Ab Initio Determination Research Articles

Image deconvolution in spherical aberration-corrected high-resolution transmission electron microscopy

The method of image deconvolution developed previously for FEG high-resolution transmission electron microscope (HRTEM) without a spherical aberration ( C s) corrector was for the first time applied to FEG HRTEM with a C s-corrector. The principle and the procedure of image deconvolution are briefly described. Four qualified [1 1 0] images of Si were selected from a through-focus series to perform image deconvolution. The projected potential is successfully derived from all the images, and the obtained “dumbbell” structure maps of Si [1 1 0] are in good agreement with the calculated potential map. The criterion of selecting qualified images for performing image deconvolution is indicated. The possibility of applying image deconvolution to defect study and to ab initio crystal structure determination is discussed.

Ab initio structure determination of novel borate NaSrBO 3

A novel orthoborate, NaSrBO 3, has been successfully synthesized by standard solid-state reaction, and the crystal structure has been determined from powder X-ray diffraction data. It crystallizes in the monoclinic space group P 2 1 / c with lattice parameters: a = 5.3 2 4 4 6 ( 7 ) Å , b = 9.2 6 8 4 ( 1 ) Å , c = 6.0 6 6 8 3 ( 8 ) Å , β = 1 0 0.5 8 9 ( 1 ) ° . The fundamental building units are isolated BO 3 groups, which are parallelly distributed along two different directions. Because of the anisotropic polarizations of planar BO 3 groups, a considerable birefringence can be expected in it. The Na atoms are six-coordinated with O atoms to form octahedra, and the Sr atoms are nine-coordinated, forming tri-capped trigonal prisms. Those polyhedra connect with each other by bridging-oxygen atoms, forming infinite three-dimensional network, which indicates that the cleaving problem is expected to be overcome during the course of single-crystal growth. The infrared spectrum has been measured, and the result is consistent with the crystallographic study. Moreover, a comparison of the new structure type with the other known orthoborates is presented here.

Characterization and ab initio XRPD Structure Determination of a Novel Silicate with Vierer Single Chains: The Crystal Structure of NaYSi2O6.

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Extension to 2268 atoms of direct methods in theab initiodetermination of the unknown structure of bacteriophage P22 lysozyme

The X-ray crystal structure of the previously unknown bacteriophage P22 lysozyme, the product of gene 19, has been determined ab initio by direct methods using the program SIR2002. The presence of several partially occupied iodine anions and samarium cations augmented the ability of direct methods to locate all 2268 non-H protein atoms in the asymmetric unit, making this one of the largest structures to date to be determined ab initio. The iodides were introduced from a quick soak, which the crystal survived sufficiently well to diffract to 1.04 angstroms resolution. The complete heavy-atom substructure contributed 6.6% of the total scattering power. The initial determination of the structure assumed that there were two iodide ions in the asymmetric unit, although it was later determined that these sites correspond to partially occupied samarium ions. Tests suggested that it is better to overestimate rather than underestimate the heavy-atom content. While experimental phases from all of the successful tests were of high quality, the best results came from a SAD experiment using the programs SHELXD and SHELXE. Nonetheless, ab initio structure determination by direct methods was found to be a viable alternative to traditional protein crystallographic methods provided that the X-ray data extend to atomic resolution and heavy atoms with sufficient scattering power are present in the crystal.

Structure and intermolecular interactions of glipizide from laboratory X-ray powder diffraction

The crystal structure of glipizide, used as a major treatment of type-2 diabetes, has been determined ab initio using variable-temperature laboratory X-ray powder diffraction combined with a direct-space Monte Carlo/simulated annealing methodology. The strengths of the intermolecular interactions (van der Waals, pi-pi stacking, hydrogen bonding and steric interlock) were quantitatively estimated using the thermal expansion data, which were collected in the same set of experiments as those used to determine the structure.

