Experimental determination of electrostatic properties of Na-X zeolite from high resolution X-ray diffraction.

High-resolution single crystal X-ray diffraction is used for the first time to obtain the charge density distribution in dehydrated Na-X zeolite. The electron density is extracted according to the Hansen & Coppens multipolar-model, from which Pval-κ-type atomic charges are derived. In order to compare the experimental electron density with theoretical calculations on zeolites and other minerals, a topological analysis is performed to derive AIM charges and electron density properties at bond critical points. The results are compared with that described in the literature. Finally, the electrostatic potential is evaluated in a periodic, mean field approach (disordered cation distribution in the Fd3[combining macron] space group) and for a given distribution of the cations (space group P1). The electrostatic energy is, then, derived in the neighbourhood of cation sites where the molecules are usually physisorbed.

Combined charge and spin density experimental study of the yttrium(III) semiquinonato complex Y(HBPz3)2(DTBSQ) and DFT calculations.

High-resolution X-ray diffraction and polarized neutron diffraction experiments have been performed on the Y-semiquinonate complex, Y(HBPz3)2(DTBSQ), in order to determine the charge and spin densities in the paramagnetic ground state, S = (1/2). The aim of these combined studies is to bring new insights to the antiferromagnetic coupling mechanism between the semiquinonate radical and the rare earth ion in the isomorphous Gd(HBPz3)2(DTBSQ) complex. The experimental charge density at 106 K yields detailed information about the bonding between the Y3+ ion and the semiquinonate ligand; the topological charge of the yttrium atom indicates a transfer of about 1.5 electrons from the radical toward the Y3+ ion in the complex, in agreement with DFT calculations. The electron density deformation map reveals well-resolved oxygen lone pairs with one lobe polarized toward the yttrium atom. The determination of the induced spin density at 1.9 K under an applied magnetic field of 9.5 T permits the visualization of the delocalized magnetic orbital of the radical throughout the entire molecule. The spin is mainly distributed on the oxygen atoms [O1 (0.12(1) mu B), O2(0.11(1) mu B)] and the carbon atoms [C21 (0.24(1) mu B), C22(0.20(1) mu B), C24(0.16(1) mu B), C25(0.12(1) mu B)] of the carbonyl ring. A significant spin delocalization on the yttrium site of 0.08(2) mu B is observed, proving that a direct overlap with the radical magnetic orbital can occur at the rare earth site and lead to antiferromagnetic coupling. The DFT calculations are in good quantitative agreement with the experimental charge density results, but they underestimate the spin delocalization of the oxygen toward the yttrium and the carbon atoms of the carbonyl ring.

Recovering experimental and theoretical electron densities in corundum using the multipolar model: IUCr Multipole Refinement Project.

This electron-density study on corundum (alpha-Al2O3) is part of the Multipole Refinement Project supported by the IUCr Commission on Charge, Spin and Momentum Densities. For this purpose, eight different data sets (two experimental and six theoretical) were chosen from which the electron density was derived by multipolar refinement (using the MOLLY program). The two experimental data sets were collected on a conventional CAD4 and at ESRF, ID11 with a CCD detector, respectively. The theoretical data sets consist of static, dynamic, static noisy and dynamic noisy moduli of structure factors calculated at the Hartree-Fock (HF) and density functional theory (DFT) levels. Comparisons of deformation and residual densities show that the multipolar analysis works satisfactorily but also indicate some drawbacks in the refinement. Some solutions and improvements during the refinements are proposed like contraction or expansion of the inner atomic shells or increasing the order of the spherical harmonic expansion.

Refinement of framework disorder in dehydrated CaA zeolite from single-crystal synchrotron data.

An accurate knowledge of zeolite structure is required for understanding their selective sorption capacities and their catalytic properties. In particular, the positions of the exchangeable cations and their interactions with the framework are essential. The present study deals with the accurate crystal structure determination of a fully exchanged and fully dehydrated CaA zeolite (Ca(48)Al(96)Si(96)O(384), Fm3c, a = 24.47 A) using single-crystal high-resolution synchrotron X-ray diffraction [(sin straight theta/lambda)(max) = 1.4 A(-1)]. It is shown that cation exchange severely distorts the skeleton, especially around the O2 atom. The high-resolution synchrotron data reveal that this latter O atom is disordered and lies out of the mirror plane it occupies in other A-type zeolites. This feature is related to that observed for Ca(2+) cations.

Electron density and electrostatic properties of two peptide molecules: tyrosyl-glycyl-glycine monohydrate and glycyl-aspartic acid dihydrate.

