bluuebunny/crossref_metadata_2025 huggingface dataset:
Architecture of crystal structures from square planes
Authors: Hauck J. , Mika K.
Published: July 2004

The crystal structures of ordered b.c.c. (body-centered cubic), f.c.c. (face-centered cubic) or primitive cubic alloys A_xB_y and related NaCl, ZnS or CaF_2 derivative structures are characterized by the self-coordination numbers T_1, T_2 of the A atoms with A atoms. Structures with identical T_1 and T_2 values for all A atoms are at the corners of T_1 and T_2 structure maps, and can be analyzed for attractive or repulsive interactions of A atoms. Most observed structures are at the borders of the structure map and can be obtained by ∼10 different combinations of structural units. The different combination mechanisms explain e.g. the shear structures of CuAu II or \rm Nb_2O_5 and the occurrence of vacancies in NaCl-related structures like NbO.
Orthorhombic τ-Zn–Mg–Dy phase related to a Frank-Kasper type decagonal quasicrystal
Authors: Abe Eiji , Tsai An Pang
Published: July 2004

We report a novel Zn–Mg–Dy phase, denoted as the τ-phase, whose structure is related to that of the Frank-Kasper type decagonal Zn–Mg–Dy phase, based on electron diffraction and high-resolution transmission electron microscopy studies. A plausible atomic model is proposed, which is constructed by two types of atomic clusters related to those in the Zn7Mg4 crystalline compound.
X-ray diffraction study of K3NdSi7O17: a new framework silicate with a linear Si—O—Si bond
Authors: Haile S. M. , Wuensch B. J.
Published: July 2004

Hydrothermal investigations in the high-silica region of the K2O–Nd2O3–SiO2 system, carried out in a search for novel fast-ion conductors (FICs), yielded the new compound tripotassium neodymium heptasilicate, K3NdSi7O17. Single-crystal X-ray methods revealed that K3NdSi7O17 crystallizes in space group P\bar 3, has lattice constants a = 16.131 (2) and c = 7.7146 (19) Å, Z = 4, and 22 atoms in the asymmetric unit. Refinement was carried out to a residual, R(F), of 0.0253 and a weighted residual, wR(F

2
), of 0.0702 using anisotropic displacement parameters for all atoms. The silicate anion forms an interrupted framework, within which both Nd octahedra and K polyhedra are situated. The structure is unusual in that it contains a symmetry-constrained Si—O—Si bond angle of 180°. No isomorphs to K3NdSi7O17 are known.
Two-dimensional incommensurately modulated structure of (Sr0.13Ca0.87)2CoSi2O7 crystals
Authors: Bagautdinov B. , Hagiya K. , Kusaka K. , Ohmasa M. , Iishi K.
Published: July 2004

The incommensurate structure of (Sr0.13Ca0.87)2CoSi2O7 at room temperature has been determined from single-crystal X-ray diffraction data. The compound has a non-centrosymmetric tetragonal basic cell of a = 7.8743 (4) and c = 5.0417 (2) Å with the space group P4¯21
m. The refinements of the basic structure converged to R = 0.038 for 757 main reflections. The two-dimensional incommensurate structure is characterized by the wavevectors q
1 = 0.286 (3)(a* + b*) and q
2 = 0.286 (3)(−a* + b*), where a*, b* are the reciprocal lattice vectors of the basic structure. With the (3 + 2)-dimensional superspace group P

p4mg

P4¯21

m

, the refinements converged to R = 0.071 for 1697 observed reflections (757 main and 940 satellite reflections). The structure is described in terms of displacement of the atoms, rotation, distortion of CoO4 and SiO4 tetrahedra, and the partial ordering of the Sr and Ca atoms accompanied with the modulation. Correlated evolution of these features throughout the crystal gives rise to various oxygen coordination around Ca/Sr. Comparison of the derived modulated structure to that of Ca2CoSi2O7 clarified that the partial substitution of Ca by large alkaline-earth atoms such as Sr should decrease the distortion of the polyhedra around the cations.
Refinement of framework disorder in dehydrated CaA zeolite from single-crystal synchrotron data
Authors: Porcher Florence , Souhassou Mohamed , Graafsma Heinz , Puig-Molina Anna , Dusausoy Yves , Lecomte Claude
Published: July 2004

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 (Ca48Al96Si96O384, Fm\bar 3c, a = 24.47 Å) using single-crystal high-resolution synchrotron X-ray diffraction [(sin θ/λ)max = 1.4 Å−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 Ca2+ cations.
Conformational preferences and supramolecular aggregation in 2-nitrophenylthiolates: disulfides and thiosulfonates
Authors: Glidewell Christopher , Low John N. , Wardell James L.
Published: July 2004

In each of the asymmetrically substituted disulfides 2-nitro-4′-methyldiphenyl disulfide, C13H11NO2S2 (1), 2-nitro-4′-chlorodiphenyl disulfide, C12H8ClNO2S2 (2), 2,4-dinitro-4′-methyldiphenyl disulfide, C13H10N2O4S2 (3), and 2,4-dinitrophenyl-2′-methoxycarbonylmethyl disulfide, C9H8N2O6S2 (4), and in both of the symmetrically substituted disulfides bis(2-nitrophenyl) disulfide, C12H8N2O4S2 (5), and bis(2-nitro-4-trifluoromethylphenyl) disulfide, C14H6F6N2O4S2 (6), the 2-nitro groups are essentially coplanar with the adjacent aryl ring and the S atom remote from the nitrated aryl ring is also essentially coplanar and transoid to the nitro group. In S-(2-nitrophenyl) 2-nitrobenzene thiosulfonate, C12H8N2O6S2 (7), which contains three independent molecules in the asymmetric unit, all six of the independent nitro groups are twisted out of the plane of the adjacent aryl rings. The crystal structures of (1)–(3) contain isolated molecules, that of (4) contains centrosymmetric dimers held together by C—H...O hydrogen bonds, while in the structures of (5)—(7), respectively, the C—H...O hydrogen bonds generate one-, two- and three-dimensional arrays. The interplay between molecular conformation and supramolecular aggregation is discussed.
Graph-set and packing analysis of hydrogen-bonded networks in polyamide structures in the Cambridge Structural Database
Authors: Motherwell W. D. Samuel , Shields Gregory P. , Allen Frank H.
Published: July 2004