A comment on “Accurate ab initio determination of binding energies for rare-gas dimers by basis set extrapolation”

In this work we comment on an extrapolation scheme presented by Lee in Theoretical Chemistry Accounts, which is based on an extrapolation of energy differences instead of actual energies. In particular, we show that a very similar scheme had been introduced already in 1999, and used to estimate the MP5, CCSDT and FCI complete basis set limits of He2.

The Coordination of Uranyl in Water: A Combined Quantum Chemical and Molecular Simulation Study

The coordination environment of uranyl in water has been studied using a combined quantum mechanical and molecular dynamics approach. Multiconfigurational wave function calculations have been performed to generate pair potentials between uranyl and water. The quantum chemically determined energies have been used to fit parameters in a polarizable force field with an added charge transfer term. Molecular dynamics simulations have been performed for the uranyl ion and up to 400 water molecules. The results show a uranyl ion with five water molecules coordinated in the equatorial plane. The U-O(H(2)O) distance is 2.40 A, which is close to the experimental estimates. A second coordination shell starts at about 4.7 A from the uranium atom. No hydrogen bonding is found between the uranyl oxygens and water. Exchange of waters between the first and second solvation shell is found to occur through a path intermediate between association and interchange. This is the first fully ab initio determination of the solvation of the uranyl ion in water.

Pd8(CH3COO)8(NO)8]: solution from X-ray powder diffraction data

The water-insoluble title compound, octakis(mu-acetato-kappa2O:O)octakis(mu-nitroso-kappa2N:O)octapalladium(II), [Pd8(CH3COO)8(NO)8], was precipitated as a yellow powder from a solution of palladium nitrate in nitric acid by adding acetic acid. Ab initio crystal structure determination was carried out using X-ray powder diffraction techniques. Patterson and Fourier syntheses were used for atom locations, and the Rietveld technique was used for the final structure refinement. The crystal structure is of a molecular type. The skeleton of the [Pd8(CH3COO)8(NO)8] molecule is constructed as a tetragonal prism with Pd atoms at the vertices. The eight NO- groups are in bridging positions along the horizontal edges of the prism. The N and O atoms of each nitroso group coordinate two different Pd atoms. The vertical edges present PdPd contacts with a short distance of 2.865 (1) A. These Pd atoms are bridged by a pair of acetate groups in a cis orientation with respect to each other. The complex has crystallographically imposed 4/m symmetry; all C atoms of the acetate groups are on mirror planes. The unique Pd atom lies in a general position and has square-planar coordination, consisting of three O and one N atom.

Ab-initio structure determination of C18H19N4S from powder X-ray diffraction

Ab-initio structure determination of C₁₈H₁₉N₄S from powder X-ray diffraction

Ab initio determination of the heat of formation of ketenyl (HCCO) and ethynyl (CCH) radicals

The heats of formation of ketenyl (HCCO) and ethynyl (CCH) radicals have been obtained from high level ab initio calculations. A set of reactions involving HCCO, CCH and species with well-known heats of formation has been considered. The reaction enthalpies have been calculated from the total energy of the species involved. These calculations include a non-relativistic electronic energy from extrapolated coupled-cluster calculations (up to CCSDTQ), corrections for scalar relativistic and spin-orbit effects, as well as the diagonal Born-Oppenheimer correction. This study also presents an accurate equilibrium geometry for HCCO as well as harmonic and fundamental frequencies for both HCCO and CCH.

Ab initio determination of the framework structure of the heavy-metal oxide Cs xNb 2.54W 2.46O 14 from 100 kV precession electron diffraction data

The present work deals with the ab initio determination of the heavy metal framework in Cs x (Nb, W) 5O 14 from precession electron diffraction intensities. The target structure was first discovered by Lundberg and Sundberg [Ultramicroscopy 52 (1993) 429–435], who succeeded in deriving a tentative structural model from high-resolution electron microsopy (HREM) images. The metal framework of the compound was solved in this investigation via direct methods from h k 0 precession electron diffraction intensities recorded with a Philips EM400 at 100 kV. A subsequent (kinematical) least-squares refinement with electron intensities yielded slightly improved co-ordinates for the 11 heavy atoms in the structure. Chemical analysis of several crystallites by EDX is in agreement with the formula Cs 0.44Nb 2.54W 2.46O 14. Moreover, the structure was independently determined by Rietveld refinement from X-ray powder data obtained from a multi-phasic sample. The compound crystallises in the orthorhombic space group Pbam with refined lattice parameters a = 27.145 ( 2 ) , b = 21.603 ( 2 ) , and c = 3.9463 ( 3 ) Å . Comparison of the framework structure from electron diffraction with the result from Rietveld refinement shows an average agreement for the heavy atoms within 0.09 Å.

