Ab Initio Determination Research Articles

Novel microporous zirconium silicate (K 2ZrSi 3O 9·2H 2O) from high temperature phase transformation

A new microporous zirconosilicate K 2ZrSi 3O 9·2H 2O (AV-15) has been prepared by high-temperature phase transformation at 910 °C. Its structure has been determined ab initio from powder X-ray diffraction data. The unit cell is orthorhombic, space group C222 1 (no. 20), Z=4 with cell dimensions: a=8.105(3), b=10.684(5), c=12.030(5) Å, V=1041.76(7) Å 3. The framework connection of AV-15 is essentially the same as the previously reported sodium stannosilicate AV-10 while the locations of potassium and water molecules in the former are quite different from those of the sodium and water molecules in AV-10. In AV-10 sodium and water molecules form a sinucoidal chain, while potassium and water molecules build up a linear chain in AV-15. The water molecules in AV-15 are lost on heating with a typical zeolitic behaviour. SEM shows that the particle sizes and habits of AV-15 and parent umbite material are the same. The 29Si MAS NMR spectrum of AV-15 displays two resonances at ca. −89.4 and −90.1 ppm in a 1:2 intensity ratio. Thermogravimetry analysis confirms the existence of water in this material.

Synthesis and Crystal Structure from X-ray Powder Diffraction Data of Two Zirconium Diphosphonates Containing Piperazine Groups

Two new zirconium aminophosphonates have been obtained by reaction of Zr(IV) with piperazine-N,N'-bis(methylenephosphonate) building blocks. Their crystal structure has been determined ab initio from X-ray powder diffraction data collected with a conventional diffractometer. Although prepared in similar conditions, their composition and crystal structure is markedly different. Compound 1, of formula Zr(2)H(4)[(O(3)PCH(2))(2)N(2)C(4)H(8)](3)·9H(2)O, has a three-dimensional structure (trigonal, space group R3 (No. 148), a = 19.9400(9) Å, c = 9.5728(6) Å, Z = 3), made of infinite inorganic chains of ZrO(6) octahedra and PO(3)C tetrahedra, running along the c-axis direction, connected by piperazine groups in the ab plane, and generating channels running along the c axis. Compound 2, of formula ZrF(2)(O(3)PCH(2))(2)(NH)(2)C(4)H(8), has a pillared-layered structure (monoclinic, space group P2(1)/c (No. 14), a = 8.7148(2) Å, b = 8.1731(1) Å, c = 9.0134(2) Å, β = 105.175(1)° Z = 2) in which inorganic layers, made of the connectivity of Zr octahedra and P tetrahedra, are covalently connected by piperazine groups, that act as pillars. The effect of the various synthesis parameters is discussed. A probable structure directing parameter seems to be the pH value of the starting precipitation solution, that can influence the protonation of N atoms of piperazine moiety.

YNi and its hydrides: Phase stabilities, electronic structures and chemical bonding properties from first principles

Within density functional theory, establishing the equations of states of YNi in two different controversial structures in the literature, leads to determine the orthorhombic FeB-type as the ground state one with small energy difference. For YNiH 3 and YNiH 4 hydrides crystallizing in the orthorhombic CrB-type structure the geometry optimization and the ab initio determination of the H atomic positions show that the stability of hydrogen decreases from the tri- to the tetra- hydride. New states brought by hydrogen within the valence band lead to its broadening and to enhanced localization of metal density of states. The chemical bonding analysis shows a preferential Ni–H bonding versus Y–H.

An experimental study of the Fe–Sn–Zr ternary system at 900 °C

The partial isothermal section of the Fe–Sn–Zr system at 900 °C reported in Ref. [7] was completed. As compared with this section, three new ternary compounds were evidenced (Y, C36 and Fe6Sn6Zr), one compound previously reported with a homogeneity domain (X) was shown to consist in fact of two separate compounds with close compositions (X′ and X″). The crystal structure of the previously reported N phase was determined ab initio from powder diffraction data.

