Accurate Crystal Structure Research Articles

Synthesis, Characterization, and Bonding Properties of Polymeric Fullerides AC70×nNH3 (A: Ca, Sr, Ba, Eu, Yb).

Reduction of C70 with alkaline earth and rare earth metals dissolved in liquid ammonia results in metal fulleride solvates AC70.nNH3 (A = Ca, Sr, Ba, Eu, Yb) containing linear polymeric, anionic chains infinity 1 [C70(2-)]. The compounds were characterised by means of Raman spectroscopy and single-crystal structure determination. The accurate crystal structure of [Sr(NH3)8]C70.3NH3, determined with atomic resolution, allowed for a comparison with results of quantum chemical calculations. The nature of the C-C bonds in the fulleride is analysed in detail leading to a model explaining the unexpected polymerisation of C70(2-).

Study of crystal structure at high temperature phase in KIO 3 crystal by synchrotron powder X-ray diffraction

The accurate crystal structure of the I-phase in KIO 3 crystal has been obtained at 530 K, for the first time, by the MEM/Rietveld analysis from high-energy X-ray powder-diffraction data. The crystal structure of the I-phase is the rhombohedral perovskite structure (space group R3m; Z=1). The MEM charge-density distributions reveal that the shorter I–O bond exhibits a covalent bonding character and others (I–K, K–O and longer I–O bonds) an ionic.

Synthesis, characterization, and bonding properties of polymeric fullerides AC70.nNH3 (A = Ca, Sr, Ba, Eu, Yb).

Reduction of C70 with alkaline earth and rare earth metals dissolved in liquid ammonia results in metal fulleride solvates AC70.nNH3 (A = Ca, Sr, Ba, Eu, Yb) containing linear polymeric, anionic chains infinity 1 [C70(2-)]. The compounds were characterised by means of Raman spectroscopy and single-crystal structure determination. The accurate crystal structure of [Sr(NH3)8]C70.3NH3, determined with atomic resolution, allowed for a comparison with results of quantum chemical calculations. The nature of the C-C bonds in the fulleride is analysed in detail leading to a model explaining the unexpected polymerisation of C70(2-).

Structural Change of Cu(HCOO) 2 ·4H 2 O Associated with the Antiferroelectric Phase Transition

An accurate x-ray crystal structure analysis and an incoherent inelastic neutron scattering measurement of Cu(HCOO) 2 4H 2 O have been performed above and below the antiferroelectric phase transition temperature T t = 235.5 K. We confirmed the water layer is disordered above T t but could not find the reported hydrogen site called H(6). The obtained structure below T t can be understood by the condensation of the disordered structure above T t . We conclude that the structural change at T t is induced by the hindered rotation of water molecules about the two kinds of the ordered O-H bonds.

Structural Change of Cu(HCOO) 2 ·4H 2 O Associated with the Antiferroelectric Phase Transition

An accurate x-ray crystal structure analysis and an incoherent inelastic neutron scattering measurement of Cu(HCOO) 2 ·4H 2 O have been performed above and below the antiferroelectric phase transition temperature T t = 235.5 K. We confirmed the water layer is disordered above T t but could not find the reported hydrogen site called H(6). The obtained structure below T t can be understood by the condensation of the disordered structure above T t . We conclude that the structural change at T t is induced by the hindered rotation of water molecules about the two kinds of the ordered O-H bonds.

Electronic Properties of the Axial Co−C and Co−S Bonds in B12 Systems − A Density Functional Study