Radiative association of He+ with H2 at temperatures below 100 K

The paper presents a theoretical study of the low-energy dynamics of radiative association processes in the He+ + H2 collision system. Formation of the triatomic HeH2(+) ion in its bound rotation-vibration states on the potential-energy surfaces of the ground and of the first excited electronic states is investigated. Close-coupling calculations are performed to determine detailed state-to-state characteristics (bound <-- free transition rates, radiative and dissociative widths of resonances) as well as temperature-average characteristics (rate constants, photon emission spectra) of the two-state (X <-- A) reaction He+(2S) + H2(X1sigma(g)+) --> HeH2(+)(X2A') + h nu and of the single-state (A <-- A) reaction He+(2S) + H2(X1sigma(g)+) --> HeH2(+)(A2A') + h nu. The potential-energy surfaces of the X- and A-electronic states of HeH2(+) and the dipole moment surfaces determined ab initio in an earlier work [Kraemer, Spirko, and Bludsky, Chem. Phys. 276, 225 (2002)] are used in the calculations. The rate constants k(T) as functions of temperature are calculated for the temperature interval 1 < or = T < or = 100 K. The maximum k(T) values are predicted as 3.3 x 10(-15) s(-1) cm3 for the X <-- A reaction and 2.3 x 10(-20) s(-1) cm3 for the A <-- A reaction at temperatures around 2 K. Rotationally predissociating states of the He+-H2 complex, correlating with the upsilon = 0, j = 2 state of free H2, are found to play a crucial role in the dynamics of the association reactions at low temperatures; their contribution to the k(T) function of the X <-- A reaction at T < 30 K is estimated as larger than 80%. The calculated partial rate constants and emission spectra show that in the X <-- A reaction the HeH2(+)(X) ion is formed in its highly excited vibrational states. This is in contrast with the vibrational state population of the ion when formed via the (X <-- X) reaction He(1S) + H2(+)(X2sigma(g)+) --> HeH2(+)(X2A') + h nu.

Phase transformations and phase stability of the AlCuFe alloys with low-Fe content

Phase transformation and microstructure of the AlCuFe alloys of the approximate compositional range of 20–50 at.% Cu and 1–10 Fe at.% have been investigated for annealed samples by means of differential thermal analysis, magneto-thermal analysis, scanning electron microscopy, electron probe analysis and powder X-ray diffraction. Representative phase transformations categorized as polymorphic, discontinuous precipitation, quasi-binary eutectoid, and ternary transition reaction (U-type) phase transformation are presented. These phase transformations are found to have a common feature, which is characterized by a dissolution of a primitive CsCl-type cubic phase and a formation of a face-centered orthorhombic phase. The crystal structures of the cubic and orthorhombic phases are determined from the powder diffraction data using routines for indexing DICVOL, for intensity extraction and ab initio structure determination EXPO and for Rietveld refinement FULPROF. A face-centered orthorhombic cell ( a=8.1530(3), b=14.1370(4), c=10.0736(4), Vol=1161.0(7), Z=4, at room temperature) with a starting structural model of ζ 1-Al 3Cu 4 (space group Fmm2, Z=4) approximates the observed pattern of powder sample quenched from 620 °C fairly well. Refined orthorhombic cell dimensions are obtained by in situ high-temperature X-ray diffraction at 463, 553 and 636 °C. These phase transformations are sensitive to the heat treatment and the alloy composition. They can be suppressed at moderate cooling rates. The metastable structures for both slowly cooled and as-cast alloys are found to contain the cubic phase replacing the equilibrium orthorhombic phase.