Solution structure of the N-terminal transactivation domain of ERM modified by SUMO-1

ERM is a member of the PEA3 group of the Ets transcription factor family that plays important roles in development and tumorigenesis. The PEA3s share an N-terminal transactivation domain (TADn) whose activity is inhibited by small ubiquitin-like modifier (SUMO). However, the consequences of sumoylation and its underlying molecular mechanism remain unclear. The domain structure of ERM TADn alone or modified by SUMO-1 was analyzed using small-angle X-ray scattering (SAXS). Low resolution shapes determined ab initio from the scattering data indicated an elongated shape and an unstructured conformation of TADn in solution. Covalent attachment of SUMO-1 does not perturb the structure of TADn as indicated by the linear arrangement of the SUMO moiety with respect to TADn. Thus, ERM belongs to the growing family of proteins that contain intrinsically unstructured regions. The flexible nature of TADn may be instrumental for ERM recognition and binding to diverse molecular partners.

Comment on “On the Electron Affinity of Nitromethane (CH3NO2)”

Nitrogen dioxide, NO2, being a stable free radical is a reactive gaseous species that is well-known as an anthropogenic pollutant; it is the major initiator of photochemical smog in the troposphere and is an ozone-depleting agent in the stratosphere.(1) Recently, following the successful multireference ab initio determination of an accurate value for the adiabatic electron affinity (AEA) of nitromethane, CH3NO2,(2) it has come to our attention that a similar high-level multiconfigurational convergence of theory and experiment has not been reported for NO2. The previous CH3NO2 study utilizing the N-state multiconfigurational quasi-degenerate perturbation theory of second order method, NS-MCQDPT,(3) showed that for CH3NO2 electron capture is dominated by the -NO2 group, and the level of theory in that study should also apply to gas-phase NO2.

ChemInform Abstract: X-Ray Powder Structure Determination of Li6P6O18×3H2O.

Abstract Preparation, characterization by X-ray diffraction, IR absorption, DTA-GTA analysis and ab-initio crystal structure determination are reported for a new lithium cyclohexaphosphate hydrate Li6P6O18·3H2O. It crystallizes in a trigonal (rhomboedral) cell (space group R 3¯m No 166, Z = 6) with a = 15.7442(2) A, c = 12.5486(2) A. X-ray powder diffraction pattern data was refined by Rietveld profile technique and lead to RBragg = 0.09. The crystal structure of Li6P6O18·3H2O is built up from [P6O18]6- ring anions, having the 3m symmetry, alternating along the 3¯ axis with rings made of six LiO4 tetrahedra and six LiO5 pseudo square pyramids sharing common edges.

ChemInform Abstract: Hydrothermal Synthesis and Characterization of an Ethylenediamine-Templated Mixed Valence Titanium Phosphate.

The mixed-valence compound TiIIITiIV(HPO4)4·C2N2H9·H2O (1) is synthesized hydrothermally from titanium powder, phosphoric and boric acids, and ethylenediamine. The compound is structurally stable up to 650 °C. It loses the template and the water molecule above 250 °C, all titanium becomes TiIV at 600 °C, and the result is the new compound TiIVTiIV(HPO4)4 (2). The structures of the two compounds were determined ab initio from powder diffraction data. Crystal data: TiIIITiIV(HPO4)4·C2N2H9·H2O, I41, a = 6.371(2), c = 16.571(1) A, V = 672.5(1) A3, Z = 2; TiIVTiIV(HPO4)4, I41/a, a = 6.335(2), c = 16.389(1) A, V = 657.7(1) A3, Z = 2. Both structures are of the open type, and the frameworks are nearly identical. Compound 2, τ-Ti(HPO4)2, is the first three-dimensional titanium hydrogen phosphate. Results of magnetization, TGA, BET, X-ray thermodiffractometry, and density measurements are also presented.

