Ab Initio Determination Research Articles

Determination of symmetry reduced structures using a soft phonon analysis for magneticshape memory alloys (abstract only)

Ni2MnGa is a typical example of a Heusler alloy that undergoes a martensitictransformation. In the high temperature austenitic phase it has a cubicL21 structure, whereas below 200 K the symmetry is reduced by an orthorhombicdistortion. Despite lattice deformations of more than 6% and largestrains connected to this change, it is completely reversible. Therefore,Ni2MnGa serves as a shape memory compound. The fact thatNi2MnGa additionally orders ferromagnetically below 360 K makes the material particularly attractivefor applications in actuators and sensors. Nevertheless, its structural details in themartensitic phase are still a subject of much debate. Several shuffling structures havebeen observed experimentally. The temperature and magnetic field dependenttransformations between these structures need to be understood for improvement of themagnetic switching (e.g. operation with higher reliability and smaller magnetic fields).Our tool for identifying the stable structures and the low energy transition paths is thecalculation of free energy surfaces as functions of key reaction coordinates (e.g. the ratio c/a) in density functional theory. (The generalized gradient approximation to theexchange–correlation functional and the projector augmented wave approach implementedin VASP (Vienna Ab initio Simulation Package) were used in these investigations.) Thedifferent variants of the low symmetry orthorhombic structures lead to characteristicminima on this surface. However, the ab initio determination of the experimentallyobserved shuffling structures is challenging, due to the large phase space of possible atomicpositions and the small shuffling formation energies of only a few meV per unitcell. Hence, we used the quasiharmonic approximation in order to compute andanalyze phonon spectra. Starting with the symmetric structure of the austenite, theTA2 (TA standing for transverse acoustic) phonon dispersion shows a phonon softening alongthe [110] direction. We were able to extract detailed information about the type of thislattice instability from the eigenvectors of the unstable phonon modes. By setting up thecorresponding modulated harmonics in supercell calculations, we systematically andefficiently identified stable shuffling structures. The resulting structural phases (austenite,martensite, pre-martensite) allow us to assign and to interpret the experimentalobservations.

Ab initio determination of lattice dynamics and thermodynamics of β - BC 2N

Using the pseudopotential density functional method, an ab initio study has been performed to determine the lattice dynamics and thermodynamics of β-BC 2N, including phonon dispersion, phonon density of states, and thermodynamic properties. A considerable energetic overlap between the LO-, TO-, and LA-phonons is revealed in the phonon dispersion. The total phonon density of states shows four main regions arising from different relative motions among the B, C1, C2, and N atoms. The calculation shows that β-BC 2N has more vibration states in the low frequency region than diamond and hence, its heat capacity C v is greater than that of diamond. The Debye temperature Θ D of β-BC 2N, which determines the Debye stiffness, is found to be smaller and larger than those of diamond and c -BN, respectively.

Relativistic calculations of the lifetimes and hyperfine structure constants in 67Zn+

This work presents accurate ab initio determination of the magnetic dipole (M1) and electric quadrupole (E2) hyperfine structure constants for the ground and a few low-lying excited states in 67Zn+, which is one of the interesting systems in fundamental physics. The coupled-cluster (CC) theory within the relativistic framework has been used here in these calculations. Long-standing demands for a relativistic and highly correlated calculation like CC can be able to resolve the disagreements among the lifetime estimations reported previously for a few low-lying states of Zn+. The roles of different electron correlation effects in the determination of these quantities are discussed and their contributions are presented.

Crystal structure of [NBu4]2[Pd2{C4(COOMe)4}2(μ-OH)2] determined ab initio by charge flipping

The crystal structure of bis(tetra-n-butylammonium)bis(mu(2)-hydroxo)-bis(1,2,3,4-tetrakis(methoxycarbonyl)-1,3-butadiene-1,4-diyl)-di-palladium, [NBu4](2)[Pd-2{C-4(COOMe)(4)}(2) (mu-OH)(2)], was determined ab initio by X-ray single-crystal diffractometry using the charge flipping method. The compound crystallizes in the monoclinic system with P2(1/c) as space group and the following cell parameters: a = 12.8481(6) angstrom, b = 63.744(3) angstrom, c = 16.6102(8) angstrom, beta = 111.943(10). The asymmetric unit is formed by two molecules, and the unit cell contains eight molecules (Z=8) giving a density of 1.369 g cm(-3). The coordination around the Pd(II) atoms is approximately planar, the methoxycarbonyl groups at the alpha and beta positions relative to Pd are perpendicular and parallel to the palladacycle ring, respectively, and the {Pd(mu-O)}(2) core has a bent conformation. The structure closely resembles the features reported previously for other palladacyclopentadiene complexes. (C) 2007 Elsevier B.V. All rights reserved.

