bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystal engineering in the gem-alkynol family: interplay between strong and weak interactions in structures of 2,3,5,6-tetrahalo[F,Cl,Br]-trans-1,4-diethynylcyclohexa-2,5-diene-1,4-diols
Authors: Madhavi N. N. L. , Desiraju Gautam R. , Bilton Claire , Howard Judith A. K. , Allen Frank H.
Published: July 2002

Structures of the title compounds are all mediated by strong cooperative arrangements of O—H...O hydrogen bonds, supported by a variety of weaker interactions which affect the type of O—H...O synthon that is formed. The tetrafluoro compound contains hexameric O—H...O synthons in a supramolecular chair conformation, together with C≡C—H...F interactions. However, the tetrachloro and tetrabromo compounds both form tetrameric O—H...O synthons. This dominant pattern is supported by halogen...halogen interactions having one C—Cl[Br]...Cl[Br] angle close to 180° and the other close to 90°, and by C≡C—H...Cl[Br] interactions.
Halogen trimer synthons in crystal engineering: low-temperature X-ray and neutron diffraction study of the 1:1 complex of 2,4,6-tris(4-chlorophenoxy)-1,3,5-triazine with tribromobenzene
Authors: Broder Charlotte K. , Howard Judith A. K. , Keen David A. , Wilson Chick C. , Allen Frank H. , Jetti Ram K. R. , Nangia Ashwini , Desiraju Gautam R.
Published: July 2002

The title complex has been studied using low-temperature X-ray (150 K) and neutron (100 K) diffraction. Molecules of the triazine host form a two-dimensional hexagonal network mediated by trigonally symmetric Cl3 synthons having Cl...Cl interactions of 3.441 (3) Å, a C—Cl...Cl angle of 165° and a Cl...Cl—C angle of 105°, close to the ideal values of 180 and 90°, respectively. The guest molecules are of an appropriate size to fit the hexagonal networks and interact with the host via C—H...π (phenyl) and C—Br...π (phenyl) interactions which stabilize the overall structure. Both C-donor bond vectors are directed more closely towards the mid-point (X) of an individual aromatic bond, rather than the ring centroid, with H...X 2.817 (9) Å and C—H...X 174.0 (9)°, and Br...X 3.353 (4) Å and C—Br...X 158.1 (2)°.
Superspace description of the structure of the composite crystal urea/n-octane at room temperature
Authors: Peral I. , Madariaga G. , Petricek V. , Breczewski T.
Published: July 2002

A structural model for the composite crystal urea/n-octane is proposed. Despite the lack of information from the largely disordered guest substructure, the final model is consistent with the collected diffraction pattern. The use of the superspace approach stresses the composite character of the inclusion compounds and makes easier a unified view of the whole urea/n-alkane family. In particular, a comparison between the octane and heptadecane derivatives shows a common pattern for the origin of the modulation of the guest chains based on the distribution of the NH_{2} groups within each tunnel wall.
Hydrated metal complexes of N-(6-amino-3,4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)glycinate: interplay of molecular, molecular–electronic and supramolecular structures
Authors: Low John N. , Moreno Sánchez Jose M. , Arranz Mascarós Paloma , Godino Salido M. Luz , López Garzon Rafael , Cobo Domingo Justo , Glidewell Christopher
Published: July 2002

The title anion, (C7H8N5O4)−, L
−, forms hydrated metal complexes with a range of metal ions M
+ and M
2+. Lithium and manganese(II) form finite molecular aggregates [Li(L)(H2O)3] (1) and [Mn(L)2(H2O)4].6H2O (4) in which the molecular aggregates are linked into three-dimensional frameworks by extensive hydrogen bonding. The sodium and potassium derivatives, [Na2(L)2(H2O)3] (2) and [K(L)(H2O)] (3) both form organic–inorganic hybrid sheets in which metal–oxygen ribbons are linked by strips containing only organic ligands: these sheets are linked by hydrogen bonds into three-dimensional frameworks. In (2) the metal–oxygen ribbon is built from pairs of edge-shared trigonal bipyramids linked by water molecules, while in (3) it consists of a continuous chain of vertex-sharing octahedra. The nitroso group in the anion acts as an η1 ligand towards Na+ and as an η2 ligand towards K+. In all cases the anion L
− shows the same unusual pattern of interatomic distances as the neutral parent LH.
Inclusion compounds of binaphthol with picolines: structures, selectivity and kinetics of desolvation
Authors: Nassimbeni Luigi R. , Su Hong
Published: July 2002

The crystal structures of the inclusion compounds formed between the host 2,2′-dihydroxy-1,1′-binaphthyl and the three picoline isomers have been elucidated and their lattice energies calculated. The selectivities of enclathration by the host have been measured by competition experiments. The thermal stabilities and activation energies of desolvation of the compounds have been determined. The kinetics of desolvation are correlated to the structures.
Influence of hydrogen bonding on the second harmonic generation effect: neutron diffraction study of 4-nitro-4′-methylbenzylidene aniline
Authors: Cole Jacqueline M. , Howard Judith A. K. , McIntyre Garry J.
Published: July 2002

A neutron diffraction study of the non-linear optical (NLO) material 4-nitro-4′-methylbenzylidene aniline (NMBA) is presented. NMBA exhibits a large macroscopic second-order NLO susceptibility, χ(2), and this study shows that hydrogen bonding is, in part, responsible for this. No hydrogen bonding was reported in the X-ray study [Ponomarev et al. (1977). Sov. Phys. Crystallogr.
22, 223–225], whereas the present work shows that C—H...X hydrogen bonds (where X = N, O or π) direct the nature of the three-dimensional lattice. C—H...X (X = N or O) hydrogen bonds are common; however, C—H...π hydrogen-bond motifs are relatively rare. Such intermolecular interactions help extend the molecular charge transfer into the supramolecular realm, the charge transfer originating as a consequence of the high level of molecular planarity and strong donor-to-acceptor interactions. Molecular planarity, coupled with the favourable nature of the hydrogen bonds, results in parallel stacking of molecules in both the a and c crystallographic directions with extremely close interplanar spacings. Such a combination of influential hydrogen-bonding characteristics accounts, in part, for the large second-order NLO output of the material since the phenomenon is so critically dependent upon the nature of the charge transfer.
Interplay between dipolar, stacking and hydrogen-bond interactions in the crystal structures of unsymmetrically substituted esters, amides and nitriles of (R,R)-O,O′-dibenzoyltartaric acid
Authors: Rychlewska Urszula , Warżajtis Beata
Published: July 2002