Four New Dysprosium and Neodymium Octamolybdate Hydrates: Assembly of RE2(Mo8O27) Sheets and Topotactic Transformations

Four new Dy and Nd hydrated octamolybdate materials have been prepared: [Dy(2)(H(2)O)(12)](Mo(8)O(27)) x 8 H(2)O, [Dy(2)(H(2)O)(6)](Mo(8)O(27)), [Nd(2)(H(2)O)(12)](Mo(8)O(27)) x 6 H(2)O, and [Nd(2)(H(2)O)(6)]Mo(8)O(27) x 3 H(2)O. They adopt one known and three new structure types, which we have determined ab initio from powder X-ray diffraction data. The four compounds contain the same basic structural building block, in the form of RE(2)Mo(8)O(27) (RE = Dy, Nd) chains, which are arranged differently for the two rare earths in the fully hydrated precursor materials. [Dy(2)(H(2)O)(12)](Mo(8)O(27)) x 8 H(2)O comprises isolated Dy(2)Mo(8)O(27) chains assembled in a zigzag manner along the a axis with interspersed crystallized water molecules, which differs from the parallel arrangements of isolated Nd(2)Mo(8)O(27) chains in [Nd(2)(H(2)O)(12)](Mo(8)O(27)) x 6 H(2)O. Partial dehydration of the two precursors leads to new phases [Dy(2)(H(2)O)(6)](Mo(8)O(27)) and [Nd(2)(H(2)O)(6)]Mo(8)O(27) x 3 H(2)O, respectively, prior to complete dehydration, which leads to initially amorphous and eventually crystalline rare-earth molybdenum mixed metal oxides. Both initial transformations occur topotactically. Partial dehydration of the Dy phase condenses the assembly of the Dy(2)Mo(8)O(27) chains principally along the a axis, leading to a 3-dimensional (3D) framework, with each Dy bridging two (Mo(8)O(27))(6-) sheets in the product. The partial dehydration of the Nd precursor condenses the assembly of Nd(2)Mo(8)O(27) chains along the [110] axis, leading to a 3D framework where each Nd bridges three (Mo(8)O(27))(6-) units. Both new dysprosium octamolybdates adopt noncentrosymmetric polar structures in space group P2(1) and are second harmonic generation (SHG) active.

Ab-initio determination of X-ray structure factors and the Compton profiles of CdO

X-ray structure factors and Compton profiles of CdO are presented in this work. The theoretical calculations are performed employing the first-principles linear combination of atomic orbitals (LCAO) method using the CRYSTAL code. The computations are made considering the Perdew–Burke–Ernzerhof (PBE) correlation energy functional and Becke's ansatz for the exchange. The computed X-ray structure factors for B1 structure are compared with the available experimental data. To compare the averaged theoretical Compton profile, first ever measurement on polycrystalline CdO is reported using 5Ci 241Am Compton spectrometer. The ionic model calculations have been used to estimate charge transfer in CdO. The agreement is, however, better with the LCAO calculation. The first-principles calculations of equilibrium lattice constants, bulk moduli and its pressure derivative of competing B1 and B2 phases of CdO are also reported and compared with the available results. The computed transition pressure for B1 → B2 structural phase transition is in good agreement with the experimental findings. Moreover, the electronic band structures show that B1 phase has indirect band gap of 0.43 eV in reasonable agreement with the experiments and B2 phase exhibits negative band gap of 0.9 eV.

Structure-Function Study of the N-terminal Domain of Exocyst Subunit Sec3

The exocyst is an evolutionarily conserved octameric complex involved in polarized exocytosis from yeast to humans. The Sec3 subunit of the exocyst acts as a spatial landmark for exocytosis through its ability to bind phospholipids and small GTPases. The structure of the N-terminal domain of Sec3 (Sec3N) was determined ab initio and defines a new subclass of pleckstrin homology (PH) domains along with a new family of proteins carrying this domain. Respectively, N- and C-terminal to the PH domain Sec3N presents an additional alpha-helix and two beta-strands that mediate dimerization through domain swapping. The structure identifies residues responsible for phospholipid binding, which when mutated in cells impair the localization of exocyst components at the plasma membrane and lead to defects in exocytosis. Through its ability to bind the small GTPase Cdc42 and phospholipids, the PH domain of Sec3 functions as a coincidence detector at the plasma membrane.