The numerous accurate structural data of cobalamins now available allows us to optimize the geometry of these systems, based on a simplified model by using density functional theory (DFT) calculations. This approach, which reproduces the trend of the experimental distances derived from EXAFS and X-ray crystal structures in the corrin macrocycle, permit us to interpret the electronic properties in the NB3−Co−X axial system. In particular, the results are analyzed for cobalamins containing a sulfur ligand which exhibits a “regular” trans influence, i.e., when the Co−S bond shortens, the trans Co−NB3 bond lengthens. This feature appears in contrast with an anomalous effect (“inverse” trans influence) postulated a few years ago by analyzing the structural data of several alkylcobaloximes, LCo(DH)2R, a simple B12 model, and attributed principally to the electronic properties of the alkyl group R. The present study on the NB3−Co−S fragment does not indicate that the “inverse” trans influence is a general rule in cobalamins. The accurate crystal structures of the [(SO3)Cbl](NH4) and [(thiourea)Cbl](PF6) cobalamins based on synchrotron diffraction data at 100 K are also reported for comparison with the theoretical study. The former crystal structure, including one co-crystallized glycerol molecule, presents “for the first time” an ordered hydrogen-bonding pattern for the solvent molecules.

Electronic Properties of the Axial Co−C and Co−S Bonds in B12 Systems − A Density Functional Study

The numerous accurate structural data of cobalamins now available allows us to optimize the geometry of these systems, based on a simplified model by using density functional theory (DFT) calculations. This approach, which reproduces the trend of the experimental distances derived from EXAFS and X-ray crystal structures in the corrin macrocycle, permit us to interpret the electronic properties in the NB3−Co−X axial system. In particular, the results are analyzed for cobalamins containing a sulfur ligand which exhibits a “regular” trans influence, i.e., when the Co−S bond shortens, the trans Co−NB3 bond lengthens. This feature appears in contrast with an anomalous effect (“inverse” trans influence) postulated a few years ago by analyzing the structural data of several alkylcobaloximes, LCo(DH)2R, a simple B12 model, and attributed principally to the electronic properties of the alkyl group R. The present study on the NB3−Co−S fragment does not indicate that the “inverse” trans influence is a general rule in cobalamins. The accurate crystal structures of the [(SO3)Cbl](NH4) and [(thiourea)Cbl](PF6) cobalamins based on synchrotron diffraction data at 100 K are also reported for comparison with the theoretical study. The former crystal structure, including one co-crystallized glycerol molecule, presents “for the first time” an ordered hydrogen-bonding pattern for the solvent molecules.

Calculation of 13C chemical shifts in rna nucleosides: structure-13C chemical shift relationships.

Isotropic 13C chemical shifts of the ribose sugar in model RNA nucleosides are calculated using SCF and DFT-GIAO ab initio methods for different combinations of ribose sugar pucker, exocyclic torsion angle, and glycosidic torsion angle. Idealized conformations were obtained using structures that were fully optimized by ab initio DFT methods starting with averaged parameters from a collection of crystallographic data. Solid-state coordinates of accurate crystal or neutron diffraction structures were also examined directly without optimization. The resulting 13C chemical shifts for the two sets of calculations are then compared. The GIAO-DFT method overestimates the shifts by an average of 5 ppm while the GIAO-SCF underestimates the shifts by the same amount. However, in the majority of cases the errors appear to be systematic, as the slope of a plot of calculated vs experimental shifts is very close to unity, with minimal scatter. The values of the 13C NMR shifts of the ribose sugar are therefore sufficiently precise to allow for statistical separation of sugar puckering modes and exocyclic torsion angle conformers, based on the canonical equation model formulated in a previous paper.

Molecular mechanics simulations of charge-transfer molecular superconductors

We report a detailed computational lattice statics study of the organic superconducting charge-transfer BEDT-TTF salts, using molecular mechanics methods. Our calculations show that standard, transferable forcefields yield accurate crystal structures for these complex materials within the constant volume regime.

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.

Similarities and differences between cobalamins and cobaloximes. Accurate structural determination of methylcobalamin and of LiCl- and KCl-containing cyanocobalamins by synchrotron radiation.