The hydrogen-bond networks and crystal packing of 81 unique secondary di- and polyamides in the Cambridge Structural Database are investigated. Graph-set analysis, as implemented in the RPluto program, is used to classify network motifs. These have been rationalized in terms of the relative dispositions of the amide groups. Peptide and retropeptides exhibit significant conformational flexibility, which permits alternative hydrogen-bonding patterns. In peptides, dihedral angles of −ψ ≃ φ ≃ 105° allow an antiparallel ladder arrangement, containing rings of either the same or alternating sizes. For retropeptides, and diamides with an odd number of CH2 spacers, this conformation leads to a parallel ladder with rings of equal size. If φ approaches −60° and ψ 180°, ladders adopt a helical twist, and if the conformation is distorted further, a three-dimensional network is usually adopted. Diamides with aromatic or an even number of CH2 spacers generally form either antiparallel ladders or sheets, although some exhibit both polymorphs. Symmetry relationships within and between hydrogen-bonded chains, ladders and sheets in the crystal packing have also been analysed. Polyamides form considerably more complex networks, although many of the structural motifs present in the diamides occur as components of these networks.
Systematic prediction of new ferroelectrics in space group P3
Authors: Abrahams S. C.
Published: July 2004

The current release of the Inorganic Crystal Structure Database contains a total of 57 entries under space group P3 that correspond to 50 different materials. There are 21 structures reported with this space group that satisfy the criteria for ferroelectricity, at a confidence level that depends on the reliability of the underlying structural determination. One ferroelectric discovered earlier is also listed. In addition, the database contains 19 entries that probably should be assigned to a centrosymmetric space group, seven that are polar but probably not ferroelectric and two that are without atomic coordinates. Seven entries are either duplicates or present additional structural studies of the same material. Structures in space group P3 identified as potentially new ferroelectrics include LiAsCu0.93, Na2UF6, BiTeI, BaGe4O9, α-UMo2O8, Cu2SiS3, Co(IO3)2, Sr7Al12O25, KSn2F5, YbIn2S4, Na5CrF2(PO4)2, Sn(ClO2)2(ClO4)6, Eu3BWO9, Li(H2O)4B(OH)4·2H2O, Mn3V1/2(SiO4)O(OH)2, Ca6(Si2O7)(OH)6, Na6.9(2)[Al5.6(1)Si6.4(1)O24](S2O3)1.0(1)·2H2O, BaCa2In6O12, Ni(H2O)6[Sb(OH)6]2, Sr4Cr3O9 and Cu5O2(VO4)2·CuCl2.
Ferroelastic structures of n-pentyl-, n- hexyl- and n-nonylammonium dihydrogenphosphate crystals
Authors: Fábry Jan , Petříček Václav , Kroupa Jan , Císařová Ivana
Published: July 2004

This study reports the structure redeterminations of C5H11NH3
+·H2PO4
− (n-pentylammonium dihydrogenphosphate, C5ADP), C6H13NH3
+·H2PO4
− (n-hexylammonium dihydrogenphosphate, C6ADP) and C9H19NH3
+·H2PO4
− (n-nonylammonium dihydrogenphosphate, C9ADP). The structures are monoclinic (P21/n), belonging to the series of previously studied structures C2ADP–C8ADP and C10ADP. The structures exhibit reproducible ferroelastic switching. There are hydrogen bonds between the dihydrogenphosphates and the n-alkylammonium groups. Among them there are two hydrogen bonds with hydrogens which hop from the donor to the acceptor oxygens during the ferroelastic switching. C5ADP as well as C3ADP differ from the other members of the series by packing of the double layers of the dihydrogenphosphates. Moreover, the packing of n-alkylammonium molecules in all these structures depends on the parity of the number of atoms in the n-alkylammonium chains. All the samples contained two domains and their structures were refined as twins.
U
equiv: its past, present and future
Authors: Watkin David
Published: July 2004

The reporting of U
equiv and its standard uncertainty has a chequered history. In spite of the recommendation of the IUCr Commission on Journals that authors use the definition of U
equiv of their own choice, possibly without standard uncertainties, there still seems to be some confusion amongst referees and editors about the status of this derived parameter. It is shown that neither of the common definitions are very useful, and that the standard uncertainty computed from the refinement normal matrix is almost worthless. A potential alternative derived parameter is proposed.
Two-dimensional packing and pseudosymmetry
Authors: Britton Doyle
Published: July 2004

It is possible to understand, or at least rationalize, the occurrence of pseusosymmetry elements in some crystals as a consequence of a higher symmetry in a two-dimensional layer being obscured by the three-dimensional packing of the layers. Six examples, including both simple compounds and co-crystals and involving six different symmetries, are described.
X-ray structure of barium titanate – missed opportunities
Authors: Chandrasekaran K. S. , Mohanlal S. K. , Saravanan R. , Israel S.
Published: July 2004

Anomalous X-ray scattering effects are quite extensive in the noncentrosymmetric ferroelectric structure of barium titanate, and typical estimates for three published X-ray diffraction experiments are computed. These data show that the Bijvoet pairs should not be averaged before least-squares refinement for this polar crystal with small atomic displacements from a higher symmetric space group.
Synthesis, structure, thermal and non-linear optical properties of L-argininium hydrogen selenite
Authors: de Matos Gomes E. , Nogueira E. , Fernandes I. , Belsley M. , Paixão J. A. , Matos Beja A. , Ramos Silva M. , Martín-Gil J. , Martín-Gil F. , Mano J. F.
Published: July 2004