The compounds analysed are the O,O′-dibenzoyl derivatives of (R,R)-tartaric acid, asymmetrically substituted by ester, amide and nitrile groups. Benzoylation does not introduce drastic changes to the molecular conformation. All investigated molecules adopt the planar T conformation of the four-carbon chain with noticeably smaller departures from the ideal conformation than observed in the nonbenzoylated analogs. Primary and secondary amides always orient the C=O bond antiperiplanar (a) with respect to the nearest C*—O bond, while methylester groups adjust their conformation to that adopted by the amide substituent situated at the other end of the molecule. Tertiary amides and carboxyl groups place their carbonyls at the same side as the nearest C*—O bond (the s form), but often deviations from coplanarity of the two bonds are significant and higher than those observed in the nonbenzoylated series. The results presented demonstrate the importance of dipole/dipole interactions between CO and βC*H groups in stabilizing the molecular conformation, and between carbonyl groups in stabilizing crystal packing of the molecules that lack classical hydrogen-bond donor groups. An illustration is provided as to how a small change in mutual orientation of molecules arranged in a close-packed fashion causes a change in the character of intermolecular interactions from van der Waals to sandwich stacking between the benzoyloxy phenyls, and to dipolar between the benzoyloxy carbonyls. Hydrogen-bonded molecules tend to orient in a head-to-tail mode; the head-to-head arrangement being limited to cases in which terminal carbonyl groups are situated at one side of the molecule. The orientation of the benzoyloxy substituents with respect to the carbon main chain is such that the (O=)C—O—C—H bond system often deviates significantly from planarity.
Variable-temperature crystal structure studies of m-nitroaniline
Authors: Wójcik Grażyna , Holband Jolanta
Published: July 2002

The crystal structure of m-nitroaniline has been examined at several temperatures over the 90–350 K range. Thermal evolution of the lattice parameters reveals a weak anomaly at 110 K and an important one at 300 K. The thermal expansion coefficients have been calculated at several temperatures and the principal axes cross-sections of the tensor were drawn. The lattice contraction along the b axis direction has been observed. The rigid-body analysis including an attached rigid group has provided the values of the translation and libration tensors at temperatures studied. The results indicate that m-nitroaniline undergoes a glass transition around 130 K arising from freezing molecular librations and translations. From above 340 K the growing plasticity of the m-nitroaniline crystal results in the loss of X-ray diffraction reflections. This is probably a second-order phase transition. It is coupled with a considerable increase in the nitro group torsion amplitude, but the NH...O hydrogen bonds are preserved. Analysis of the temperature evolution of short intermolecular distances enabled us to consider the occurrence of reorienting aggregates of hydrogen-bonded molecules in the high-temperature plastic phase.
Systematic generation of all nonequivalent closest-packed stacking sequences of length N using group theory. Erratum
Authors: Thompson Richard M. , Downs Robert T.
Published: July 2002

In the paper by Thompson & Downs (2001) the last line in Table 1 is missing. The correct table is reprinted here.The two nonequivalent sequences for N = 4 and their symmetrical equivalentsABAB
ABAC
ACAC
ABCB
BABA
ACAB
BCBC
ACBC
CACA
BABC
CBCB
BACA
BCBA
BCAC
CACB
CABA
CBCA
CBAB
Novel, predicted patterns of supramolecular self-assembly, afforded by tetrameric R_4^4(12) rings of C
2 symmetry in the crystal structures of 2-hydroxy-1-cyclopentanecarboxylic acid, 2-hydroxy-1-cyclohexanecarboxylic acid and 2-hydroxy-1-cycloheptanecarboxylic acid
Authors: Kálmán Alajos , Fábián László , Argay Gyula , Bernáth Gábor , Gyarmati Zsuzsanna
Published: July 2002

Determination of the crystal structures of the homologous (1R*,2R*)-trans-2-hydroxy-1-cyclopentanecarboxylic acid (5T), (1R*,2S*)-cis-2-hydroxy-1-cyclohexanecarboxylic acid (6C) and (1R*,2S*)-cis-2-hydroxy-1-cycloheptanecarboxylic acid (7C) proved a predicted pattern of supramolecular close packing. The prediction was based on the common features observed in the crystal structures of six related 2-hydroxy-1-cyclopentanecarboxylic acids and analogous carboxamides [Kálmán et al. (2001). Acta Cryst. B57, 539–550]. This pattern is characterized by tetrameric R_4^4(12) rings of C
2 symmetry formed from dimeric R_2^2(12) rings. The C
2 symmetry of such tetramers is not common in the literature, usually they have Ci
symmetry. Both types of tetramers are formed from dimers with similar or opposite orientation. The R_2^2(12) dimers differ in their hydrogen bonds. In 5T the monomers are joined by a pair of O1—H...O2=C bonds, whereas in 7C they are joined by a pair of O3—H...O1-H bonds. In 6C 60% of the disordered R_2^2(12) dimers are similar to those in 7C, while 40% resemble those in 5T. Apart from these hydrogen-bonding differences and the ring-size differences, the three crystals exhibit isostructurality.
The Cambridge Structural Database: a quarter of a million crystal structures and rising
Authors: Allen Frank H.
Published: July 2002