Structural characterization of anhydrous naloxone‐ and naltrexone hydrochloride by high resolution laboratory X‐ray powder diffraction and thermal analysis

The crystal structures of the analgesic compounds anhydrous naloxone and naltrexone hydrochloride were determined ab initio from high resolution laboratory X-ray powder diffraction data. Both compounds crystallize in the orthorhombic space group P2(1)2(1)2(1) with lattice parameters of a = 14.6588(10) A, b = 17.4363(9) A, c = 7.96200(22) A, and V = 2035.06(23) A(3) for naloxone hydrochloride and a = 15.4560(5) A, b = 14.9809(4) A, c = 7.84121(18) A, and V = 1815.58(11) A(3) for naltrexone hydrochloride. The crystal structure of anhydrous naloxone hydrochloride forms one-dimensional chains through hydrogen bonds. In the crystal structure of anhydrous naltrexone hydrochloride, two-dimensional sheets are formed by hydrogen bonds. The dehydration processes of naloxone hydrochloride dehydrate and naltrexone hydrochloride tetrahydrate was analyzed by DTA, DSC, TG, and MG.

Structure of calcium aluminate decahydrate (CaAl2O4·10D2O) from neutron and X-ray powder diffraction data

Calcium aluminate decahydrate is hexagonal with the space group P6(3)/m and Z = 6. The compound has been named CaAl(2)O(4).10H(2)O (CAH(10)) for decades and is known as the product obtained by hydration of CaAl(2)O(4) (CA) in the temperature region 273-288 K - one of the main components in high-alumina cements. The lattice constants depend on the water content. Several sample preparations were used in this investigation: one CAH(10), three CAD(10) and one CA(D/H)(10), where the latter is a zero-matrix sample showing no coherent scattering contribution from the D/H atoms in a neutron diffraction powder pattern. The crystal structure including the positions of the H/D atoms was determined from analyses of four neutron diffraction powder patterns by means of the ab initio crystal structure determination program FOX and the FULLPROF crystal structure refinement program. Additionally, eight X-ray powder diffraction patterns (Cu Kalpha(1) and synchrotron X-rays) were used to establish phase purity. The analyses of these combined neutron and X-ray diffraction data clearly show that the previously published positions of the O atoms in the water molecules are in error. Thermogravimetric analysis of the CAD(10) sample preparation used for the neutron diffraction studies gave the composition CaAl(2)(OD)(8)(D(2)O)(2).2.42D(2)O. Neutron and X-ray powder diffraction data gave the structural formula CaAl(2)(OX)(8)(X(2)O)(2).gammaX(2)O (X = D, H and D/H), where the gamma values are sample dependent and lie between 2.3 and 3.3.

Crystal Structure of the NS3 Protease-Helicase from Dengue Virus

Several flaviviruses are important human pathogens, including dengue virus, a disease against which neither a vaccine nor specific antiviral therapies currently exist. During infection, the flavivirus RNA genome is translated into a polyprotein, which is cleaved into several components. Nonstructural protein 3 (NS3) carries out enzymatic reactions essential for viral replication, including proteolysis of the polyprotein through its serine protease N-terminal domain, with a segment of 40 residues from the NS2B protein acting as a cofactor. The ATPase/helicase domain is located at the C terminus of NS3. Atomic structures are available for these domains separately, but a molecular view of the full-length flavivirus NS3 polypeptide is still lacking. We report a crystallographic structure of a complete NS3 molecule fused to 18 residues of the NS2B cofactor at a resolution of 3.15 A. The relative orientation between the protease and helicase domains is drastically different than the single-chain NS3-NS4A molecule from hepatitis C virus, which was caught in the act of cis cleavage at the NS3-NS4A junction. Here, the protease domain sits beneath the ATP binding site, giving the molecule an elongated shape. The domain arrangement found in the crystal structure fits nicely into an envelope determined ab initio using small-angle X-ray scattering experiments in solution, suggesting a stable molecular conformation. We propose that a basic patch located at the surface of the protease domain increases the affinity for nucleotides and could also participate in RNA binding, explaining the higher unwinding activity of the full-length enzyme compared to that of the isolated helicase domain.