Comprehensive conformational analysis of N-acetyl- l-tryptophane- N-methylamide. An ab initio and DFT study

A comprehensive conformational analysis has been carried out on N-acetyl- l-tryptophane- N-methylamide. The complete set of minima has been located on the Potential Energy Hypersurface (PEHS) using ab initio (RHF/6-31G(d)) and DFT (B3LYP/6-31G(d)) calculations. Previous ab initio structure determinations at the RHF/3-21G level of theory resulted in 36 different structures. In the present work, a total of 35 and 34 different conformations were obtained at RHF/6-31G(d) and DFT (B3LYP/6-31G(d)) levels, respectively. Diamide conformers, similar to structural building units of the right-handed helix (α L) as well as of polyproline II type structures (ε L) were found. However, C 7 eq (γ L) and extended C 5 (β L) conformations were the preferred forms for this compound. Sidechain structural (i.e. χ 1 and χ 2 conformer interconversions) are also discussed in this paper.

Ab‐initio Powder Structure Determination of Dichloro[1,2‐ethanediylbis(iminomethylene)bis(phosphonato)]trizinc Dihydrate

The reaction of zinc chloride with 1,2-ethanediylbis(iminomethylene)bis(phosphonic acid) in acidic conditions yieldeddichloro[1,2-ethanediylbis(iminomethylene)bis(phosphona-to)]trizinc dihydrate, Zn3Cl2(HO3PCH2NHCH2CH2NHCH2-PO3H)2·2 H2O which crystallizes in the monoclinic system and space group P21/n, with the unit cell parameters a = 9.94316(4), b = 10.44577(5), c = 24.3240(1) A, β = 90.003(1)°, and Z = 4. The crystal structure was determined ab initio from its powder pattern using the programs EXPO and GSAS. The zinc atoms are in tetrahedral environment and form 16-membered rings with the phosphonate groups. The structure is clearly different from that of the corresponding Cd complex in that the Cd is sixfold coordinated and of different ligand to metal ratio. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

Approaching the basis set limit for transition metal compounds with highly polar bonds: A benchmark coupled-cluster study of the ScF3 and FeF3 molecular structures and spectra

The molecular equilibrium geometries, quadratic and cubic force constants, vibrational frequencies, and infrared intensities of scandium and iron trifluorides are determined ab initio with a sequence of atomic natural orbital basis sets using the CCSD(T) treatment of electron correlation. The largest basis set of spdf ghi quality contains 462 contracted Gaussian functions. Relativistic corrections are applied to compute the equilibrium geometries and vibrational frequencies. The cubic force constants are used to estimate vibrational corrections to the effective r(g) internuclear distances determined in the gas electron diffraction experiments. The computed molecular properties are extrapolated to the complete basis-set limit. The predicted values are compared to the available experimental data; uncertainties and inconsistencies in these data are then discussed.

Rate constants for D + C 2H 4 → C 2H 3D + H at high temperature: implications to the high pressure rate constant for H + C 2H 4 → C 2H 5

The shock tube technique with H- and D-atom atomic resonance absorption spectrometry detection has been used to study the reaction, D + C 2 H 4 → C 2 H 3 D + H over the temperature range, 1153–1616 K. The rate constants for this reaction were found to be temperature dependent with k = (2.56 ± 0.46) × 10 −10 exp (−2797 ± 239K/ T) cm 3 molecule −1 s −1 with the errors being at the one standard deviation level. The present data have been combined with earlier lower temperature determinations, and the joint database has been examined with theory that includes both an ab initio determination of the potential energy surface and an evaluation of the rate constants using the RRKM theory. Similar calculations have been made for the analogous all-H reaction. For both isotopic combinations, the agreement between theory and experiment is good, allowing a new estimate from theory for the high-pressure limit for H + C 2H 4 → C 2H 5 of 0.420 × 10 −15 T 1.75 exp (−604.9 K/ T) cm 3 molecule −1 s −1 for 200–2000 K. Since the D + C 2H 4 measurements reported here are the only high temperature measurements for either isotopic combination, the new high-pressure limiting estimate should be the best available at high temperatures.