The accurate crystal structure determinations of MeCbl (1), CNCbl.2LiCl (2), and CNCbl.KCl (3), based on synchrotron diffraction data collected at 100 K and using high-quality single crystals, are reported. Refinements gave R1 indices of 0.0834 (1), 0.0434 (2), and 0.0773 (3). The influence of the water of crystallization and ion content on the crystal packing of these and other cobalamins (XCbl) is discussed, and a relationship between the crystal packing and the corrin side chain conformations is presented. An analysis of the bond lengths within the corrin moiety, based on 13 accurate structures with several X groups, shows that the trend of the C-C and C-N distances can be interpreted in terms of electronic and steric factors. The variation in structural, NMR and IR spectroscopic, and electrochemical properties are compared with those of cobaloximes, the B12 model, when X is varied. This comparison indicates that the pi-back-donation from metal to the CN axial ligand and the transmission of the trans influence of the X ligand are more effective in cobalamins than in cobaloximes. These findings are consistent with a significantly greater availability of electron charge on Co in cobalamins, and, hence, a semiquantitative evaluation of the electronic difference between the cobalt centers in the two systems is allowed.

A Molecular Mechanics Force Field for Alkylcobaloximes, a Model of Vitamin B12 Coenzyme – Implications of Steric and Electronic Factors in the Co–C Bond Cleavage

Molecular mechanics force field constants have been derived for alkylcobaloximes, (alkyl)Co(DH)2L (DH = monoanion of dimethylglyoxime and L = planar N-donor ligand), implementing the AMBER force field. Atomic charges have been calculated by the semiempirical ZINDO/1 method. Stretching and bending constants have been calculated by the Badger and Halgren equations, with the introduction of simple functions for the description of the electronic influence of the axial ligands on the coordination geometry. 26 parameters have been optimized, by the Simplex method, to fit 4523 bond lengths and angles of 52 alkylcobaloxime accurate crystal structures. In spite of the oversimplification of the adopted method for the description of the electronic effects, this approach provides a good description of the metal coordination geometries. The root-mean-square deviations of the calculated bond lengths and angles from the experimental values average to 0.023 Å and 1.4°, respectively. The molecular mechanics results are discussed in terms of the steric properties of the axial ligands and correlated with their calculated cone angles. The force field has been used to analyse some conformational features of these compounds, such as the influence of the rotation of the axial ligands on their coordination geometry. The calculated energy for the Co–N rotational barrier agrees well with the experimetal ones derived from dynamic and saturation 1H-NMR spectroscopy in (alkyl)Co(DH)2(2-NH2-py). In order to have more experimental data for this analysis, the crystal structures of two new cobaloximes, (CH2Cl)Co(DH)2L with L = py, 1, and 1-Me-Im, 2) have been determined. The results of a conformational analysis on ribosyl-imidazole derivatives, taken as a suitable vitamin B12 coenzyme model, suggest that the 1-Me-imidazole-like ligands have a significantly greater rotation freedom with respect to the benzimidazole-like ones, but cause similar stretchings of the Co–C bond, and a significantly less stretching of the Co–N one. Implications for the recent findings on the binding mode of the coenzyme B12 in the enzyme active site are discussed.

Polysulfonylamines. CIX. 1,2,4-Triazolium di(methanesulfonyl)amidate

The first accurate crystal structure involving the discrete unsubstituted 1,2,4-triazolium cation is reported. In the title salt, C 2 H 4 N + 3 .C 2 H 6 NO 4 S - 2 , the cation is linked to five adjacent anions by a set of N-H…N/O hydrogen bonds and C-H…O interactions, one of the latter being remarkably short and acceptably linear [H…O 2.26 (2), C…O 3.046 (2) A, C-H…O 161 (2)°]. We suggest on the basis of bond lengths, hydrogen bonding and U values that the X-ray structure of C 2 H 4 N + 3 .Sb 2 F - 7 [Udovenko, Gorbunova, Zemnukhova, Mikhailov & Davidovich (1998). Koord. Khim. 24, 655-657; Russ. J. Coord. Chem. 24, 611-613] contains an incorrectly refined cation in which both C atoms have been assigned as N and two N atoms as C.

Experimental charge density and electrostatic potential in nicotinamide.