X-ray powder study of cis-dichloridobis(methylamine)platinum(II)

The title compound, cis-[PtCl2(CH3NH2)2], was obtained from the reaction of K2PtCl4 with CH3NH2·HCl and CH3COOK. The single-crystal structure has been reported previously [Wimmer, Wimmer, Jaud, Johnson & Castan (1988). Inorg. Chim. Acta, 144, 25–30], but no three-dimensional coordinates are available. We have carried out an ab initio crystal structure determination using X-ray powder diffraction techniques. The crystal structure consists of discrete molecules, with the PtII atom in a slightly distorted square-planar coordination environment. The methyl groups lie on the same side of the plane defined by the two N and two Cl atoms. Molecules are connected via intermolecular N—H...Cl hydrogen bonds to form two-dimensional layers perpendicular to the b axis. The methylamine groups protrude from these layers, forming organic interlayers.

Theoretical calculations of hypersurfaces of the 13C chemical shift anisotropy in the C [dbnd]O⋯H [sbnd]N hydrogen bond and the benefit for the ab initio structure determination

We investigated the influence of structural changes on the anisotropic part of the carbonyl 13C chemical shift tensor in a model complex containing hydrogen bonded cyanuric acid and pyrrole. The model was chosen for its chemical resemblance to cyameluric acid. In the solid state this compound comprises three different hydrogen bonds which are well distinguishable based on the anisotropy parameters δ aniso and η of the carbonyl 13C atoms. The variation of six relevant structural variables in the model system produced hypersurfaces for the isotropic shift, δ aniso and η. Our goal was to investigate whether such surfaces can be used for the ab initio structure determination of hydrogen bonds. With a medium size basis set it could be shown that although the absolute values differ DFT describes the relative change in δ aniso and η close to the quality of MP2 calculations. Due to the high dimensionality of the hypersurface we had to reduce the number of variables in our study. We systematically created subsurfaces each described by three of the six variables and investigated their isolated influence on the NMR observables. We identified the most important structure parameters and on this base built a minimal model. For a fixed NO distance the hydrogen bond arrangement was altered by two angular variations and one dihedral distortion. In this model evidence was found that the η surfaces for different NO distances exhibit a uniform shape and can be transformed into one another by a simple shift and multiplication by a mean factor. Furthermore, the experimental parameters δ aniso and η of cyameluric acid were taken as a base for the extraction of structures from the hypersurfaces. δ aniso and η unequivocally selected ensembles of similar structure and the COHN arrangement in two of the three cyameluric hydrogen bonds could be predicted with good quality from the theoretical model. Our results show that it is possible to predict the distance and at least qualitatively the orientation in a hydrogen bond environment from an analysis of the anisotropic part of the 13C chemical shift tensor.

Novel Intermetallic Compound UFe5Si3: A New Room‐Temperature Magnet with an Original Atomic Arrangement.

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The charge flipping method: a new approach to solve periodic and aperiodic structures

The talk summarizes the current state of charge flipping, a recently developed and deceptively simple algorithm of ab initio structure determination [1,2]. This algorithm is iterative and works in dual spaces. Its operation is based on the presence and perturbation of large plateaus of low electron density, but not directly on atomicity or statistical phase relations. Such a working principle radically differs from that of classical direct methods, and offers complementary applications. Charge flipping can be used at different stages of the structure solution process. It can either operate in a truly ab inito manner, without utilizing any preliminary structural information (atom types, chemical composition or space group symmetry), or can be applied to complete a partially known structure or phase set, it can check the stability of a solution, but it can also be adapted to work as an ingredient of other dualspace schemes. The list of already successful structure solution cases includes periodic and aperiodic crystals using single crystal and powder diffraction data measured with X-ray and neutron radiation [3-12]. Apart from counting applications, the talk mainly deals with algorithmic issues: it describes the basic algorithm and its properties, introduces and compares new improvements of the iteration scheme in real and reciprocal space, helps to identify convergence by new figures of merit, defines the computational cost of a single solution and helps to find parameters that maximize the efficiency of the algorithm. It also discusses the present limitations of structure size, data completeness and of utilizing known information. Finally, we try to foretell what is the future of such an alternative among well-established direct methods. □This research was supported by OTKA 67980K.