The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500000 crystal structures by the year 2010.
Crystal Engineering Using Trisphenols. Three-Dimensional Hydrogen-Bonding Networks in 1,1,1-Tris(4-hydroxyphenyl)ethane, its Hydrated Adduct with 1,4-Diazabicyclo[2.2.2]octane (1/1/1) and its Adduct with Piperazine (4/3)
Authors: Ferguson G. , Bell W. , Coupar P. I. , Glidewell C.
Published: July 2002

In 1,1,1-tris(4-hydroxyphenyl)ethane, C20H18O3 (1), monoclinic la, a = 7.9781 (10), b = 18.558 (3), c = 11.1995 (13) Å, \beta–101.668 (9)°, with Z = 4, each of the hydroxyl groups acts as both a donor and an acceptor of hydrogen bonds of the type O—H...O. The molecules are thus connected into square nets, graph set R^4_4(38), pairs of which are then interwoven; the nets are themselves interconnected by further hydrogen bonds to give a continuous three-dimensional network. In 1,1,1-tris(4-hydroxyphenyl)ethane-l,4-diazabicyclo[2.2.2]octane–water (1/1/1), C20H18O3.C6H12N2.H2O (2), triclinic P\overline 1, a = 10.421 (2), b = 10.734 (2), c = 10.9756 (13) Å, \alpha = 76.645 (12), \beta 74.513 (11), \gamma = 89.305 (13)°, with Z = 2, the water molecules are linked to the trisphenol and the diamine units by O—H...O and O—H...N hydrogen bonds, respectively, to form a linear aggregate. These aggregates are linked into chains by the formation of O—H...N hydrogen bonds between the trisphenol and the neighbouring diamine; however, alongside hydrogen-bond formation between the trisphenol and the diamine, there is also partial transfer of a proton, so that the intra-chain links between trisphenol and diamine units are in fact a mixture of O—H...N and N—H...O hydrogen bonds. These chains in the [101] direction are cross-linked by further O—H...O hydrogen bonds, involving only trisphenol O atoms, which form chains in both the [010] and [001] directions, thus generating a continuous three-dimensional network. Adduct (3), 1,1,1-tris(4-hydroxyphenyl)ethane–piperazine (4/3), (C20H18O3)4.(C4H10N2)3, triclinic P\overline 1, a = 12.5049 (11), b = 12.7046 (10), c = 14.6226 (9) Å, \alpha = 113.738 (6), \beta = 100.839 (6), \gamma = 102.438 (7)°, with Z = 1, has two independent trisphenol molecules in general positions and three independent piperazine molecules lying about centres of inversion. The five independent components of the asymmetric unit are linked together by means of three O—H...N and one O—H...O hydrogen bonds to form an open aggregate containing no hydrogen-bonded rings. These aggregates are connected into three sets of interlinked chains in the [010], [001] and [\overline 110] directions: the [010] and [\overline 110] chains employ only O—H...O hydrogen bonds, while the [001] chains employ both O—H...N and N—H...O hydrogen bonds. Additionally, the inversion symmetry at each piperazine unit gives rise to further interlinks.
A New Structural Transformation Mechanism in Catalytic Oxides
Authors: Gai P. L.
Published: July 2002

During dynamic reduction of vanadyl pyrophosphate using in situ electron microscopy and diffraction under controlled reaction conditions, recurrent dislocation of atoms is observed, which leads to the formation of extended defects by a glide shear mechanism. Ordering of the glide shear defects leads to a new structure by transforming the orthorhombic vanadyl pyrophosphate into an anion-deficient tetragonal structure. These defects are formed close to the surface and the nature of the defects is such that they accommodate the misfit between the reduced surface layers containing anion vacancies and the underlying unreduced bulk. The glide shear planar defects (GS) essentially preserve anion vacancies and do not lead to a lattice collapse, and are distinct from the well known crystallographic shear planes (CS, which eliminate anion vacancies leading to lattice collapse). In important complex oxides such as vanadyl pyrophosphates, and in a variety of model ReO3- and V2O5-based oxides used as catalysts, my in situ studies suggest that glide shear is the most effective defect mechanism by which the catalysts accommodate nonstoichiometry and continue to operate in partial oxidation reactions. Anion vacancy formation resulting from the oxide reduction is the driving force for the generation of glide misfit defects and their ordering can give rise to new phases or structures in oxides. The studies have important implications in oxide catalysis and, more generally, in oxide crystallography.
Structure and Thermal Vibrations of Spermine Phosphate Hexahydrate from Neutron Diffraction Data at 125K
Authors: Cohen A. E. , Craven B. M. , Klooster W. T.
Published: July 2002

Spermine phosphate hexahydrate crystallizes in space group P21/a with unit-cell dimensions a = 7.931 (1), b = 23.158 (5), c = 6.856 (2) Å, and \beta = 113.44 (2)° at 125 K with unit-cell contents [(C10H30N4)^{4+}_{2} (HPO4)^{2-}_{4}.12H2O]. The packing of spermines and monohydrogen phosphates in this crystal structure has features which may be relevant to the binding of spermine to DNA. Another important structural feature is the presence of channels containing water that is hydrogen bonded as in ice-Ih with disordered protons. The channels occur between sheets of spermine long chains and are also bordered by hydrogen-bonded monohydrogen phosphate chains. The hydrogen-bonding scheme of these water chains proposed on the basis of an earlier X-ray study is now confirmed. Nuclear positions, anisotropic mean-square (m.s.) displacements, an overall scale factor and two extinction parameters (\rho and g) were refined using full-matrix least-squares giving values of R(F^{2}_{o}) = 0.09, Rw(F^{2}_{o}) = 0.11 and S = 1.02. Thermal vibrational analysis revealed that the backbone of the spermine cation can be described as a single rigid segment with a substantial libration of 27 deg2 around the spermine molecular long axis.
Re-Refinement of Composite Modulated Nb2Zr
x−2O2x+1 (x = 8) Using Synchrotron Radiation Data
Authors: Schmid S. , Thompson J. G. , Withers R. L. , Petříček V. , Ishizawa N. , Kishimoto S.
Published: July 2002