The accurate crystal structure of nicotinamide, 3-pyridinecarboxamide, was determined from X-ray and neutron diffraction experiments: C(6)H(6)N(2)O, M(r) = 122.13, monoclinic, P2(1)/c, Z = 4. The electron distribution at 150 K was determined by the maximum entropy method and the electrostatic potential in the crystal was calculated by Fourier convolution of the electron distribution. The electrostatic properties of the nicotinamide molecule depend on the molecular conformation. The asymmetric electrostatic potential field observed above and below the pyridine-ring plane is related to the rotation of the carboxamide group with respect to the pyridine plane. The positive potential peak at the C4 atom of the pyridine ring extends to the C=O-group side of the plane. The asymmetry of the potential on the C4 atom is consistent with the stereospecificity of hydride transfer in NAD(+)/NADH oxidoreduction.

Structures of Furanosides: Density Functional Calculations and High-Resolution X-ray and Neutron Diffraction Crystal Structures

Highly accurate and precise crystal structures of methyl R-D-arabinofuranoside, methyl ‚-D-ribofuranoside, methyl R-D-lyxofuranoside, and methyl R-D-xylofuranoside have been determined at 100 K by X-ray crystallography. The structures of methyl R-D-arabinofuranoside and methyl ‚-D-ribofuranoside have also been determined at 15 K by neutron diffraction. Equilibrium (re) geometries of the same compounds were computed by means of density functional methods using a variety of exchange-correlation functionals and a sequence of basis sets. The validity of the computed results was assessed by several criteria including agreement between computed and observed bond distances and bond angles, agreement between computed and observed ring conformations, and basis set convergence of the computed geometrical parameters. Particular reference was made to computed internal hydrogen bond parameters, which are especially sensitive to the quality of the theoretical treatment. Because of the intrinsic sensitivity of the conformation of the five-membered ring to bond lengths and bond angles, molecular mechanics and small basis set SCF treatments are wholly inadequate. Local density functional theory also fails because of a tendency to strongly underestimate internal hydrogen bond distances. When the B3LYP exchange-correlation functional is used, bond lengths and bond angles agree with the neutron diffraction values to within their experimental uncertainty and the ring conformation is qualitatively correct, as long as a basis set of at least double- œ plus polarization quality (such as cc-pVDZ) is used. Further expansion of the basis set leads to more accurate equilibrium bond lengths and bond angles but does not appreciably affect the ring conformation. For methyl R-D-arabinofuranoside, methyl ‚-D-ribofuranoside, and methyl R-D-xylofuranoside, there is very good correspondence between the best computed and observed ring conformations, even though some intermolecular hydrogen bonds in the crystal give way to internal hydrogen bonds in the predicted gas-phase structures. On the other hand, in the case of methyl R-D-lyxofuranoside, an O2H‚‚‚O4 internal hydrogen bond between the ring oxygen O4 and the hydroxyl hydrogen of a ring carbon (O2H) in the computed structure leads to a very large change of ring conformation from the northeast corner of the pseudorotation pathway (P ) 28°, crystal) to the southeast corner ( P ) 130°, computed).

Lattice-Dynamical Estimation of Atomic Displacement Parameters in Carbonates: Calcite and Aragonite CaCO3, Dolomite CaMg(CO3)2 and Magnesite MgCO3

Using crystallographic information and empirical potentials derived from fitting the vibrational frequencies of all the substances under study, together with those of a group of silicates and oxides, a Born–von Karman rigid-ion lattice-dynamical model has been applied to the whole Brillouin zone in calcite, aragonite (α- and β-CaCO3, respectively), magnesite (MgCO3) and dolomite [CaMg(CO3)2]. The Raman and IR spectra are satisfactorily reproduced and interpreted by these calculations; there is also very good agreement with atomic anisotropic displacement parameters (a.d.p.'s) derived from accurate crystal structure refinement by various authors and with the experimental values of thermodynamic functions over a wide range of temperatures. On these vibrational grounds, the stability of calcite with respect to aragonite at high temperature can be accounted for.

First Accurate Molecular and Crystal Structure of the Meisenheimer Complex of 2,4,6-Trinitrobenzene

The first accurate and reliable molecular and crystal structure of the Meisenheimer complex of 2,4,6-trinitrobenzene (potassium (1,4-dioxolane)-2-spiro-1′-2′,4′,6′-trinitrocyclohexadienide) has been obtained by X-ray diffraction. The C–NO2 bond length for the substituent in the para position of the six-membered ring is shorter than for the other ones, and the bond lengths in the unsaturated parts of the anion are not equal. These facts indicate an essential contribution of the 1,4-diene geometry of the ring as well as of the aci resonance forms of the nitro groups to the structure of the anion.