Understanding the trend in the Curie temperatures ofCo2-based Heusler compounds:Ab initiocalculations

The Curie temperatures for the Heusler compounds Co{sub 2}TiAl, Co{sub 2}VGa, Co{sub 2}VSn, Co{sub 2}CrGa, Co{sub 2}CrAl, Co{sub 2}MnAl, Co{sub 2}MnSn, Co{sub 2}MnSi, and Co{sub 2}FeSi are determined ab initio from the electronic structure obtained with the local-density functional approximation and/or the generalized gradient approximation. Frozen spin spirals are used to model the excited states needed to evaluate the spherical approximation for the Curie temperature. The spherical approximation is found to describe the experimental Curie temperatures very well which, for the compounds selected, extend over the range from 95 to 1100 K; as a function of the valence electron count, they show an approximately linear trend which finds an explanation by our calculations.

Novel Intermetallic Compound UFe5Si3: A New Room-Temperature Magnet with an Original Atomic Arrangement

The new compound UFe5Si3 was prepared by rapid solidification of the melt using a splat cooling technique, followed by annealing at 1173 K for 10 days. Its crystal structure was determined ab initio from powder X-ray diffraction data. It crystallizes in the tetragonal space group P4/mmm, with lattice parameters at room temperature of a = 3.9298(3) A and c = 7.7133(6) A. The structure of UFe5Si3, which is new among intermetallic compounds, can be viewed as built up from an infinite three-dimensional framework of Fe and Si atoms defining along the a direction, tunnels of hexagonal sections, where the U atoms lie. Alternating and direct current magnetic measurements reveal that UFe5Si3 behaves as a hard ferromagnet with a Curie temperature of about 310 K. Measurements on magnetically oriented powder suggest that UFe5Si3 has a uniaxial anisotropy with c as the easy axis. The electrical resistivity decreases monotonously with decreasing temperature suggesting no other magnetic transition below 300 K. In line w...

Wannier functions and exchange integrals: The example ofLiCu2O2

Starting from a single band Hubbard model in the Wannier function basis, we revisit the problem of the ligand contribution to exchange and derive explicit formulas for the exchange integrals in metal oxide compounds in terms of atomic parameters that can be calculated with constrained LDA and $\mathrm{LDA}+\mathrm{U}$. The analysis is applied to the investigation of the isotropic exchange interactions of $\mathrm{Li}{\mathrm{Cu}}_{2}{\mathrm{O}}_{2}$, a compound where the Cu-O-Cu angle of the dominant exchange path is close to 90\ifmmode^\circ\else\textdegree\fi{}. Our results show that the magnetic moments are localized in Wannier orbitals which have strong contribution from oxygen atomic orbitals, leading to exchange integrals that considerably differ from the estimates based on kinetic exchange only. Using $\mathrm{LSDA}+\mathrm{U}$ approach, we also perform a direct ab initio determination of the exchange integrals $\mathrm{Li}{\mathrm{Cu}}_{2}{\mathrm{O}}_{2}$. The results agree well with those obtained from the Wannier function approach, a clear indication that this modelization captures the essential physics of exchange. A comparison with experimental results is also included, with the conclusion that a very precise determination of the Wannier function is crucial to reach quantitative estimates.

THE DETERMINATION OF ENERGY BY AB INITIO METHODS: ESTIMATION OF ERRORS AND SOME IMPROVEMENTS

This work presents a statistical analysis of errors in the ab initio determination of molecular energy. These sets of analyses have allowed us to separate the errors in systematic and random components and also to realize that differences between experimental data and theoretical calculations are larger than those initially suspected. Although there is a limit to how small this difference can be analyzed by our methods, procedures to improve ab initio molecular energies are proposed. This has been achieved by reducing the systematic error obtained by correlating the calculated results to the most accurate data (in this case CCSD (T)), as well as by reducing the random error by mixing the results of different standard procedures.