The crystal structure of Nb2Zr_{x-2}O_{2x + 1}, x = 8, has been re-refined as a composite modulated structure using synchrotron radiation data measured at energies below the Zr K absorption edge. The structure comprises one-atom thick layers of two substructures stacked alternately along the b direction. The two component substructures are, in general, mutually incommensurable along their common a-axis directions and are referred to as the metal substructure (M), space group Amma, aM
= 5.1348 (2), bM
= 4.9590 (2), cM
= 5.2908 (3) Å, and the oxygen substructure (O), space group Imam, aO
= 2.4164, bO
= bM
= b, cO
= cM
= c, respectively. The four basis vectors used to index reciprocal space, based on the more strongly scattering metal substructure, are a^{\ast}_{M}, b*, c* and q

M
. The primary modulation wavevector q

M
= ^{\ast}_{M} − 2a^{\ast}_{M} + b* - 1/8 a^{\ast}_{M} + b* for x = 8. The overall superspace-group symmetry is Amma(\alpha10)0s0. Two sets of intensity data recorded at room temperature, 8 eV (\lambda_n = 0.6892 Å) and 1450 eV (\lambda_f = 0.7492 Å) below the Zr K absorption edge, were refined to an overall R(\lambda_n) = 0.0377 and R(\lambda_f) = 0.0439. The displacive modulation wave amplitudes obtained from these refinements agree well with those previously obtained for an x = 12 member. Difference Fourier maps show that metal-atom ordering is virtually negligible.
Electron Density Distribution in LiB3O5 at 293 K
Authors: Le Hénaff C. , Hansen N. K. , Protas J. , Marnier G.
Published: July 2002

The electron density distribution in lithium triborate LiB3O5 has been studied at room temperature by X-ray diffraction using Ag K
\alpha radiation up to 1.02 Å−1 [1439 unique reflections with I > 3\sigma(I)]. Conventional refinements with a free-atom model yield R(F) = 0.0223, wR(F) = 0.0299, S = 1.632. Atom charge refinements show that the lithium should be considered a monovalent ion. Multipolar refinements were undertaken up to fourth order, imposing local non-crystallographic symmetry constraints in order to avoid phase problems leading to meaningless multipole populations due to the non-centrosymmetry of the structure (space group: Pn
a21). The residual indices decreased to: R(F) = 0.0147, wR(F) = 0.0193, S = 1.106. The net charges are in good agreement with what can be expected in borate chemistry. Deformation density maps are analysed in terms of \sigma and \pi bonding. The experimental electron distribution in the p

z
orbitals of triangular B atoms and surrounding O atoms has been analysed by introducing idealized hybridized states. In parallel, the electron density has been determined from ab initio Hartree–Fock calculations on fragments of the structure. Agreement with the X-ray determination is very good and confirms the nature of bonding in the crystal. The amount of transfer of \pi electrons from the oxygen to the triangular B atoms is estimated to be 0.22 electrons by theory.
Crystallographic and Molecular Mechanics Study of Imidooxy Anticonvulsants
Authors: Ciechanowicz-Rutkowska M. , Lieberman H. F. , Hursthouse M. B. , Scott K. R.
Published: July 2002

X-ray crystal structures have been determined of five compounds closely related to N-benzyl-2-azaspiro[4.4]-nonane-l,3-dione (1), which is inactive as an anticonvulsant, and N-(benzyloxy)-2-azaspiro[4.4]nonane-1,3-dione (2), which is active. Conformational analyses have been carried out with (1), (2) and the new compounds N-(2′,4′-dichlorobenzyloxy)-2-azaspiro[4.4]nonane-l,3-dione (3), N-(2′-bromobenzyloxy)-2-azaspiro[4.4]nonane-l,3-dione (4), N-(4′-(trifluoromethyl)benzyloxy)-2-azaspiro[4.4]nonane-l,3-dione (5), which are all active anticonvulsants, and N-(4′-chlorobenzyloxy)-2-azaspiro[4.4]nonane-l,3-dione (6) and N-(4′-bromobenzyloxy)-2-azaspiro[4.4]nonane-1,3-dione (7), which are inactive. Regardless of the substitution pattern, the conformations of compounds (2)–(7) in the crystals are very similar. Among the low-energy conformations, which are well distributed in the conformational space, that present in its solid state is dominant. Ortho-substitution considerably cuts down the number of conformations accessible within the set energy limit. The results of these studies alone do not explain the differences in activity.
Crystal Engineering Using Bis- and Tris-phenols. Adducts with 1,4,8,11-Tetraazacyclotetradecane (Cyclam): Isolated Ladders in the Adduct with 4,4'-Thiodiphenol, Tethered Ladders in the Adduct with 4,4'-Sulfonyldiphenol and Two Interwoven Three-Dimensional Networks in the Adduct with 1,1,1-Tris(4-hydroxyphenyl)ethane
Authors: Ferguson G. , Glidewell C. , Gregson R. M. , Meehan P. R.
Published: July 2002