The electron density and electrostatic properties of Tyr-Gly-Gly and Gly-Asp molecules have been determined from high-resolution X-ray diffraction data at 123 K. Topological properties of the charge distribution are discussed and compared with those derived from other experimental studies on peptide molecules, and the characteristics of the (3,-1) critical points of the C=O, C-N, C-C bonds are analysed. Crystal data for Tyr-Gly-Gly: C13H17N3O5.H2O, Mr = 313, orthorhombic, P2(1)2(1)2(1), Z = 4, T = 123 +/- 2 K; lattice parameters: a = 7.984 (2), b = 9.535 (3), c = 18.352 (5) A, V= 1397.1 (6) A3, Dx = 1.49 g cm(-3), mu = 1.2 cm(-1) for lambdaMo = 0.7107 A. Crystal data for Gly-Asp: C6H10N2O5.2H2O, Mr = 212, orthorhombic, P2(1)2(1)2(1), Z = 4, T = 123 +/- 2 K; lattice parameters: a = 9.659 (1), b = 9.672 (1), c = 10.739 (1) A, V= 1003.3 (4) A3, Dx = 1.40 g cm(-3), mu = 1.3 cm(-1) for lambda(Mo)= 0.7107 A.

Electron density in ammonium dihydrogen phosphate: non-uniqueness of the multipolar model in simple inorganic structures.

X-ray and neutron diffraction data of a single crystal of ammonium dihydrogen phosphate have been used for the determination of the electron density using multipolar expansion of the density around each nucleus. As the ammonium group was found to be nearly neutral from unconstrained multipole refinement, constrained refinements have been performed with the charge of the ammonium group ranging from zero to one. On the other hand, the expansion of the radial functions of the phosphorus atom was varied. All refinements led to almost the same agreement factors and residual densities. The consequences of such uncertainties on the topology of the electron density are discussed, namely the topology of the P-O bond critical point.

Topological analysis of the electron density in hydrogen bonds.

Topological analysis of the experimental electron density rho(r) in hydrogen-bonding regions has been carried out for a large number of organic compounds using different multipole models and techniques. Relevant systematic relationships between topological properties at the critical points and the usual geometric parameters are pointed out. Results involving X-ray data only and joint X-ray and neutron data, as well as special hydrogen bonding cases (symmetric, bifurcated, peptide bonds, etc.) are included and analysed in the same framework. A new classification of hydrogen bonds using the positive curvature of the electron density at the critical point [lambda(3)(r(CP))] is proposed.

Structure of tris(cyclohexylammonium) phosphoenolpyruvate monohydrate and crystal chemistry of phosphoenolpyruvates.

The crystal structure of (C6H11NH3+)3. Pep3-.H2O, where Pep3- = (O-)2P(O)-O-C(CH2)-CO2-, is reported and the systematic structural variations among 19 crystallographic occurrences of H3Pep, H2Pep-, HPep2- and Pep3- species, which are important phosphate donors in the ATP cycle of bioenergetics, are reviewed. Tris(cyclohexylammonium) phosphoenolpyruvate monohydrate, (C6H11NH3+)3.-[O3POC(CH2)CO2]3-.H2O, M(r) = 483.6, m.p. 418-420K; T = 296(1)K; orthorhombic, P2(1)2(1)2(1); a = 16.7042(5), b = 24.4881 (6), c = 6.38910 (10) A; V = 2613.49(11) A3, Z = 4, Dx = 1.23, Dm = 1.22 mg mm-3, mu = 0.14 mm-1 for lambda(MoK alpha) = 0.7107 A; F(000) = 1056 e; R(magnitude of F) = 0.0608 for 6056 hkl and hkl data with (sin theta)/lambda < or = 0.65 A-1.

Computational studies of crystalline H3PO4.

A polarized split-valence wavefunction was computed for the H3PO4 molecule at its neutron crystallographic valence geometry, and the wavefunction was used to map the molecular electron-density distribution and to simulate X-ray crystal structure factors for both static, at-rest and dynamic thermally averaged structures. The thermal vibrational averaging was approximated using anisotropic mean-square atomic displacements from approximately 300 K neutron diffraction data. The simulated X-ray data were used to test pseudoatom multipole modeling of the valence electron-density distribution, in particular, radial modeling of the M valence shell of the P atom, and deconvolution of the nonspherical density features from anisotropic vibrational smearing.

Experimental electron density in crystalline H3PO4.