L-Argininium hydrogen selenite (C6H15N4O2HSeO3) is a new semiorganic compound of the hydrogen selenite family with non-linear optical properties. The crystal lattice is monoclinic with unit-cell parameters a = 22.493 (5), b = 5.1624 (13), c = 9.730 (4) Å, β = 95.68 (3)°, V = 1124.3 (6) Å3, Z = 4, space group C2. Second-harmonic generation measurements performed on powder samples, using a Q-switched Nd:Yag laser (λ = 1064 nm), showed the second-harmonic power to be about twice that of urea. Differential scanning calorimetry measurements revealed the existence of a phase transition with onset at 289 K.
Bis(hfac)-copper(II) complexes bridged by pyrimidines showing magnetic interactions
Authors: Yasui Masanori , Ishikawa Yoshimitsu , Ishida Takayuki , Nogami Takashi , Iwasaki Fujiko
Published: July 2004

Crystals of bis(1,1,1,5,5,5-hexafluoropentane-2,4-dionato)bispyrimidinecopper(II) (1), bis(1,1,1,5,5,5-hexafluoropentane-2,4-dionato)bis(4-methylpyrimidine)copper(II) (2), bis(1,1,1,5,5,5-hexafluoropentane-2,4-dionato)bis(quinazoline)copper(II) (3) showed ferromagnetic interactions at extremely low temperature. Crystal structure analyses revealed that these complexes were catena-bis(1,1,1,5,5,5-hexafluoropentane-2,4-dionato)[μ-pyrimidine-N
1:N
3]copper(II), [Cu(hfac)2(pm)2]
n
, catena-bis(1,1,1,5,5,5-hexafluoropentane-2,4-dionato)[μ-4-methylpyrimidine-N
1:N
3]copper(II), [Cu(hfac)2(4-Me-pm)]
n
, and catena-bis(1,1,1,5,5,5-hexafluoropentane-2,4-dionato)[μ-pyrimidine-N
1:N
3]copper(II), [Cu(hfac)2(qz)]
n
, for (1), (2) and (3), respectively. In (1) and (2) the pyrimidines bridge the Cu atoms with an axial–equatorial mode to form one-dimensional spiral chains. Complex (3) also forms a one-dimensional chain structure. The coordination mode of (3) is axial–axial at room temperature, while axial–equatorial at 120 K. On the other hand, the structure of the other modification of the 4-methylpyrimidine complex (4), showing paramagnetic properties, was revealed to be a trinuclei complex bridged by two 4-methylpyrimidines, tris[bis-(1,1,1,5,5,5-hexafluoropentane-2,4-dionato)copper(II)][bis-μ-4-methyl-pyrimidine-N
1:N
3]. The chain structures with an axial–equatorial coordination mode of the bridging organic moieties should play an important role in the appearance of the ferromagnetic interactions.
Rules governing the crystal packing of mono- and dialcohols
Authors: Taylor Robin , Macrae Clare F.
Published: July 2004

A new program, Mercury, has been used to survey 144 monoalcohol (C
m
H
n
OH) and 101 dialcohol [C
m
H
n
(OH)2] crystal structures. Results show that their hydrogen-bonding patterns are strongly correlated with steric effects. Primary monoalcohols have a strong preference to form infinite ...OH...OH... chains. Secondary monoalcohols form chains and rings of hydrogen bonds with about equal facility. Tertiary monoalcohols very often form isolated OH...O hydrogen bonds or structures containing no OH...O hydrogen bonds at all. In the latter case, however, the structures almost invariably contain CH...O and/or OH...π interactions. Substitution on the β-carbon(s) of monoalcohols has a profound effect on packing patterns, with increased substitution disfavouring chains and rings. Dialcohols show a much stronger preference for chains of hydrogen bonds, compared with monoalcohols. This is particularly so when at least one of the hydroxyl groups is primary, in which case chains are overwhelmingly preferred. Once again, substitution on the β-C atoms is influential, heavy substitution tending to lead to packing arrangements that involve isolated or intramolecular OH...O hydrogen bonds. Dialcohols almost never crystallize without at least some OH...O hydrogen-bond formation. In both monoalcohols and dialcohols, chains show a stronger preference to be helical (usually threefold helices) as steric hindrance increases. Hydrogen-bonded rings usually contain four OH...O hydrogen bonds. It is possible that empirical observations such as these may aid crystal-structure prediction.
Temperature-dependent neutron powder diffraction study of the Ba(OD)2 polymorphs: a new low-temperature phase
Authors: Friedrich Alexandra , Kunz Martin , Suard Emmanuelle
Published: July 2004

The structural behaviour of both low-temperature β- and high-temperature α-Ba(OD)2, barium dihydroxide-d, was investigated at temperatures between 10 and 552 K by neutron powder diffraction. While the β phase (P21/n) remains stable to the lowest temperature investigated, the quenchable α phase (Pnma) shows a reversible orthorhombic-to-monoclinic phase transition between 100 and 150 K. The structure of the new α
m
phase (P21/n) is quite similar to that of the α phase. This behaviour is unusual as a metastable phase transforms to another metastable phase. The Pnma ↔ P21/n low-temperature phase transition is driven by an order–disorder mechanism, mainly caused by one of the D atoms, which is disordered on positions off the mirror plane, mimicking a special position on the mirror plane in the orthorhombic phase. Refinements of the α phase above the phase transition indicate this disorder across the mirror plane through a conspicuously high isotropic displacement parameter if compared to the other D atoms. At low temperature the energy of the vibration is lowered and the D atom is frozen at a general position in a correlated way, thus violating the mirror plane and reducing the space-group symmetry.
X-ray studies on crystalline complexes involving amino acids and peptides. XXXVIII. Crystal structures of the complexes of L-arginine and L-histidine with glutaric acid and a comparative study of amino acid–glutaric acid complexes
Authors: Saraswathi N. T. , Vijayan M.
Published: July 2004

