrodispiro[cyclohexane-1,2,-quinazoline-4,,1,,-cyclohexane]-8,-carbodithioate (I) was solved and refined from powder synchrotron X-ray diffraction data. The initial model for the structural solution in direct space using the simulated annealing algorithm implemented in DASH [David et al. (2006). J. Appl. Cryst.39, 910,915] was obtained performing a conformational study on the fused six-membered rings of the octahydroquinazoline system and the two spiran cyclohexane rings of (I). The best model was chosen using experimental evidence from 1H and 13C NMR [Contreras et al. (2001). J. Heterocycl. Chem.38, 1223,1225] in combination with semi-empirical AM1 calculations. In the refined structure the two spiran rings have the chair conformation, while both of the fused rings in the octahydroquinazoline system have half-chair conformations compared with in-vacuum density-functional theory (DFT) B3LYP/6-311G*, DFTB (density-functional tight-binding) theoretical calculations in the solid state and other related structures from X-ray diffraction data. Compound (I) presents weak intramolecular hydrogen bonds of the type N,H...S and C,H...S, which produce delocalization of the electron density in the generated rings described by graph symbols S(6) and S(5). Packing of the molecules is dominated by van der Waals interactions. [source] Inverse bilayer structure of mononuclear CoII and NiII complexes of the type M(H2O)3(SO4)(4-CNpy)2ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2009Birinchi K. Das Two new metal compounds of the formula [M(H2O)3(SO4)(4-CNpy)2]·H2O [M = Ni (1) and Co (2), 4-CNpy = 4-cyanopyridine] have been prepared and studied by X-ray diffraction. In both of these compounds the 4-CNpy ligands are coordinated via pyridyl-N atoms to the metal ions in a cis fashion. The neutral complexes along with the uncoordinated H2O molecules are glued together preferentially into inverse bilayers by non-covalent interactions, including unique interlayer ,,, interactions between antiparallel nitrile groups. Hartree,Fock and density-functional theory (DFT) calculations indicate that the ,,, interactions are energetically significant. The unit-cell similarity index (,) of 0.0046 for the compounds suggests their isostructurality, which is also supported by their X-ray powder diffraction patterns that can be almost superimposed. [source] Ab initio determination of the valence electron distribution in the average structure of the incommensurately modulated calaverite AuTe2ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2001Razvan Caracas The valence-electron density distribution of the average structure of incommensurately modulated calaverite, AuTe2, has been computed using density-functional theory. High-density regions, centered around the Au and Te atoms, are not spheric, but present charge concentrations along the Au,Te and Te,Te bonds. The electronic band structure and its corresponding density of states reveal the presence of three electronic band groups, constituted mainly by Te 5s, Au 5d and hybrids of Te 6p + Au 6s + Au 5d orbitals. The electrons belonging to the last block are responsible for the chemical bonds. [source] Modeling Na clusters in Ar matricesANNALEN DER PHYSIK, Issue 7 2005F. Fehrer Abstract We present a microscopic model for Na clusters embedded in raregas matrices. The valence electrons of the Na cluster are described by time-dependent density-functional theory at the level of the local-density approximation (LDA). Particular attention is paid to the semi-classical picture in terms of Vlasov-LDA. The Na+ ions and Ar atoms are handled as classical particles whereby the Ar atoms carry two degrees of freedom, position and dipole polarization. The interaction between Na+ ions and electrons is mediated through local pseudo-potentials. The coupling to the Ar atoms is described by (long-range) polarization potentials and (short-range) repulsive cores. The ingredients are taken from elsewhere developed standards. A final fine-tuning is performed using the NaAr molecule as benchmark. The model is then applied to embedded systems Na8ArN. By close comparison with quantum-mechanical results, we explore the capability of the Vlasov-LDA to describe such embedded clusters. We show that one can obtain a reasonable description by appropriate adjustments in the fine-tuning phase of the model. [source] Oxidation of Diiron and Triiron Sulfurdithiolato Complexes: Mimics for the Active Site of [FeFe]-HydrogenaseCHEMISTRY & BIODIVERSITY, Issue 10 2008Jochen Windhager Abstract The oxidation of the hexacarbonyl(1,3-dithiolato- S,S,)diiron complexes 4a,4c with varying amounts of dimethyldioxirane (DMD) was systematically studied. The chemoselectivity of the oxidation products depended upon the substituent R (R=H, Me, 1/2 (CH2)5). For R=H, four oxidation products, 6a,6d, have been obtained. In the case of R=Me, three products, 7a,7c, were formed, and for R=1/2 (CH2)5, only complex 8 was observed. These observations are due to steric and electronic effects caused by the substituent R. Additionally, oxidation of the triiron complex 5 with DMD was performed to yield the products 9a and 9b. X-Ray diffraction analyses were performed for 6a,6d, 7a, and 7c, as well as for 9a and 9b. The electronic properties were determined by density-functional theory (DFT) calculations. [source] X-Ray Absorption Spectroscopy of Cuprous-Thiolate Clusters in Saccharomyces cerevisiae MetallothioneinCHEMISTRY & BIODIVERSITY, Issue 10 2008Limei Zhang Abstract Copper (Cu) metallothioneins are cuprous-thiolate proteins that contain multimetallic clusters, and are thought to have dual functions of Cu storage and Cu detoxification. We have used a combination of X-ray absorption spectroscopy (XAS) and density-functional theory (DFT) to investigate the nature of Cu binding to Saccharomyces cerevisiae metallothionein. We found that the XAS of metallothionein prepared, containing a full complement of Cu, was quantitatively consistent with the crystal structure, and that reconstitution of the apo-metallothionein with stoichiometric Cu results in the formation of a tetracopper cluster, indicating cooperative binding of the Cu ions by the metallothionein. [source] | |||||||||||||||||||||||||