Lubomir Smrcok

Refinement of the crystal structure of Cronstedtite-1T

The crystal structure of cronstedtite-2H2 was refined in a hexagonal cell, space group P63, Z = 2, using two acicular crystals from Wheal Maudlin, Cornwall, England, and from Pribram, Czech Republic. The Wheal Maudlin sample has the chemical composition

Ab initio periodic Hartree-Fock study of lizardite 1T

\left( {{\rm{Fe}}_{2.291}^{2 + }{\rm{Fe}}_{0.709}^{3 + }} \right)\left( {{\rm{S}}{{\rm{i}}_{1.298}}{\rm{Fe}}_{0.707}^{3 + }{\rm{A}}{{\rm{l}}_{0.004}}} \right){{\rm{O}}_5}{\left( {{\rm{OH}}} \right)_4}

HYDROGEN BONDING AND VIBRATIONAL SPECTRA IN KAOLINITE-DIMETHYLSULFOXIDE AND -DIMETHYLSELENOXIDE INTERCALATES –A SOLID-STATE COMPUTATIONAL STUDY

(Fe2.2912+Fe0.7093+)(Si1.298Fe0.7073+Al0.004)O5(OH)4 and the Příbram sample has the composition

A new rietveld refinement of κ-Al2O3

\left( {{\rm{Fe}}_{2.269}^{2 + }{\rm{Fe}}_{0.731}^{3 + }} \right)\left( {{\rm{S}}{{\rm{i}}_{1.271}}{\rm{Fe}}_{0.724}^{3 + }{\rm{A}}{{\rm{l}}_{0.005}}} \right){{\rm{O}}_5}{\left( {{\rm{OH}}} \right)_4}

Crystal and electronic structure of aqua(N-salicylidene-methylester-L-glutamato)Cu(II) monohydrate

(Fe2.2692+Fe0.7313+)(Si1.271Fe0.7243+Al0.005)O5(OH)4. The results of refinements are as follows: a = 5.500(1), c = 14.163(2) Å, V = 371.08(8) Å3, R = 3.83%, from 381 independent reflections, and a = 5.4927(1), c = 14.1481(2) Å, V = 369.70(4) Å3, R = 4.77%, from 1088 independent reflections for the Wheal Maudlin and Příbram samples, respectively. The best Fovs.Fc agreement was achieved when the structure was interpreted as merohedral twin; several possible twinning laws are discussed. The cronstedtite layer consists of one tetrahedral sheet and one octahedral sheet. There is one octahedral (M1) position, occupied by Fe only, and two tetrahedral (T1, T2) positions in the structure. Refinement of occupancy of tetrahedral sites led to values Si:Fe = 0.45:0.55(1) (Wheal Maudlin) and 0.432:0.568(8) (Příbram) in T1, and Si: Fe = 0.99:0.01(1) (Wheal Maudlin) and 0.888:0.112(7) (Příbram) in 72. Whereas the size of T1 is reasonable (average dT1-O = 1.693 Å (Wheal Maudlin), 1.691 Å (Příbram)), T2 is unusually large: (dT2-O= 1.740 Å (Wheal Maudlin), 1.737 Å (Příbram)) with respect to the small or almost zero Fe content. As an explanation, an alternative structure model comprising a certain amount of vacancies in T2 is presented. The tetrahedral rotation angle α is highly positive (+12.1° and +12.5° for the Wheal Maudlin and Příbram samples, respectively), and the layer belongs to the Franzini type A. Distortion parameters of octahedra and tetrahedra are given for both samples. One hydrogen atom engaged in the hydrogen bond was located in the Wheal Maudlin sample.

Pseudo-merohedrally twinned praseodymium hexacyanoferrate(III) tetrahydrate

Abstract A periodic ab initio Hartree-Fock LCAO study was performed on the 1:1 sheet silicate lizardite, Mg3Si2O5(OH)4, which has P31m symmetry. A total of 258 atomic orbitals were described using double-zeta-quality basis sets augmented with polarization d (Si, Mg, O) and p (H) functions. Density of states and electron charge-density maps were calculated to investigate the electronic properties. The majority of the valence states are composed of O and Si atomic orbitals with little contribution from H atoms. Calculations showed that although there are about 0.5|e| in Si d and about 0.1|e| in Mg d orbitals, the population of O d orbitals is negligible. The maps of charge density show that interlayer hydrogen bonds fix adjacent 1:1 layers. Positions of the main O peaks in projected density of states evaluated for both three-dimensional (3D) and two-dimensional (2D) calculations were influenced by layer-to-layer interactions, especially hydrogen bonds.