MSLS, a Least-Squares Procedure for Accurate Crystal Structure Refinement from Dynamical Electron Diffraction Patterns

In X-ray crystallography, a least-squares structure refinement is used to two purposes: to prove the correctness of the proposed model and to improve it. In electron crystallography, the same tool would be desirable. However, the standard programs for least-squares structure refinement used in X-ray diffraction may give wrong results using electron diffraction data because the kinematically calculated diffracted intensity is not valid for the interaction of electrons and crystals thicker than about 20 Å for strong scatterers. In this paper, a new approach is presented that overcomes this problem and in addition takes into account all the advantages contained in dynamic scattering. The multislice method, well known in high-resolution electron microscopy (HREM), was combined with a least-squares algorithm, resulting in the multislice least-squares (MSLS) procedure. Experiments show that the atomic positions obtained by the new procedure are of the same accuracy as those obtained from single-crystal X-ray diffraction. However, the size of the single crystals used is much smaller (diameters down to ±100 Å). Also, light-atom positions can be determined with high precision by using data sets from crystal areas with different thicknesses. The multislice refinement gave good results up to 150 to 400 Å depending on the composition of the crystal, with R values based on the intensities of less than 5%. An additional advantage of the approach is that some extra quantities (e.g. crystal thickness, crystal orientation) can be refined at the same time.

Cytldlne Cyclic (3′, 5′) Monophosphate: Cyclic Nucleotide With a Non-Characteristic Ribose Ring Conformation

Cytidine 3′,-5′-cyclic phosphate (cCMP) occurs in nature and has growth stimulatory activity on L-1210 cells. The initiation of cell growth by cCMP, under conditions where CAMP, cGMP and cUMP delay the onset of proliferation suggests that cCMP may play a regulatory role in the cell metabolism. It has been reported that in 3′,5′-cyclic nucleotides, the phosphate ring fused to the furanose ring resuicts the conformation of the furanose ring to the twist form C(3′) endo C(4′) exo (3T4), in contrast to the C(2′) endo C(3′) endo (2T3) and C(3′) endo C(2′) exo (3T2) twist forms normally found in nucleotides and nucleosides. We have carried out an accurate crystal structure of cCMP and found that the furanose ring in cCMP has the C(3′) endo C(2′) exo conformation (3T2), with a pseudo rotation amplitude (P) of 44° and phase angle τm of 12°. cCMP is in low anti conformation (XCN = 15.4°) and O(5′) has the fixed g conformation. The phosphate ring is constrained to the chair conformation, as in other cyclic nucleotides. The two exocyclic P-O bond distances are short (1.489, 1.476Å) and the ring angle at N(3) is large (125.2°) suggesting that the molecule in the solid state is a zwitterion with a plus charge on N(3). The crystals are hydrated and highly unstable. The three water molecules are highly disordered in ten locations. The crystals of cCMP 3H2O are hexagonal, a = 16.294(3), b = c = 11.099(4)Å, space group P61, final R value is 0.067 for 1620 reflections 230.

Derivation of Class II Force Fields. 4. van der Waals Parameters of Alkali Metal Cations and Halide Anions

A critical survey of previously reported van der Waals parameters for alkali metal cations and halide anions is presented. A new set of force field parameters is proposed, derived by fitting the experimental lattice constants and lattice energies of 20 ionic alkali halide crystals. These parameters are constrained to satisfy two relationships connecting the ions with the isoelectronic noble gasesthe relative van der Waals radii R* and the coefficients of the London dispersion energies C6using the experimentally determined noble gas van der Waals parameters. In addition to reproducing physical trends in common with atoms of isoelectronic species, the present parameters predict more accurate crystal structures and energies and, when combined with a molecular force field for water, also quite accurate gas-phase ion−water interaction energies and aqueous solution structures compared to the computed results previously reported by other authors.