The complexes of glutaric acid with L-arginine and L-histidine (two crystal forms) exhibit different stoichiometries and ionization states. The aggregation patterns in two of the crystals are remarkably similar to those observed earlier in similar structures, while the pattern in the remaining one has not been seen earlier. The variability in the ionization state and stoichiometry observed in amino acid–dicarboxylic acid complexes appears to represent subtle differences in the response of a molecule to the presence in its neighbourhood of another type of molecule. The glutaric acid molecules (or glutarate or semiglutarate ions) in their complexes and in other crystals favour a fully extended conformation, albeit with frequent departures from it. The change in the chirality of the component molecules in the complex could lead to drastic changes in the aggregation pattern; alternatively, the effects of the change are accommodated through small adjustments in essentially the same pattern.
Influence of aromatic sulfonation on the geometry of [2.2]paracyclophane: crystal structures of one sulfonate, one disulfonic anhydride and five disulfonimides
Authors: De Ridder Dirk J. A. , Goubitz Kees , Fontijn Margot , Čapková Pavla , Dova Eva , Schenk Henk
Published: July 2004

The crystal structures of potassium [2.2]paracyclophane-4-sulfonate (1), [2.2]paracyclophane-4,15-disulfonic anhydride (2), [2.2]paracyclophane-4,15-disulfonimide (3), N-n-propyl-[2.2]paracyclophane-4,15-disulfonimide (4), N-isopropyl-[2.2]paracyclophane-4,15-disulfonimide (5), N-cyclopropyl-[2.2]paracyclophane-4,15-disulfonimide (6) and N-phenyl-[2.2]paracyclophane-4,15-disulfonimide (7) were established by single-crystal X-ray diffraction. The structural changes caused by sulfonation are discussed with respect to the parent [2.2]paracyclophane (tricyclo[8.2.2.24,7]hexadeca-4,6,10,12,13,15-hexaene). The main features are a change in the non-bonding distances between the para-phenylene rings and a rotation of these rings with respect to the molecular symmetry plane. The rings are rotated away from each other in the case of monosulfonation (1), but are rotated in the opposite way in the case of the disulfonic anhydride (2) or the disulfonimide compounds (3)–(7). The results are also discussed in terms of the parameters proposed by Keehn [(1983), Organic Chemistry, A Series of Monographs 45, edited by P. H. Keehn & S. M. Rosenfeld, Vol. 1, pp. 69–238. New York: Academic Press] showing that (bonded and non-bonded) angles involving the para-phenylene rings are mainly affected.
Superlattice formation in the lithiated vanadium oxide phases Li0.67V6O13 and LiV6O13
Authors: Björk Helen , Lidin Sven , Gustafsson Torbjörn , Thomas John O.
Published: July 2004

Two new lithiated phases of V6O13 were formed by carefully tuning the temperature of electrochemical lithiation in a `coffee-bag' type Li-ion battery at 2.78 V versus Li/Li+. These were studied by single-crystal X-ray diffraction. A phase with the composition Li2/3V6O13 was obtained at 308 K with a unit cell three times the volume of the original V6O13 cell. A single crystal discharged at ambient temperature was shown to be LiV6O13 and twice the unit-cell volume of the original V6O13 cell. On lithiation, the structures retain their basic V6O13 structure of alternating single and double layers of VO6 octahedra. The lithium ions occupy chemically equivalent sites, where they coordinate fivefold to O atoms, and associate with the single layers of VO6 octahedra. The insertion of lithium causes a significant elongation of one of the V—O bonds in each structure, which expands from 1.65 to 1.89 Å; this is due to the charge reduction of a specific V atom.
Hydrogen-bond network in cyclodecaamylose hydrate at 20 K; neutron diffraction study of novel structural motifs band-flip and kink in α-(1→4)-D-glucoside oligosaccharides
Authors: Imamura K. , Nimz O. , Jacob J. , Myles D. , Mason S. A. , Kitamura S. , Aree T. , Saenger W.
Published: July 2004

A single-crystal neutron diffraction study of cyclodecaamylose (CA10) was carried out at 20 K. CA10 crystallizes with 27.18 water molecules [(C6H10O5)10·27.18H2O] in space group C2 with unit-cell constants a = 29.31 (5), b = 9.976 (10), c = 19.34 (2) Å, β = 121.07 (2)°. The asymmetric unit contains a half molecule of CA10 and 13.59 water molecules, the other half being related by a crystallographic twofold rotation axis. All H atoms except two water H atoms could be located from difference neutron-density maps; structure refinement converged at R = 0.635. Two of the five CH2—O6 groups and one of the 15 O2, O3 hydroxyl groups of CA10 are twofold orientationally disordered. A total of 13.59 water molecules in the asymmetric unit are distributed over 23 positions; 20 of which are in the CA10 cavity, and the other three occupy intermolecular interstices. Of the 123 symmetry-independent hydrogen bonds, 25 (= 20%) are three-centered and 7 (= 6%) are four-centered. Water molecules and O—H groups of CA10 form an extended network with cooperative O—H...O—H...O—H hydrogen bonds. They are arranged in 11 polygons with three, four, five, six and eight O—H bonds and in homodromic, antidromic and heterodromic arrangements. Nine polygons are located within the cavity and the others are outside.
Use of software to search for higher symmetry: space group C2
Authors: Marsh Richard E. , Spek Anthony L.
Published: July 2004

From a search of the October 2000 release of the Cambridge Structural Database we find coordinate data for approximately 1500 entries under space group No. 5: C2 or, occasionally, A2, I2 or B112. Software designed to detect cases of missed higher symmetry identified 144 entries for detailed inspection. Of these, 50 should, we believe, be revised to space groups of higher symmetry. The most common revision is to space group C2/m, which entails adding a center of inversion and usually results in important changes in bond lengths and angles.
Associations of squaric acid and its anions as multiform building blocks of hydrogen-bonded molecular crystals
Authors: Gilli Gastone , Bertolasi Valerio , Gilli Paola , Ferretti Valeria
Published: July 2004