Identification of possible Lewis acid sites on the β-AlF3(100) surface: an ab initio total energy study

Strong Lewis acid catalysts are widely used in a variety of industrial processes including Cl/F exchange reactions. Aluminium fluorides (AlF3) have great potential for use in such reactions. Despite the importance of the surface in the catalytic process little is known about the detailed atomic scale structure of AlF3 surfaces. In the current study we employ state of the art total energy calculations based on hybrid-exchange density functional theory to predict the composition and structure of the (100) surface of beta-AlF3 for the first time. We examine six possible terminations of the beta-AlF3 (100) surface and demonstrate that there are two relatively low energy terminations that result in the formation of under co-ordinated Al3+ ions at the surface. Such under co-ordinated ions are expected to be strong Lewis acid sites. This is the first ab initio determination of the atomic scale structure of such sites on the surface of beta-AlF3.

Structure solution of zeolites from powder diffraction data

AbstractThis article reviews methods in structure determination of zeolites from powder diffraction data. First, examples of different model building techniques are discussed. Then the applications and limitations of conventional direct methods in zeolite structure solution are examined. Methods for partitioning overlapping peak intensities are also discussed, and examples are given to illustrate improvements in structure elucidation when these techniques are applied.Ab initiostructure determination of zeolites from powder data has made great progress within the past 10 years. In particular, the developments of the ZEFSAII, FOCUS, and XLENS algorithms have allowed rapid structure solutions of zeolites, in some cases a few days after their initial discoveries.

Studying the structure of metal-organic polymers using in-house powder X-ray diffraction data: structural transformations induced by thermal treatment

Abstract The use of X-ray powder diffraction for the structure determination of inorganic, organic and metal-organic compounds has grown impressively over the last ten years. In supramolecular chemistry, the knowledge of the three-dimensional structure of a material is essential for the discussion of its macroscopic behaviour, and as a result the design of new functionalized materials. The ab initio crystal structure determination of previously unknown metal-organic compounds is still rare but is a field of high interest and activity. Here we describe the formation of 1D coordination polymers and the phase transformation processes that lead to the formation of 3D polymers on heating, accompanied by colour changes. The reaction of pyrazine-2,5-dimethyl-3,6-dicarboxylic acid with first row transition metal salts lead to the formation of coordination polymers always in the form of microcrystalline powders. With manganese and nickel salts isostructural 1D coordination polymers were obtained. With zinc chloride and copper chloride isomorphous 1D coordination polymers were obtained. The thermal decomposition of the nickel and copper polymers were studied and it was shown that on the loss of the coordinated water molecules new 3D coordination polymers could be obtained. In both the 1D and 3D coordination polymers the metal atoms have octahedral geometry in N2O4 environments. The crystal structures of all six complexes have been determined from powder X-ray diffraction data. Crystal data: (1) crystal symmetry monoclinic [space group P21/c, a = 7.4645(1), b = 8.9472(2), c = 7.6166(1) Å, β = 92.198(2)°]; (2) crystal symmetry orthorhombic [space group Pmna, a = 7.4060(2), b = 7.1857(2), c = 9.0661(2) Å]; (3) crystal symmetry monoclinic [space group P21/c, a = 6.9376(9), b = 7.1306(12), c = 8.5852(20) Å, β = 113.299(18)°]; (4) crystal symmetry orthorhombic [space group Pbcn, a = 9.0593(2), b = 7.4410(1), c = 14.6697(2) Å]; (5) crystal symmetry orthorhombic [space group Pbcn, a = 8.9727(1), b = 7.2354(1), c = 15.0444(2) Å]; (6) crystal symmetry monoclinic [space group P21/c, a = 6.9133(4), b = 7.9927(6), c = 8.2084(6) Å, β = 110.066(6)°].