The structure of 4,4′-thiodiphenol–1,4,8,11-tetraazacyclotetradecane (2/1), (C12H10O2S)2.C10H24N4 (1), monoclinic, P21/c, a = 11.1602 (12), b = 10.8084 (12), c = 14.001 (2) Å, β = 103.127 (10)°, with Z = 2, contains phenolate anions [HOC6H4SC6H4O]− and diprotonated cyclam cations [C10H26N4]2+: these cations have the centrosymmetric trans-III conformation and the two additional protons are contained within the N4 cavity of the macrocycle, held by three-centre hydrogen bonds. The phenolate anions form chains, held together by O—H...O hydrogen bonds, and pairs of these chains are cross-linked into ladders by the [cyclamH2]2+ cations by means of N—H...O hydrogen bonds. The structure of 4,4′-sulfonyldiphenol–1,4,8,11-tetraazacyclotetradecane (2/1), (C12H10O4S)2.C10H24N4 (2), triclinic, P1¯, a = 10.9345 (10), b = 11.0060 (10), c = 14.350 (2) Å, α = 79.532 (10), β = 86.739 (10), γ = 87.471 (10)°, with Z = 2, contains phenolate anions [HOC6H4SO2C6H4O]− and cyclam dications [C10H26N4]2+: the phenolate anions are linked into antiparallel chains, cross-linked by the cyclam cations. There are two distinct types of ladder in the structure running along (0, y, 0) and (1\over2, y, 1\over2), respectively, and these bundled ladders are tied together by C—H...O hydrogen bonds to form a continuous three-dimensional array. In 1,1,1-tris(4-hydroxyphenyl)ethane–1,4,8,11-tetraazacyclotetradecane–methanol (2/1/1), (C20H18O3)2.C10H24N4.CH4O (3), triclinic, P1¯, a = 8.2208 (11), b = 16.245 (2), c = 17.337 (2) Å, α = 81.694 (13), β = 89.656 (14), γ = 86.468 (12)°, with Z = 2, the structure contains centrosymmetric diprotonated cyclam cations of precisely the same type as found in (1), phenolate anions [(HOC6H4)2C(CH3)C6H4O]− and neutral methanol molecules. The molecular components are linked together by nine different types of hydrogen bond, five of O—H...O type and four of N—H...O type, to form chains running in the [001], [010] (two sets), [211] and [211¯] directions. The combination of these chain motifs generates two independent three-dimensional networks which are fully interwoven, but not bonded to one another.
Ab Initio Structure Determination of Ammonium Hydrogen Alkyl Phosphates from X-ray Powder Diffraction Data
Authors: Neels A. , Stoeckli-Evans H. , Neels J. , Clearfield A. , Poojary D.
Published: July 2002

The structures of three ammonium hydrogen alkyl phosphates, NH4PO2(OH)(OR) [R = Me (1), Et (2), Pr
i
(3)], have been solved ab initio from X-ray powder diffraction data. The structure determinations were based on Patterson search methods combined with difference-Fourier techniques and the refinement was carried out using Rietveld methods. Powder diffraction data were first collected for all three compounds in the reflection mode using Cu K
α1+α2 radiation. A pronounced preferred orientation effect was found for all the samples, even by side-loading into a flat sample holder. A random orientation of the powder particles was obtained for (1) using a special suspension chamber for the sample preparation, while for (2) and (3) data were remeasured in capillaries using the transmission mode. Crystals of the ammonium hydrogen methyl phosphate (1) and the ammonium hydrogen ethyl phosphate (2) both belong to the monoclinic space group P21/c, Z = 4, with a = 9.9645 (4), b = 7.1801 (3), c = 7.8897 (3) Å and β = 96.243 (3)° for (1), and a = 12.6453 (4), b = 7.1502 (2), c = 7.9738 (2) Å and β = 108.875 (2)° for (2). The ammonium hydrogen isopropyl phosphate (3) crystallizes in space group An, Z = 4, with a = 6.2475 (2), b = 29.3825 (6), c = 4.6305 (1) Å and β = 100.904 (2)°. All three compounds are characterized by an extended hydrogen-bonding network involving the hydrogen phosphate units and the ammonium ions, forming double layers. The methyl (1), ethyl (2) and isopropyl groups (3), which point into the interlayer space, connect the layers by van der Waals interactions.
Ideal and Real Structure of Ti5O4(PO4)4: X-ray and HRTEM Investigations
Authors: Reinauer F. , Glaum R.
Published: July 2002

The crystal structure of pentatitanium tetraoxide tetrakis(phosphate), Ti5O4(PO4)4, has been determined and refined from X-ray diffraction single-crystal data [P212121 (No. 19), Z = 4, a = 12.8417 (12), b = 14.4195 (13), c = 7.4622 (9) Å (from Guinier photographs); conventional residual R
1 = 0.042 for 2556 Fo
> 4σ(Fo
), R
1 = 0.057 for all 3276 independent reflections; 282 parameters; 29 atoms in the asymmetric unit of the ideal structure]. The structure is closely related to those of β-Fe2O(PO4)-type phosphates and synthetic lipscombite, Fe3(PO4)4(OH). While these consist of infinite chains of face-sharing MO6 octahedra, in pentatitanium tetraoxide tetrakis(phosphate) only five-eighths of the octahedral voids are occupied according to □3Ti5O4(PO4)4. Four of the five independent Ti4+O6 show high radial distortion [1.72 ≤ d(Ti−O) ≤ 2.39 Å] and a typical 1 + 4 + 1 distance distribution. The fifth Ti4+O6 is an almost regular octahedron [1.91 ≤ d(Ti−O) ≤ 1.98 Å]. Partial disorder of Ti4+ over the available octahedral voids is revealed by the X-ray structure refinement. High-resolution transmission electron microscopy (HRTEM) investigations confirm this result.
Multipole Analysis of the Electron Density in Topaz Using X-ray Diffraction Data
Authors: Ivanov Yu. V. , Belokoneva E. L. , Protas J. , Hansen N. K. , Tsirelson V. G.
Published: July 2002