Squaric acid, H2C4O4 (H2SQ), is a completely flat diprotic acid that can crystallize as such, as well as in three different anionic forms, i.e. H2SQ·HSQ−, HSQ− and SQ2−. Its interest for crystal engineering studies arises from three notable factors: (i) its ability of donating and accepting hydrogen bonds strictly confined to the molecular plane; (ii) the remarkable strength of the O—H...O bonds it may form with itself which are either of resonance-assisted (RAHB) or negative-charge-assisted [(−)CAHB] types; (iii) the ease with which it may donate a proton to an aromatic base which, in turn, back-links to the anion by strong low-barrier N—H+...O1/2− charge-assisted hydrogen bonds. Analysis of all the structures so far known shows that, while H2SQ can only crystallize in an extended RAHB-linked planar arrangement and SQ2− tends to behave much as a monomeric dianion, the monoanion HSQ− displays a number of different supramolecular patterns that are classifiable as β-chains, α-chains, α-dimers and α-tetramers. Partial protonation of these motifs leads to H2SQ·HSQ− anions whose supramolecular patterns include ribbons of dimerized β-chains and chains of emiprotonated α-dimers. The topological similarities between the three-dimensional crystal chemistry of orthosilicic acid, H4SiO4, and the two-dimensional one of squaric acid, H2C4O4, are finally stressed.
Irreversible single-crystal to polycrystal and reversible single-crystal to single-crystal phase transformations in cyanurates
Authors: Kaftory Menahem , Botoshansky Mark , Kapon Moshe , Shteiman Vitaly
Published: July 2004

4,6-Dimethoxy-3-methyldihydrotriazine-2-one (1) undergoes a single-crystal to single-crystal reversible phase transformation at 319 K. The low-temperature phase crystallizes in monoclinic space group P21/n with two crystallographically independent molecules in the asymmetric unit. The high-temperature phase is obtained by heating a single crystal of the low-temperature phase. This phase is orthorhombic, space group Pnma, with the molecules occupying a crystallographic mirror plane. The enthalpy of the transformation is 1.34 kJ mol−1. The small energy difference between the two phases and the minimal atomic movement facilitate the single-crystal to single-crystal reversible phase transformation with no destruction of the crystal lattice. On further heating, the high-temperature phase undergoes methyl rearrangement in the solid state. 2,4,6-Trimethoxy-1,3,5-triazine (3), on the other hand, undergoes an irreversible phase transformation from single-crystal to polycrystalline material at 340 K with an enthalpy of 3.9 kJ mol−1; upon further heating it melts and methyl rearrangement takes place.
Amino and cyano N atoms in competitive situations: which is the best hydrogen-bond acceptor? A crystallographic database investigation
Authors: Ziao Nahossé , Graton Jérôme , Laurence Christian , Le Questel Jean-Yves
Published: July 2004

The relative hydrogen-bond acceptor abilities of amino and cyano N atoms have been investigated using data retrieved from the Cambridge Structural Database and via ab initio molecular orbital calculations. Surveys of the CSD for hydrogen bonds between HX (X = N, O) donors, N—T—C≡N (push–pull nitriles) and N—(Csp
3)
n
—C≡N molecular fragments  show that the hydrogen bonds are more abundant on the nitrile than on the amino nitrogen. In the push–pull family, in which T is a transmitter of resonance effects, the hydrogen-bonding ability of the cyano nitrogen is increased by conjugative interactions between the lone pair of the amino substituent and the C≡N group: a clear example of resonance-assisted hydrogen bonding. The strength of the hydrogen-bonds on the cyano nitrogen in this family follows the experimental order of hydrogen-bond basicity, as observed in solution through the pK
HB scale. The number of hydrogen bonds established on the amino nitrogen is greater for aliphatic aminonitriles N—(Csp
3)
n
—C≡N, but remains low. This behaviour reflects the greater sensitivity of the amino nitrogen to steric hindrance and the electron-withdrawing inductive effect compared with the cyano nitrogen. Ab initio molecular orbital calculations (B3LYP/6-31+G** level) of electrostatic potentials on the molecular surface around each nitrogen confirm the experimental observations.
Systematic generation of all nonequivalent closest-packed stacking sequences of length N using group theory
Authors: Thompson Richard M. , Downs Robert T.
Published: July 2004

An algorithm has been developed that generates all of the nonequivalent closest-packed stacking sequences of length N. There are 2
N
+ 2(−1)
N
different labels for closest-packed stacking sequences of length N using the standard A, B, C notation. These labels are generated using an ordered binary tree. As different labels can describe identical structures, we have derived a generalized symmetry group, Q ≃ D

N
× S
3, to sort these into crystallographic equivalence classes. This problem is shown to be a constrained version of the classic three-colored necklace problem.
X-ray investigations of sulfur-containing fungicides. III. Intramolecular forces governing the conformation of a novel orthorhombic polymorph of benzoylmethyl phenyl sulfone, benzoylmethyl 4-chlorophenyl sulfone and benzoylphenylmethyl phenyl sulfone
Authors: Wolf W. M.
Published: July 2004