Generation and performance of special quasirandom structures for studying the elastic properties of random alloys: Application to Al-Ti

The performance of special-quasirandom structures (SQSs) for the description of elastic properties of random alloys was evaluated. A set of system-independent 32-atom-fcc SQS spanning the entire concentration range was generated and used to determine ${C}_{11}$, ${C}_{12}$, and ${C}_{44}$ of binary random substitutional AlTi alloys. The elastic properties of these alloys could be described using the set of SQS with an accuracy comparable to the accuracy achievable by statistical sampling of the configurational space of $3\ifmmode\times\else\texttimes\fi{}3\ifmmode\times\else\texttimes\fi{}3$ (108 atom, ${C}_{44}$) and $4\ifmmode\times\else\texttimes\fi{}4\ifmmode\times\else\texttimes\fi{}4$ (256 atom, ${C}_{11}$ and ${C}_{12}$) fcc supercells, irrespective of the impurity concentration. The smaller system size makes the proposed SQS ideal candidates for the ab initio determination of the elastic constants of random substitutional alloys. The set of optimized SQS is provided.

Ab initio determination of geometries and vibrational characteristics of building blocks of organic superconductors: 4,5-Ethylenedithio-1,3-dithiole-2-thione, and 4,5-ethylenedithio-1,3-dithiole-2-one

RHF and DFT calculations were carried out to study the optimized molecular geometries and vibrational characteristics of the 4,5-ethylenedithio-1,3-dithiole-2-thione (EDT-DTT) and 4,5-ethylenedithio-1,3-dithiole-2-one (EDT-DTO) molecules and their radical cations and anions. It is found that the anionic radical of the EDT-DTO molecule is unstable. Both the neutral molecules and their radical cations have non-planar structures with C 2 symmetry while the radical anion of the EDT-DTT molecule has non-planar structure with C 1 symmetry. It is found that the most of the vibrational characteristics of the radicals are similar to their corresponding neutral molecules, however, for some of the modes significant changes are noticed. As a result of anionic radicalization of EDT-DTT, the IR intensity and Raman activity increase and Raman band becomes polarized for both the CH 2 twisting modes. Drastic enhancements in the Raman activity and reduced IR intensity are noticed for the C S/O stretching mode in going from neutral molecules to their radical ions consistent with charge separation along this bond. The C S and C C stretching wavenumber changes are consistent with corresponding bond length changes in going from neutral to their radical ions.

Synthesis, structure and solid state NMR analysis of a new templated titanium(III/IV) fluorophosphate

Abstract The title compound MIL-131 (MIL stands for Material from Institut Lavoisier) was prepared hydrothermally (4 days, 473 K, autogenous pressure) in the presence of an organic base (N((CH2)2NH2)3). The structure of MIL-131 or TiIIITiIV(OH)F4(HPO4)·(PO4)·(N((CH2)2NH3)3) has been determined ab initio from X-Ray synchrotron powder diffraction data using simulated annealing methods and was refined in the triclinic space group P-1 (no. 2). MIL-131 exhibits a one-dimensional structure built up from inorganic chains of corner sharing TiO5(OH) titanium(III) octahedra and PO4 and HPO4 phosphate tetrahedra, related to TiO2F4 titanium octahedra. Protonated triamine cations are located between the inorganic motifs, and interact strongly with the mineral network through hydrogen bondings both with terminal fluorine atoms and hydroxo or oxo groups. Multinuclear solid state NMR has allowed a clear attribution of the protons, fluoride, and phosphate groups environment within the framework of MIL-131. The large values of chemical shift anisotropy together with the absence of any 13C NMR response confirmed the presence of paramagnetic titanium(III) species deduced from the crystal structure. Finally, 2D MAS 1H-31P CP-HETCOR NMR correlation experiment gives some insight on the nature of the intra-framework hydrogen bonding. Crystal data for MIL-131: a = 14.109(1) A, b = 8.462(3) A, c = 7.179(1) A, α = 93.772(1)°, β = 96.566(2)°, γ = 98.004(1)°, V = 840.36(2) A3, z = 2.