The static deformation electron density, Laplacian of the electron density and critical points in the electron density were analyzed in topaz Al2[SiO4]F2, using high-precision X-ray diffraction data. The electron deformation density, positive values of the Laplacian at (3,−1) bond critical points and the net atomic charges indicate a closed-shell-type interaction in the polyhedra. Anion valence-shell charge depletions are revealed. Maxima in the Laplacian of the electron density are displaced towards the close-packed plane owing to the mutual repulsion of the anion valence shells. The relationship between the topological features of the electron density and the close-packing concept is discussed. Shifts of the critical points from the internuclear vectors reflect the strain in the structure.
Distortion of Crystal Structures of Some CoIII Ammine Complexes. III. Distortion of Crystal Structure of [Co(NH3)5NO2]Cl2 at Hydrostatic Pressures up to 3.5 GPa
Authors: Boldyreva E. V. , Naumov D. Yu. , Ahsbahs H.
Published: July 2002

This contribution continues comparative studies on the anisotropy of structural distortion of some CoIII ammine complexes induced by various actions [Boldyreva, Kivikoski & Howard (1997a). Acta Cryst. B53, 394–404; Boldyreva, Kivikoski & Howard (1997b). Acta Cryst. B53, 405–414]. Changes in the cell parameters of (OC-6-22)-pentaamminenitro-N-cobalt(III) dichloride were measured by single-crystal X-ray diffraction at pressures up to 3.5 GPa in a diamond anvil cell (DAC). At several pressures (ambient, 0.24, 0.52, 1.25, 1.91 and 3.38 GPa) a full data collection was carried out, and the atomic coordinates and anisotropic atomic displacement parameters were refined. The anisotropy of structural distortion under pressure was shown to be qualitatively different compared with that on cooling (Boldyreva, Kivikoski & Howard, 1997b). The role of the non-covalent interactions, in particular hydrogen bonds, in the anisotropy of structural distortion is discussed.
Thermal vibrations in potassium 3-benzoyl-2-thiophenecarboxylate
Authors: Craven B. M. , Ballas F. L.
Published: July 2002

The atomic thermal displacement parameters at 293 K for the anion in the title salt have been analyzed in terms of a body having two rigid segments, namely the benzoyl and the 2-thiophenecarboxylate groups. These segments are each nearly planar and have a dihedral angle of 80.1° between them. The internal torsional libration of the anion is physically correlated with its overall external translational and librational motion. Bond distances involving the heavier atoms have an s.u. σ from 0.002 to 0.003 Å while librational corrections in these distances range up to 4σ. A short nonbonded intersegment C...O distance of 2.817 (2) Å becomes 2.831 Å after correction, the correction being 7σ. An intermolecular S...O distance of 3.1891 (14) Å becomes 3.215 Å after correction for independent vibration of the two molecules, the correction being 18σ.
Molecular aggregation in crystalline 1:1 complexes of hydrophobic D- and L-amino acids. I. The L-isoleucine series
Authors: Dalhus Bjørn , Görbitz Carl Henrik
Published: July 2002

The amino acid L-isoleucine has been cocrystallized with seven selected D-amino acids including D-methionine [L-isoleucine–D-methionine (1/1), C6H13NO2.C5H11NO2S, amino-acid side chain R = —CH2—CH2—S—CH3] and a homologous series from D-alanine [L-isoleucine–D-alanine (1/1), C6H13NO2.C3H7NO2, R = —CH3] through D-α-aminobutyric acid [L-isoleucine–D-α-aminobutyric acid (1/1), C6H13NO2.C4H9NO2, R = —CH2—CH3] and D-norvaline [L-isoleucine–D-norvaline (1/1), C6H13NO2.C5H11NO2, R = —CH2—CH2—CH3] to D-norleucine [L-isoleucine–D-norleucine (1/1), C6H13NO2.C6H13NO2, R = —CH2—CH2—CH2—CH3] with linear side chains, and D-valine [L-isoleucine–D-valine (1/1), C6H13NO2.C5H11NO2, R = —CH—(CH3)2] and D-leucine [L-isoleucine–D-leucine (1/1), C6H13NO2.C6H13NO2, R = —CH2—CH—(CH3)2] with branched side chains. All the crystal structures are divided into distinct hydrophilic and hydrophobic layers. In the five complexes with amino acids with linear side chains the polar parts of the D- and L-amino acids are related by pseudo-glide-plane symmetry, and four of them have remarkably similar molecular arrangements. The D-valine and D-leucine complexes, on the other hand, are structurally quite different with the polar parts of the D- and L-amino acids related by pseudo-inversion. Differences in the hydrogen-bond pattern in the two molecular arrangements are discussed.
Structure analysis of new homologous compounds Ga2O3(ZnO)
m
(m = integer) by high-resolution analytical transmission electron microscopy
Authors: Li Chunfei , Bando Yoshio , Nakamura Masaki , Kurashima Keiji , Kimizuka Noboru
Published: July 2002

The crystal structure of a new homologous compound series, Ga2O3(ZnO)
m
(m = integer), is determined by high-resolution lattice imaging and high spatial resolution energy-dispersive X-ray spectroscopy (EDS) analysis in a field-emission analytical transmission electron microscope. This work was carried out mainly on the compound with m = 9 (digallium nonazinc dodecaoxide), which belongs to the orthorhombic system and has lattice constants ao
= 0.33, bo
= 2.0 and co
= 3.4 nm. From the extinction rules three possible space groups are selected and from them a unique space group is assigned as noncentrosymmetric Cmc21 (No. 36) on the basis of structural requirements. Ga2O3(ZnO)
m
is a layered structure consisting of Ga–O and m + 1 Ga/Zn–O layers stacked alternately along the c axis. It is shown that the structure of Ga2O3(ZnO)
m
differs from that of M
2O3(ZnO)
m
(M = In, Fe; m = integer) reported previously. In Ga2O3(ZnO)
m
the Ga atoms occupy the tetrahedral sites in the Ga–O layers, whereas the M atoms in the M–O layers occupy the octahedral sites in M
2O3(ZnO)
m
(M = In, Fe).
Crystal structure of layered bis(ethylenediamine)nickel hexavanadate as a new representative of the V6O14 series
Authors: Zavalij Peter Y. , Zhang Fan , Whittingham M. Stanley
Published: July 2002