The crystal and molecular structures of three β-ketosulfones: benzoylmethyl phenyl sulfone (I), benzoylmethyl 4-chlorophenyl sulfone (II) and benzoylphenylmethyl phenyl sulfone (III) have been investigated using X-ray analysis and quantum mechanics ab initio calculations. Compound (I) crystallizes in the monoclinic and orthorhombic crystal systems. The crystal structure of the orthorhombic polymorph has not been reported previously. At room temperature and in the presence of daylight the pale yellow orthorhombic crystals undergo transformation to the stable colourless monoclinic polymorph. Hyperconjugative σ(S—C1) − π*(C2=O3) and σ*(S—C1) − π(C2=O3) stabilization energies in benzoylmethyl phenyl sulfones are highly dependent on the central dihedral angle α: S—C1—C2=O3 and are largest for a gauche arrangement, as found in both crystal forms of (I). The electron density distribution in all compounds (I), (II) and (III) is significantly affected by interactions of oxygen lone pairs with non-bonding orbitals of the adjacent S—C1 and C1—C2 bonds. The latter effect is responsible for back-donation of the electron density from O atoms towards the central part of the molecule.
Electron density and electrostatic potential of KMnF3: a phase-transition study
Authors: Ivanov Yury , Nimura Tatsuya , Tanaka Kiyoaki
Published: July 2004

Three accurate X-ray diffraction experiments (Mo Kα, T = 190, 240 and 298 K) were carried out to track the temperature dependence of the electron density in the cubic perovskite potassium manganese trifluoride, KMnF3, from room temperature to just above that of the phase transition to the tetragonal structure (186 K), and to correlate the parameters of the critical points with the phase-transition mechanism. The data obtained were approximated by the Hansen–Coppens multipole model expanded up to hexadecupoles; the anharmonicity of the atomic displacements up to the fourth level was considered. Topological analysis shows only two types of chemical bond at room temperature, Mn—F and K—F. However, at low temperature the K—F bonds blocking the rotation of the MnF6 octahedra are weakened and new Mn—K bonds are formed to keep the crystal structure from disintegrating. The Mn—K bonds become stronger as the temperature approaches 186 K. This rearrangement of chemical bonds can be regarded as a precursor effect, which starts 50–60° above the phase-transition temperature. The effective one-particle potential of the F atom has a single minimum at 298 K and four well separated minima (with a shift of 0.2 Å from the equilibrium position towards the structural holes) at 190 K. Parameters of the critical points of the electron density indicate closed-shell type interactions between K—F and Mn—K pairs, whereas the Mn—F bond can be considered as an intermediate type. The topology of the electrostatic potentials is discussed as well.
Structural manifestations of proton transfer in complexes of 2,6-dichlorophenols with pyridines
Authors: Majerz I. , Koll A.
Published: July 2004

DFT B3LYP/6-31G(d,p) calculations were performed to describe the proton transfer reaction pathway in the 2,6-dichlorophenolate of pyridine. The aim of these calculations was to establish the character of the dependence of the structure parameters on the proton transfer and comparing the results with known structures, e.g. the 2,6-dichloro-4-nitro- and pentachlorophenolates of pyridines. To make this comparison more reliable, the calculations were repeated with the use of a reaction-field correction with the Onsager radius and electric permittivity taken from the solid-state measurements. The calculations show that the second approach gives a better description of the structural modifications during the proton transfer.
Bis(1-chloro-2,2,4,4-tetramethyl-3-oxocyclobutan-1-yl)pentasulfane: an occupancy modulated structure
Authors: Rae A. David , Linden Anthony , Majchrzak Agnieszka , Mloston Grzegorz , Heimgartner Heinz
Published: July 2004

The title compound crystallizes in the space group P21/n and may be described by a partial ordering of a 1:1 disordered P21/a parent structure with the c axis halved. The pentasulfane chain completes a full turn of a helix, which gives molecules containing left- or right-handed helices similar spatial requirements and allows them to be interchanged. The structure can be redescribed as containing 0.732 (1) of an ordered P21/n structure and 0.268 (1) of a 1:1 disordered P21/a structure, implying that 0.134 (1) of the molecule sites contain molecules of the opposite hand to that predicted by an ordered P21/n structure. It is found that the average molecular position in the asymmetric unit is not the same for each component and that these structural differences must be recognized to obtain a satisfactory refinement.
Supramolecular structures of substituted α,α′-trehalose derivatives
Authors: Baddeley Thomas C. , Davidson Iain G. , Glidewell Christopher , Low John N. , Skakle Janet M. S. , Wardell James L.
Published: July 2004

The structures of five substituted α,α′-trehalose trehalose derivatives have been determined, and these are compared with those of four previously published analogues. In 2,2′,3,3′,4,4′-hexaacetato-6,6′-bis-O-methylsulfonyl-α,α′-trehalose, C26H38O21S2, where the molecules lie across twofold rotation axes in the space group C2, a single C—H...O=S hydrogen bond links the molecules into sheets. 2,2′,3,3′,4,4′-Hexaacetato-6,6′-bis-O-(4-toluenesulfonyl)-α,α′-trehalose, C38H46O21S2, crystallizes with Z′ = 2 in the space group P212121 and a combination of three C—H...O hydrogen bonds, each having a carbonyl O atom as an acceptor, and a C—H...π(arene) hydrogen bond link the molecules into a three-dimensional framework. 2,2′,3,3′,4,4′-Hexaacetato-6,6′-diazido-α,α′-trehalose, C24H32N6O15, crystallizes as a partial ethanol solvate and three C—H...O hydrogen bonds link the substituted trehalose molecules into a three-dimensional framework. In 2,2′,3,3′-tetraacetato-6,6′-bis(N-acetylamino)-α,α′-trehalose dihydrate, C24H36N2O15·2H2O, the substituted trehalose molecules lie across twofold rotation axes in the space group P21212 and a three-dimensional framework is generated by the combination of O—H...O and N—H...O hydrogen bonds. The diaminotrehalose molecules in 6,6′-diamino-α,α′-trehalose dihydrate, C12H24N2O9.2(H2O), lie across twofold rotation axes in the space group P43212: a single O—H...N hydrogen bond links the trehalose molecules into sheets, which are linked into a three-dimensional framework by O—H...O hydrogen bonds.
Variation of large-scale regularity in modulated structures of Ca2CoSi2O7 studied by a simulation method
Authors: Kusaka Katsuhiro , Hagiya Kenji , Ohmasa Masaaki , Iishi Kazuaki
Published: July 2004