X-ray diffraction data for H3PO4 crystals have been measured to dmin = 0.46 A resolution, and used to model the electron-density distribution with the hydrogen structure of the crystals adopted from an earlier neutron diffraction analysis. The molecule is asymmetric in the crystal with site symmetry 1 (C1), but the local symmetries of the pseudoatomic densities are, within experimental error, equivalent as they would be under idealized 3m (C3v) molecular symmetry. Although the experimental analysis entailed substantial problems with absorption and extinction corrections, the static deformation density from the experiment agrees very well with that from a polarized split-valence molecular orbital wavefunction for an isolated molecule with the crystallographic molecular geometry. Hydrogen bonding in the crystal polarizes the molecule's P==O acceptor group towards P(+)--O-, and appears to relocalize the lone-pair density of the P--OH donor groups. Crystal data: anhydrous orthophosphoric acid, H3PO4, M(r) = 98.00, room temperature, P2(1)/c, a = 5.7572 (13), b = 4.8310 (17), c = 11.5743 (21) A, beta = 95.274 (12) degrees, V = 320.55 (25) A3, Z = 4, dx = 2.030 mg mm-3, mu = 0.660 mm-1 for lambda(Mo K alpha) = 0.7107 A, F(000) = 200 e-, R(parallel F) = 0.026 for 3512 unique reflections.

Experimental evidence for the existence of non-nuclear maxima in the electron-density distribution of metallic beryllium. A comparative study of the maximum entropy method and the multipole refinement method.

The electron-density distribution (EDD) of metallic beryllium has been derived from the structure factors of Larsen & Hansen [(1984). Acta Cryst. B40, 169-179] using the maximum entropy method (MEM). Subsequent topological analysis reveals non-nuclear maxima (NNM) in the EDD. Plots of the gradient field of the electron density illustrates this finding. A possible critical-point network for the hexagonal close-packed (h.c.p.) structure of beryllium is suggested. It is thus demonstrated that it is possible to obtain detailed topological information about the electron density in metallic beryllium without the use of a structural model. In order to test the findings of the MEM, the same set of structure factors were analysed using the multipole refinement method (MRM). Use of the MRM also reveals NNM. The results of the two different approaches to electron-density analysis are contrasted and discussed. Expressed within the framework of the theory of atoms in molecules, our results suggest that the h.c.p. structure of beryllium has no Be atoms directly bonded to other Be atoms. The structure is held together through a three-dimensional network of bonds between the NNM and Be atoms as well as between different NNM. The topological analysis thus reveals that the beryllium structure has important interactions connecting Be atoms of different basal plane layers. The breaking of these interactions when forming a surface may explain the abnormally large expansion of the inter-layer distance in the beryllium surface structure.

Crystal chemistry of Mg2P2O7.nH2O, n = 0, 2 and 6: magnesium-oxygen coordination and pyrophosphate ligation and conformation.

The crystal structure of the hexahydrate has been determined and is compared with the known structures of the dihydrate and two forms of the anhydrous compound. Comparisons among the structures provide some insight as to the structural role of Mg2+ as a cofactor in the ATP-ADP hydrolysis reactions of bioenergetics. Crystal data for dimagnesium pyrophosphate hexahydrate: Mg2P2O7.6H2O, M(r) = 330.66, monoclinic, P2(1)/n, a = 7.189 (2), b = 18.309 (8), c = 7.665 (5) A, beta = 92.360 (14) degrees, V = 1008.1 A3, Z = 4, Dx = 2.18 mg mm-3, F(000) = 680, mu = 0.609 mm-1 for lambda(Mo K alpha) = 0.7107 A. R(magnitude of F) = 0.047 for 937 data.

Electron distributions in peptides and related molecules. 1. An experimental and theoretical study of N-acetyl-L-tryptophan methylamide.

The thermal vibrations and electron density of N-Ac-L-Trp-NHMe have been analyzed using single-crystal X-ray diffraction data measured at 103 K with Mo K alpha radiation to a resolution corresponding to (sin theta max)/ lambda = 1.17 A-1. Measurements of 10,527 reflections gave 4913 unique data [R(int)(magnitude of F2) = 0.019] of which 2641 had I greater than 3 sigma (I). A multipolar atomic density model was fitted [R(magnitude of F) = 0.028] in order to calculate phases for the crystal structure factors and map the valence-electron distribution. The phase problem for determining deformation densities by Fourier synthesis for noncentrosymmetric crystals is discussed. The experimental density agrees well with the theoretical density from an ab initio SCF molecular wave function calculated at the crystallographic molecular geometry with a split-valence basis set. Both the experimental and theoretical analyses confirm that the electron distribution is the same in the two different peptide groups in the molecule. Crystal data: C14H17N3O2, Mr = 259.31, orthorhombic, P2(1)2(1)2(1), Z = 4, F(000) = 522 e from 295 to 103 K; at 295 K, a = 8.152(2), b = 11.170 (2), c = 15.068 (3) A, V = 1372 A3, Dx = 1.26 mg mm-3; at 103 K, a = 8.209 (3), b = 11.016 (2), c = 14.760 (4) A, V = 1135 A3, Dx = 1.29 mg mm-3, mu = 0.083 mm-1 for lambda = 0.7107 A.