A new [Ni(NH2CH2CH2NH2)2](V6O14) compound has been synthesized hydrothermally and was found to crystallize in the monoclinic system. The single-crystal X-ray data leads to a disordered structure, which can be decomposed into two ordered models with different stacking of the V6O14 layers. The structure of the layer is the same in both models and represents a new member of the V6O14 series. All known structures from this series are constructed from the same chain of square pyramids (SP), which share alternatively adjacent or opposite edges of their bases. The differences lie in the orientation of the SP chains which are joined together by sharing corners with tetrahedra to form the layers. Combinatorial analysis of the V6O14 structures was conducted, yielding ten possible symmetry groups for the series of V6O14 layers. The known structures belong only to the three simplest cases with the highest symmetry.
2,4,6-Triisopropylbenzenesulfonamide: Monte Carlo structure solution from X-ray powder diffraction data for a molecular system containing four independent asymmetric rotors
Authors: Tremayne Maryjane , MacLean Elizabeth J. , Tang Chiu C. , Glidewell Christopher
Published: July 2002

The crystal structure of 2,4,6-triisopropylbenzenesulfonamide, C15H25NO2S, has been solved from X-ray powder diffraction data collected at 120 (1) K using synchrotron radiation and refined by Rietveld methods. The structure was solved by the application of a Monte Carlo method in which trial structures were generated by random movement of the molecule in the unit cell and assessed using a full-profile-fitting technique. Intramolecular flexibility was introduced into the structure solution in the form of four independent asymmetric rotors, allowing the isopropyl and sulfonamide groups to rotate freely within the molecule. The structure is monoclinic P21/c, a = 16.9600 (6), b = 8.1382 (2), c = 11.7810 (2) Å, β = 104.777 (2)° with Z = 4. The molecules are linked by N—H...O hydrogen bonds, with N...O distances of 2.77 (1) and 2.92 (1) Å, into two-dimensional sheets built from R^2_2(8) and R^6_6(20) rings.
Direct observation of deuterium migration in crystalline-state reaction by single-crystal neutron diffraction. II. 3–1 Photoisomerization of a cobaloxime complex
Authors: Ohhara Takashi , Harada Jun , Ohashi Yuji , Tanaka Ichiro , Kumazawa Shintaro , Niimura Nobuo
Published: July 2002

Single crystal neutron diffraction analysis of photo-exposed(3-cyanopropyl-d
2
α,α)-[(R)-1-phenylethylamine-d
11]bis(dimethylglyoximato-d
14)cobalt(III) was carried out in order to clarify the mechanism of the crystalline-state photoisomerization of the 3-cyanopropyl group bonded to the Co atom in some cobaloxime complexes. Before irradiation the two H atoms bonded to the C1 atom of the 3-cyanopropyl group were exchanged with the D atoms such as —CH2CH2CD2CN. On exposure to a xenon lamp, the cell dimensions of the crystal were gradually changed. After 7 d exposure the change became insignificantly small. The structure was analyzed by neutron diffraction. The 3-cyanopropyl group was transformed to the 1-cyanopropyl group such as —CD(CN)C(H1/2,D1/2)2CH3 with retention of the single-crystal form. This indicates that one of the D atoms bonded to C1 migrates to either position bonded to C2. The other atoms of the complex remained unchanged. These results indicate that photoisomerization proceeded in two steps: the 3-cyanopropyl group was isomerized to the 2-cyanopropyl group in the first place and then the 2-cyanopropyl group was transformed to the 1-cyanopropyl group. Moreover, it was made clear that the second-step isomerization was irreversible, since one of the D atoms was retained. The disordered structure at C2 is estimated to be caused by the interconversion between the 1-cyanopropyl group produced and its dehydrogenated olefin after the photoisomerization.
3,6,9,16,19,22-Hexaazatricyclo[22.2.2.211,14]triconta-1(26),11(29),12,14(30),24,27-hexaene, C24H38N6, as a building block in supramolecular chemistry: structures in two and three dimensions
Authors: Glidewell Christopher , Ferguson George , Gregson Richard M. , Lough Alan J.
Published: July 2002

The adduct (1) formed between the hexaaza macrocycle 3,6,9,16,19,22-hexaazatricyclo[22.2.2.211,14]triconta-1(26),11(29),12,14(30),24,27-hexaene, C24H38N6, and 4,4′-sulfonyldiphenol, O2S(C6H4OH)2, is a salt [(C24H40N6)2+]·2[(HOC6H4SO2C6H4O)−], and the adduct (2) formed by the same macrocyclic amine with 4,4′-biphenol is an aquated salt which also contains neutral biphenol molecules, [(C24H40N6)2+]·2[(HOC6H4C6H4O)−]·(HOC6H4C6H4OH).2H2O. In both compounds the cations lie across centres of inversion: there are two crystallographically distinct cation sites in (1) and the conformations of the cations occupying them are quite different. In (2) the single type of cation site is occupied by a conformationally disordered cation: the major and minor components represent two further distinct conformers. In (1) the anions are linked by O—H...O hydrogen bonds into chains, and each cation is linked by a total of six N—H...O hydrogen bonds to anions in four different chains, so linking the chains into continuous sheets. In (2) the anions and the water molecules are linked into sheets, which are further linked into a continuous three-dimensional framework by both the cations and the neutral biphenol units.
An analysis of recent single crystal X-ray diffraction measurements on calcium fluoride
Authors: Cooper M. J.
Published: July 2002