The period of two-dimensional modulation in Ca2CoSi2O7 varies with temperature (q = 0.285–1/3). The change in the modulated structure with the variation of q has been clarified by the construction of the structures using various q values and the modulation amplitudes determined at 293 K [q = 0.2913 (1), tetragonal]. The features of the modulated structures are characterized by the formation of CaO6 polyhedra and the variable distribution of bundles along the c-axis, composed of four arrays of CaO6 polyhedra and an array of CoO4 tetrahedra. The formation of octagonal arrangements of the bundles is a typical feature of the structures in the incommensurate phase. Large-scale regularities with sizes much larger than the modulation wavelength are also formed in the structures.
Isomeric iodo-N-(nitrobenzyl)anilines: interplay of hard and soft hydrogen bonds, iodo...nitro interactions and aromatic π...π stacking interactions
Authors: Glidewell Christopher , Low John N. , Skakle Janet M. S. , Wardell Solange M. S. V. , Wardell James L.
Published: July 2004

Molecules of 2-iodo-N-(4-nitrobenzyl)aniline, 4-O2NC6H4CH2NHC6H4I-2′ (1) are linked into chains by C—H...O hydrogen bonds. In the isomeric compound 3-iodo-N-(4-nitrobenzyl)aniline (2) a combination of N—H...O and C—H...O hydrogen bonds and iodo...nitro and aromatic π...π stacking interactions links the molecules into a three-dimensional framework structure. The two-dimensional supramolecular structure of 4-iodo-N-(4-nitrobenzyl)aniline (6) is built from a combination of C—H...O and N—H...π(arene) hydrogen bonds and aromatic π...π stacking interactions. 2-Iodo-N-(2-nitrobenzyl)aniline (7) crystallizes with two molecules in the asymmetric unit and these molecules are linked into ladders by a combination of N—H...O and C—H...O hydrogen bonds and iodo...nitro and aromatic π...π stacking interactions. Comparisons are made between the supramolecular structures of these compounds and those of other isomers, in terms both of the types of direction-specific intermolecular interactions exhibited and the dimensionality of the resulting supramolecular structures.
2-Hydroxyisophthalic acid: hydrogen-bonding patterns in the monohydrate and the tetraphenylphosphonium salt. An instance of dramatic acidity enhancement by symmetric, internally hydrogen-bonded anion stabilization
Authors: Bawa Shaleen , Coté Marie L. , Dubois Patrick , Lalancette Roger A. , Thompson Hugh W.
Published: July 2004

The monohydrate of the title phenolic diacid (C8H6O5·H2O, 2-hydroxybenzene-1,3-dioic acid or 3-carboxysalicylic acid) adopts a planar conformation, with the phenol hydrogen internally hydrogen-bonded to the carbonyl of one highly ordered carboxyl, which, in turn, donates a hydrogen bond to the oxygen of water. The second carboxyl is disordered and hydrogen-bonded both to water and to the disordered carboxyl of a centrosymmetrically related neighbor in a static disorder arrangement extending over two full asymmetric units. The water accepts either one or two hydrogen bonds and donates a long bifurcated hydrogen bond shared equally by O atoms of the phenol and the disordered carboxyl. The hydrogen bonding includes no standard carboxyl pairing and is entirely two-dimensional. The resulting planar ribbons stack translationally at a distance of 3.413 (8) Å, in an offset arrangement having non-translational interplanar distances of 0.821 (5) and 2.592 (6) Å. This structure is compared with two previously reported for this compound. The title compound forms a monoanion, whose tetraphenylphosphonium salt is described (C32H25O5P, tetraphenylphosphonium 2,6-dicarboxyphenolate, tetraphenylphosphonium 2-oxidoisophthalic acid or tetraphenylphosphonium 3-carboxysalicylate). The phenol oxygen is the site of formal negative charge on the anion, which is stabilized in a planar arrangement by symmetrical hydrogen bonds from both ortho-carboxyl groups. The energetics of this arrangement, the phenol and carboxyl acidities, and factors affecting those acidities and providing anion stabilization are discussed.
Sizes of molecules in organic crystals: the Voronoi–Dirichlet approach
Authors: Baburin Igor A. , Blatov Vladislav A.
Published: July 2004

The sizes of more than 100 000 molecules in organic crystals have been assessed as the volumes of molecular Voronoi–Dirichlet polyhedra. The average molecular volumes for all crystals are shown to be nearly equal to the corresponding values in homomolecular (consisting of identical molecules) crystals. The validity of the Voronoi–Dirichlet approach in determining molecular sizes is substantiated and the reasons for the variations in the molecular volumes are discussed. It is shown that a molecule increases its volume if it is surrounded by a good deal of high-row (i.e. an element with more than ten protons) atoms or if there is disorder in the crystal structure.
New bond-valence parameters for lanthanides. Addendum
Authors: Trzesowska Agata , Kruszynski Rafal , Bartczak Tadeusz J.
Published: July 2004

Recently, we have been informed that the part of our work [Trzesowska et al. (2004), Acta Cryst. B60, 174–178] concerning the linear correlation between the average bond-valence parameters and atomic number of a lanthanide is in agreement with the results of Chen & Hu (2002).
Structure of a high-pressure phase of vanadium pentoxide, β-V2O5
Authors: Filonenko V. P. , Sundberg M. , Werner P.-E. , Zibrov I. P.
Published: July 2004