A practical scheme for ab initio determination of a crystal structure based on the Dirac equation

An applicable formulation of ab initio crystal structure determination based on the Dirac equation is presented. For this purpose, Dirac equation without regard to electron correlation effects is reduced to its spin-free one-component form by means of regular approximations, and then, connected to crystallographic notions. Thus, a relativistically valid structural description of a crystal structure is made possible by using single crystal X-ray diffraction data. The relativistic scheme was tested with a previously reported crystal structure containing heavy elements, and the results show that accuracy of the phase assignment process increases as the order of regular approximation is raised.

Redetermination of SrTe3O8from a hydrothermally grown single crystal

The crystal structure of the mixed-valence tellurium compound strontium ditellurate(IV) tellurate(VI) was redetermined from single-crystal data. The previous structural model, determined ab initio from powder X-ray diffraction data [Barrier et al. (2006). J. Solid State Chem. 179, 3484–3488], was confirmed, but with all atoms refined with anisotropic displacement parameters and with differences in individual Te—O bond lengths up to 0.05 A. The structure is composed of [Te3O8]∞2− chains that extend parallel to [001] and [110] to form a channel structure. Whereas one half of the channel is occupied by the Sr atoms in an eightfold coordination, the other half remains unoccupied, with the electron lone pairs of TeIV protruding into the empty space. Except for one O atom, all other atoms are on special positions: Sr (\overline{4}.. symmetry), Te1 (m..), Te2 (2/m..), O1 (m..) and O2 (m..).

Ab initio crystal structure of nickel(II) hydroxy-terephthalate by synchrotron powder diffraction and magnetic study

The structure of the new hybrid compound [Ni 3(OH) 2(tp) 2(H 2O) 4]·2H 2O (tp = C 8H 4O 4 2−) has been determined ab initio from synchrotron powder diffraction data and refined with the Rietveld method: space group P-1, a = 10.2077(6) Å, b = 8.0135(5) Å, c = 6.3337(4) Å, α = 97.70 (1)°, β = 97.21(1)°, γ = 108.77(1)°, D x = 2.124 g/cm 3, Rp = 0.045, R B = 0.095 (757 independent reflections). H atoms were placed geometrically and their position optimized by DFT calculation. The repeating structural unit is the chain [Ni(1)O 6] 2Ni(2)O 6, consisting of two edges sharing octahedrons related by the symmetry center and linked via μ3-OH to a vertex of Ni(2) octahedron. The Ni(1) coordination is ensured by two oxygen atoms from two water molecules, two OH and two oxygen atoms from carboxylate groups. The linkage of the chains by the tp anions forms infinite layers parallel to the (010) planes. Interchain hydrogen bonds between the water molecules coordinating the metal ensure the cohesion of the 2D structure. The structural and magnetic properties are compared with that of the 3D fumarate-based compound [Ni 3(OH) 2(fum) 2(H 2O) 4]·2H 2O (fum = C 4H 2O 4 2−).

Structures of three dehydration products of bischofite from in situ synchrotron powder diffraction data (MgCl2·nH2O; n = 1, 2, 4)

High-quality in situ synchrotron powder diffraction data have been used to investigate the decomposition products of bischofite in the temperature range 298 </= T </= 873 K. At least eight phases could be identified: MgCl(2).nH(2)O (n = 1, 2, 4 and 6), MgOHCl.nH(2)O (0 </= n </= 1.0), MgCl(2) and MgO. The crystal structures of three magnesium chloride hydrates MgCl(2).nH(2)O (n = 1, 2, 4) were determined ab initio, replacing published Rietveld refinements from low-quality powder diffraction data based on similarity criteria. MgCl(2).4H(2)O was found to be disordered and has been correctly determined for the first time. The crystal structures of bischofite and MgCl(2).4H(2)O consist of discrete Mg(H(2)O)(6) and MgCl(2)(H(2)O)(4) octahedra, respectively. The crystal structure of MgCl(2).2H(2)O is formed by single chains of edge-sharing MgCl(2)(H(2)O)(4) octahedra, while in the case of MgCl(2).H(2)O double chains of edge-sharing MgCl(H(2)O)(5) octahedra are found. The phases in the system MgCl(2)-H(2)O are intermediates in the technologically important process of MgO and subsequently Mg production. The same phases were recently found to be of key importance in the understanding of cracks in certain magnesia concrete floors.

The Non‐Centrosymmetric Borate Oxides, MBi2B2O7 (M: Ca, Sr).

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.