An analysis of recent single-crystal X-ray diffraction measurements on calcium fluoride has been carried out by comparing the observed data with those calculated from a theoretical model. A computer program was used which can refine parameters for extinction and anharmonic thermal vibrations in addition to the conventional parameters. It is shown that for the majority of the experiments in the recent ACA project the angle-dependent deviations between the experiments are consistent with those which would be expected due to a variation in the measured contributions from thermal diffuse scattering. There are discrepancies between experiments for the strongest reflexions, presumably because of errors associated with the use of attenuators, but if these reflexions are excluded the agreement between experiments, allowing for variations in the thermal diffuse scattering contributions, is much better than was indicated by previous analyses. The two remaining experiments and that reported by Zachariasen are in poor agreement with the others and this is attributed to the techniques used, namely an ω-scan with balanced filters in one case and a stationary-crystal, stationary-detector technique in the other two. Although the effects of anharmonicity on the X-ray intensities are rather small, the data from all experiments are consistent with the magnitude of an anharmonic thermal-vibration parameter, associated with the fluorine atoms, derived from neutron-diffraction measurements.
Positional errors in (partial) structure models; their influence on the residual R
2
Authors: Van de Mieroop W. , Lenstra A. T. H.
Published: July 2002

Algebraic expressions are evaluated, from which the influence of small discrepancies between atomic positions in a structure model and the corresponding atomic sites in the observed structure on R
2 can be calculated. Theory and experiment are in good agreement. It is demonstrated that because of the effect of small positional errors, R
2 as a function of the size of a structure model does not necessarily show a monotonic decrease. The path of R
2 may even contain additional minima.
The crystal structure of 4Nb2O5.9WO3 studied by 1 MV high-resolution electron microscopy
Authors: Horiuchi S. , Muramatsu K. , Matsui Y.
Published: July 2002

Images of pale yellow crystals of 4Nb2O5. 9WO3, obtained with a 1 MV high-resolution electron microscope revealed twinned domains of a tetragonal tungsten bronze structure with a superlattice of 3 x 1 subcells. Comparison with computer calculations suggests that the cations filling the pentagonal tunnels include both Nb and W. Crystals darkened due to reduction on longer heating included no domains and were sensitive to electron irradiation; cations were knocked on from the filled to the vacant pentagonal tunnels. This suggests that some oxygens are released from the -M-O-M-O-M- strings in the tunnels on reduction to weaken the chemical bonding. The number of deficient oxygens is known from the weight gain on oxidizing the crystal. Some additional experiments reveal that there is no '6Nb2O5. 1 IWO3' phase. The resolving power of the present microscope is discussed on the basis of the analysis of the chromatic aberration.
Life-science applications of the Cambridge Structural Database
Authors: Taylor Robin
Published: July 2002

Several studies show that the molecular geometries and intermolecular interactions observed in small-molecule crystal structures are relevant to the modelling of in vivo situations, although the influence of crystal packing is sometimes important and should always be borne in mind. Torsional distributions derived from the Cambridge Structural Database (CSD) can be used to map out potential-energy surfaces and thereby help identify experimentally validated conformational minima of molecules with several rotatable bonds. The use of crystallographic data in this way is complementary to in vacuo theoretical calculations since it gives insights into conformational preferences in condensed-phase situations. Crystallographic data also underpin many molecular-fragment libraries and programs for generating three-dimensional models from two-dimensional chemical structures. The modelling of ligand binding to metalloenzymes is assisted by information in the CSD on preferred coordination numbers and geometries. CSD data on intermolecular interactions are useful in structure-based inhibitor design both in indicating how probable a protein–ligand interaction is and what its geometry is likely to be. They can also be used to guide searches for bioisosteric replacements. Crystallographically derived information has contributed to many life-science software applications, including programs for locating binding `hot spots' on proteins, docking ligands into enzyme active sites, de novo ligand design, molecular superposition and three-dimensional QSAR. Overall, crystallographic data in general, and the CSD in particular, are very significant tools for the rational design of biologically active molecules.
Comparative Studies of Protein Crystallization by Vapour-Diffusion and Microbatch Techniques
Authors: Chayen Naomi E.
Published: July 2002

Numerous reports have been published in the literature which describe the crystallization of macromolecules by a variety of crystallization methods, including the vapour-diffusion and microbatch techniques. This topical review compares the results of examples of proteins which were crystallized by both vapour-diffusion and microbatch methods. The inherent features of the vapour-diffusion and microbatch methods are discussed and some specific conditions where one method appears more favourable than the other are reported. Guidelines for the conversion of crystallization conditions from vapour diffusion to microbatch (and vice
versa) are also presented.
R
omit profile analysis for molecular replacements
Authors: Tsuchiya Daisuke , Takenaka Akio
Published: July 2002

A new procedure for evaluation of molecular replacement has been examined by using an R factor calculated from the probe structure with some omitted parts (R
omit). It has been demonstrated that changes in R
omit from the conventional R factor for the whole structure are sensitive to the local fitness in the omitted region even for large molecules such as proteins. Their profile, plotted against residues, is effective for distinguishing the most probable one from several solutions. In addition, this profile analysis exhibits useful information for model building.
Preliminary X-ray crystallographic studies of a newly defined human theta-class glutathione transferase
Authors: McKinstry William J. , Oakley Aaron J. , Rossjohn Jamie , Verger Denis , Tan Kian-Leong , Board Philip G. , Parker Michael W.
Published: July 2002

Human theta-class glutathione S-transferases (GST's) appear to play a critical role in the metabolism of a variety of environmental pollutants but in some cases the products of the reaction are carcinogenic. Crystals of a human theta-class GST, namely hGSTT2-2, have been grown from polyethylene glycol by the hanging-drop vapour-diffusion method. The crystals belong to the trigonal space group P3121 with cell dimensions of a = b = 94.0 and c = 120.5 Å. They contain two monomers in the asymmetric unit and diffract to 3.0 Å resolution.