A high-pressure phase of vanadium pentoxide, denoted β-V2O5, has been prepared at P = 6.0 GPa and T = 1073 K. The crystal structure of β-V2O5 has been studied by X-ray and neutron powder diffraction, and high-resolution transmission electron microscopy. The V atoms are six-coordinated within distorted VO6 octahedra. The structure is built up of quadruple units of edge-sharing VO6 octahedra linked by sharing edges along [010] and mutually connected by sharing corners along [001]. This arrangement forms layers of V4O10 composition in planes parallel to (100). The layers are mutually held together by weak forces. β-V2O5 is metastable and transforms to α-V2O5 at 643–653 K under ambient pressure. Structural relationships between β- and α-V2O5, and between β-V2O5 and B-Ta2O5-type structures are discussed. The high-pressure β-V2O5 layer structure can be considered as the parent of a new series of vanadium oxide bronzes with cations intercalated between the layers.
Rigid backbone moiety of KNI-272, a highly selective HIV protease inhibitor: methanol, acetone and dimethylsulfoxide solvated forms of 3-[3-benzyl-2-hydroxy-9-(isoquinolin-5-yloxy)-6-methylsulfanylmethyl-5,8-dioxo-4,7-diazanonanoyl]-N-tert-butyl-1,3-thiazolidine-4-carboxamide
Authors: Doi Mitsunobu , Kimura Tooru , Ishida Toshimasa , Kiso Yoshiaki
Published: July 2004

When crystals of kynostatin (KNI)-272, a highly selective HIV protease inhibitor containing allophenylnorstatine [(2S,3S)-3-amino-2-hydroxy-4-phenylbutyric acid], were grown in three different solvent systems (methanol, acetone and dimethylsulfoxide solutions), the local conformations around the hydroxymethylcarbonyl (HMC) moiety, which mimics the structure of the transition state, were similar in all three forms. The peptide backbones were slightly bent, but their structures differed from typical sheets, turns or helixes. Although the isoquinoline ring at the N-terminal showed conformational variations, a remarkable similarity was observed in the C-terminal region, including the HMC moiety. Moreover, the conformational characteristics of the uncomplexed forms resembled those of the inhibitor within the KNI-272–HIV protease complex. This suggests that the structure of the C-terminal region of KNI-272 is rigid or very stable.
Li3+δV6O13: a short-range-ordered lithium insertion mechanism
Authors: Höwing Jonas , Gustafsson Torbjörn , Thomas John O.
Published: July 2004

The structures of Li3V6O13 and Li3+δV6O13, δ ≃ 0.3, have been determined by single-crystal X-ray diffraction. Both compounds have the space group C2/m, with very similar cell parameters. In Li3V6O13, the Li atoms are found in the Wyckoff positions 4(i) and 2(b) with multiplicities of four and two, respectively. Since Li3V6O13 exhibits no superstructure reflections, it is concluded that Li3V6O13 contains one disordered lithium ion in an otherwise ordered centrosymmetric structure. On inserting more lithium into the structure, the Li3+δV6O13 phase is formed with the homogeneity range 0 < δ < 1. It is concluded that the site for the extra inserted lithium ion is closely coupled to the position of the disordered lithium ion in Li3V6O13. A mechanism for this behaviour and for the further formation of the Li6V6O13 end-phase in the Li
x
V6O13 system is proposed.
Structural features controlling the binding of β-carbolines to the benzodiazepine receptor
Authors: Ferretti Valeria , Gilli Paola , Borea Pier Andrea
Published: July 2004

β-Carbolines are a class of drug which can interact with a high affinity with the benzodiazepine (BDZ) binding site of the GABAA receptor. The present paper, aimed at obtaining a deeper insight into the structure–properties relationships of this class of molecules, reports the crystal structures of four β-carbolines: ZK93423 (3-carboethoxy-4-methoxymethyl-6-benzyloxy-β-carboline), ZK91296 (3-carboethoxy-4-methoxymethyl-5-benzyloxy-β-carboline), FG7142 (N-methyl-3-carbamoyl-β-carboline) and the low-affinity ligand harmine hydrochloride (1-methyl-7-methoxy-β-carboline). This set of structural data is completed by the X-ray structures of other carbolines of known biological activity retrieved from the Cambridge Crystallographic Database and by the structures of β-CCE (3-carboethoxy-β-carboline), 6-PBC (3-carboethoxy-4-methoxymethyl-6-isopropoxy-β-carboline), PRCC (3-isopropoxy-β-carboline) and ZK93426 (3-carboethoxy-4-methyl-5-isopropoxy-β-carboline), which have been obtained by molecular-mechanics simulations. The structural features of all these molecules have been compared according to the stereochemical model we proposed in 1987. The structural comparison is integrated by the Free–Wilson analysis on 32 β-carbolines of known binding affinity data.
Synchrotron X-ray and ab initio studies of β-Si3N4
Authors: du Boulay D. , Ishizawa N. , Atake T. , Streltsov V. , Furuya K. , Munakata F.
Published: July 2004

Almost absorption- and extinction-free single-crystal synchrotron X-ray diffraction data were measured at 150, 200 and 295 K for β-Si3N4, silicon nitride, at a wavelength of 0.7 Å. The true symmetry of this material has been the subject of minor controversy for several decades. No compelling evidence favouring the low-symmetry P63 model was identified in this study.
Ab initio structure determination of the hygroscopic anhydrous form of α-lactose by powder X-ray diffraction
Authors: Platteau Cyril , Lefebvre Jacques , Affouard Frederic , Derollez Patrick
Published: July 2004

Annealing of α-lactose monohydrate at 408 K yielded a mixture of this compound with hygroscopic anhydrous α-lactose. A powder X-ray diffraction pattern of this mixture was recorded at room temperature. The starting structural model of hygroscopic α-lactose was found by a Monte Carlo simulated-annealing method. The final structure was obtained through Rietveld refinements, with soft restraints on interatomic bond lengths and bond angles, and crystalline energy minimization to locate the H atoms of the hydroxy groups. The crystalline cohesion is achieved by networks of O—H...O hydrogen bonds that differ from those of the monohydrate phase. The width of the Bragg peaks is interpreted by a phenomenological microstructural approach in terms of isotropic size effects and anisotropic strain effects.