Direct Space Methods for Powder X-ray Diffraction for Guest−Host Materials: Applications to Cage Occupancies and Guest Distributions in Clathrate Hydrates

Structural determination of crystalline powders, especially those of complex materials, is not a trivial task. For non-stoichiometric guest-host materials, the difficulty lies in how to determine dynamical disorder and partial cage occupancies of the guest molecules without other supporting information or constraints. Here, we show how direct space methods combined with Rietveld analysis can be applied to a class of host-guest materials, in this case the clathrate hydrates. We report crystal structures in the three important hydrate crystal classes, sI, sII, and sH, for the guests CO(2), C(2)H(6), C(3)H(8), and methylcyclohexane + CH(4). The results obtained for powder samples are found to be in good agreement with the experimental data from single crystal X-ray diffraction and (13)C solid-state NMR spectroscopy. This method is also used to determine the guest disorder and cage occupancies of neohexane and tert-butyl methyl ether binary hydrates with CH(4) in the structure H clathrate hydrates. The results are found to be in good agreement with the results from the (13)C solid-state NMR and molecular dynamics simulations. It is demonstrated that the ab initio crystal structure determination methodology reported here is able to determine absolute cage occupancies and the dynamical disorder of guest molecules in clathrate hydrates from powdered crystalline samples.

Crystal structures of three intermetallic phases in the Mo–Pt–Si system

The crystal structures of three ternary Mo–Pt–Si intermetallic compounds have been determined ab initio from powder X-ray diffraction data. All three structures are representative of new structure types. Both the X (MoPt 2Si 3, Pmc2 1, oP12, a=3.48438(6), b=9.1511(2), c=5.48253(8) Å) and Y (MoPt 3Si 4, Pnma, oP32, a=5.51210(9), b=3.49474(7), c=24.3090(4) Å) phases derive from PtSi (FeAs type) structure while the Z phase (ideal composition Mo 32Pt 20Si 16, refined composition Mo 29.9(2)Pt 21.0(3)Si 17.1(1), Cc, mC68, a=13.8868(3), b=8.0769(2), c=9.6110(2) Å, β=100.898(1)°) present similarities with the group of Frank-Kasper phases.

Strong deviations from jellium behavior in the valence electron dynamics of potassium

We present experimental and ab initio theoretical determination of the dynamics of valence electrons in potassium by investigating the dynamical structure factor at nonvanishing momentum transfers. The spectra show large deviations from a jellium-type behavior due to the presence of $d$-type states above the Fermi level. In particular, we identify two well-defined interband excitations that have a direct correspondence with the density of states above the Fermi level.

Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations

Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical λ-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.

Topotactic Transformation of the Cationic Conductor Li4Mo5O17 into a Rock Salt Type Oxide Li12Mo5O17

Intercalation of lithium in the ribbon structure Li4Mo5O17 has been achieved, using both electrochemistry and soft chemistry. The ab initio structure determination of the “Mo−O” framework of Li12Mo5O17 shows that the [Mo5O17]∞ ribbons keep the same arrangement of edge sharing MoO6 octahedra and the same orientation as in the parent structure but that a topotactic antidistortion of the ribbons appears, as a result of the larger size of Mo4+ in “Li12” compared to Mo6+ in “Li4”. On the basis of bond valence calculations, it is observed that 12 octahedral sites are available for Li+ in the new structure so that an ordered hypothetical rock salt type structure can be proposed for Li12Mo5O17. After the first Li insertion, a stable reversible capacity of 100 mA·h/g is maintained after 20 cycles. A complete structural reversibility leading back to the ribbon type Li4Mo5O17 structure is obtained using a very low rate of C/100. The exploration of the Li mobility in those oxides shows that Li4Mo5O17 is a cationic conductor with σ = 10−3.5 S/cm at 500 °C and Ea = 0.35 eV.

Ab initiocalculation of Feshbach resonances in cold atomic collisions:s- andp-wave Feshbach resonances inL6i2

We present a model applicable to cold diatomic collisions and solve the close-coupled equations for the particular ${^{6}\text{L}\text{i}}_{2}$ system. Feshbach resonances are determined ab initio for both $s$ and $p$ waves. The $s$-wave scattering lengths are reported for all possible hyperfine states as a function of magnetic field strengths between 0 and 1500 G. In addition, $p$-wave scattering lengths are calculated for selected hyperfine states. Matrix elements for the hyperfine, Zeeman, and rotational Hamiltonian were worked out by the use of the molecular Hund's case (a) basis set. All relevant matrix elements are reported. The short-range hyperfine interaction has been included in the calculations, and its effect on the scattering length are investigated. Hyperfine parameters were obtained from separate ab initio calculations.