1,4-diazabicyclo[2.2.2]octane-1,4-diium dihydrogen phosphate monohydrate from X-ray and neutron data

The aims of this study were to obtain accurate structural information on the dimethyl sulfoxide (DMSO) and dimethylselenoxide (DMSeO) kaolinite intercalates, paying close attention to the hydrogen-bond geometries, and to provide a detailed interpretation of the individual vibrational modes of intercalates under study and relate their energies to the formation of the hydrogen bonds. Accurate positions of all the atoms in the structures of kaolinite:dimethylsulfoxide (K:DMSO) and kaolinite:dimethylselenoxide (K:DMSeO) intercalates have been obtained by the total energy minimization in solid state at density functional theory (DFT) level of the theory. The bond distances and angles in the kaolinite 1:1 layer are in good agreement with those reported in the most recent single-crystal refinement of kaolinite. Computed geometries of DMSO and DMSeO agree well with the high-quality diffraction data and independent theoretical ab initio calculations. The organic molecules are fixed in the interlayer space mainly by three moderately strong O-H⋯O hydrogen bonds, of different strengths, with the O⋯O contact distances being within 2.739–2.932 Å (K:DMSO) and 2.681–2.849 Å (K:DMSeO). Substantially weaker C-H⋯O and O-H⋯S(Se) contacts play only a supporting role. The optimized atomic coordinates were used to calculate the individual vibrational modes between 0 and 4000 cm−1. The maximum red shifts of the OH-stretching modes caused by the formation of the O-H⋯O hydrogen bonds were 407 cm− (K-DMSO) and 537 cm−1 (K-DMeSO), respectively. The Al-O-H bending modes are spread over the large interval of 100–1200 cm−1, but the dominant contributions are concentrated between 800 and 1200 cm−1. Theoretically calculated energies of the OH- and CH-stretching modes show good agreement with the previously published figures obtained from the infrared and Raman spectra of these intercalates.

Prediction of crystal structures of two monosaccharides by potential energy minimisation

Abstract Rietveld refinement and the final model for pure κ-alumina are presented. The starting model was obtained through total energy calculations based on first principles. The resulting geometry parameters are within intervals of expected values for octahedral and tetrahedral coordina-tions. This result thus serves as a validation of the compu-tational approach as a useful alternative to classical methods in the first step of structure determination.

Intramolecular hydrogen bond and proton transfer in 3-(2-benzimidazolylthio)-2,4-pentanedione. Crystallographic evidence and theoretical calculations

Abstract The absolute structure of the title compound, CuNC13H17O7, has been determined. The crystal structure consists of the molecular units Cu(N-sal-5-met-L-glu)(H2O) connected by a three-dimensional network of hydrogen bonds. The coordination polyhedron in the complex is approximately square-pyramidal with a pentacoordinated Cu(II) atom. The base of the pyramid is formed by nitrogen and oxygen atoms belonging to the molecule, while the apex of the pyramid contains a weakly bonded oxygen atom of the carboxylic group of another molecule. The B3LYP/SVP method and basis set in Gaussian98 was used for quantum chemical calculation of the nature of Cu–X (X = O, N) bonds. While the calculated dissociation energy of the weakly bonded crystalline water is only 17.2 kJ/mol, the bonding energy of the water molecule coordinating to the Cu atom is 62.3 kJ/mol.

(E)-Methyl 2-[(2-fluorophenyl)aminomethylene]-3-oxobutanoate: X-ray and density functional theory (DFT) study.

Crystals of the title compound, diaquahexa-mu-cyano-ferrate(III)praseodymium(III) dihydrate, Pr[Fe(CN)(6)].4H(2)O or [PrFe(CN)(6)(H(2)O)(2)].2H(2)O, are twinned with three components. The Pr atom is coordinated by eight atoms, viz. six N and two symmetry-related water O atoms. The Pr polyhedron (Pr has site symmetry m2m, Wyckoff position 4c) is linked to an FeC(6) octahedron (Fe located on a site with imposed 2/m symmetry, Wyckoff position 4b) through N atoms, forming an infinite array. The second (symmetry independent) water molecule lies on a mirror plane, is not included in coordination and is weakly hydrogen bonded to N atoms.