Interesting Solvent Area in Crystal Structures of Two Natural Ergot Alkaloids

2005 ◽  
Vol 70 (1) ◽  
pp. 41-50 ◽  
Author(s):  
Blanka Klepetářová ◽  
Jan Čejka ◽  
Bohumil Kratochvíl ◽  
Svetlana Pakhomova ◽  
Ivana Císařová ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Three Dimensional ◽  
Ergot Alkaloids ◽  
Unit Cell ◽  
Dimensional Structure ◽  
Chemical Similarity ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Benzene Solvate ◽  
Similarity Structures

The structures of ergotamine bis(benzene) solvate (1) and ergocristine bis(benzene) solvate (2) are reported. Both structures crystallise in theP212121space group with cell parameters:1,a= 14.2968(3) Å,b= 15.4700(2) Å,c= 17.8123(4) Å, andV= 3939.57(13) Å3;2,a= 11.8358(2) Å,b= 17.6469(3) Å,c= 19.7125(3) Å, andV= 4117.25(12) Å3. Unexpectedly, despite the chemical similarity, structures of1and2significantly differ not only in the unit cell parameters, but also in the packing. Whereas in1solvent cavities are separated, there is only one unusual continuous solvent area in2filled with benzene, forming independent three-dimensional structure.

Three Dimensional Structure of UMo8O26: Ordering of U-Vacancies

2002 ◽  
Vol 718 ◽  
Author(s):  
N.D. Zakharov ◽  
P. Werner
Keyword(s):  
Low Temperatures ◽  
Driving Force ◽  
Three Dimensional ◽  
Solid State Reaction Method ◽  
Dimensional Structure ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Selected Area Electron Diffraction ◽  
Transmission Electron ◽  
Edx Microanalysis

AbstractThe structure and composition of UMo8O26 synthesized by solid state reaction method have been investigated by High Resolution Transmission Electron Microscopy (HRTEM), Selected Area Electron Diffraction, and EDX microanalysis. The ordering of U vacancies results in considerable enlargement of unit cell parameters: an=6.44 nm, bn=1.45 nm, cn=1.6 nm. It is build up of four layers piled up in c direction. Each following layer is shifted relative to previous one by vector bn/4. Eight hexagonal tunnels in each layer are filled by U atoms, while the eight others are vacant (V). Interaction between U cations and vacancies is driving force for ordering. The variation of stoichiometry can be a reason for appearance of incommensurate modulations in these crystals. It seems plausible that this structure might also exhibit superconductivity at low temperatures.

scholarly journals New crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 in two conformations

2014 ◽  
Vol 70 (11) ◽  
pp. 1468-1471
Author(s):  
Trung Thanh Thach ◽  
Sangho Lee
Keyword(s):  
Crystal Structures ◽  
Adenylate Kinase ◽  
Bound States ◽  
Critical Role ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
Ligand Free ◽  
Adenylate Kinases

Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groupsP21andP1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space groupC2, with unit-cell parametersa= 73.5,b= 54.3,c= 62.7 Å, β = 118.8°. The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on Cαatoms of 1.4 Å. The new crystal of the complex with the two-substrate-mimicking inhibitorP1,P5-bis(adenosine-5′-)pentaphosphate (Ap5A) belonged to space groupP1, with unit-cell parametersa= 53.9,b= 62.3,c= 63.0 Å, α = 101.9, β = 112.6, γ = 89.9°. Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.

The structures of marialite (Me6) and meionite (Me93) in space groups P42/n and I4/m, and the absence of phase transitions in the scapolite series

2011 ◽  
Vol 26 (2) ◽  
pp. 119-125 ◽  
Author(s):  
Sytle M. Antao ◽  
Ishmael Hassan
Keyword(s):  
Phase Transitions ◽  
High Resolution ◽  
Crystal Structures ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Space Groups ◽  
Cell Parameters ◽  
The Mean

The crystal structures of marialite (Me6) from Badakhshan, Afghanistan and meionite (Me93) from Mt. Vesuvius, Italy were obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinements. Their structures were refined in space groups I4/m and P42/n, and similar results were obtained. The Me6 sample has a formula Ca0.24Na3.37K0.24[Al3.16Si8.84O24]Cl0.84(CO3)0.15, and its unit-cell parameters are a=12.047555(7), c=7.563210(6) Å, and V=1097.751(1) Å3. The average ⟨T1-O⟩ distances are 1.599(1) Å in I4/m and 1.600(2) Å in P42/n, indicating that the T1 site contains only Si atoms. In P42/n, the average distances of ⟨T2-O⟩=1.655(2) and ⟨T3-O⟩=1.664(2) Å are distinct and are not equal to each other. However, the mean ⟨T2,3-O⟩=1.659(2) Å in P42/n and is identical to the ⟨T2′-O⟩=1.659(1) Å in I4/m. The ⟨M-O⟩ [7]=2.754(1) Å (M site is coordinated to seven framework O atoms) and M-A=2.914(1) Å; these distances are identical in both space groups. The Me93 sample has a formula of Na0.29Ca3.76[Al5.54Si6.46O24]Cl0.05(SO4)0.02(CO3)0.93, and its unit-cell parameters are a=12.19882(1), c=7.576954(8) Å, and V=1127.535(2) Å3. A similar examination of the Me93 sample also shows that both space groups give similar results; however, the C–O distance is more reasonable in P42/n than in I4/m. Refining the scapolite structure near Me0 or Me100 in I4/m forces the T2 and T3 sites (both with multiplicity 8 in P42/n) to be equivalent and form the T2′ site (with multiplicity 16 in I4/m), but ⟨T2-O⟩ is not equal to ⟨T3-O⟩ in P42/n. Using different space groups for different regions across the series implies phase transitions, which do not occur in the scapolite series.

Crystal structure of three diaza-crowns-18

1997 ◽  
Vol 212 (5) ◽  
Author(s):  
P. Dokurno ◽  
R. Trokowski ◽  
B. Kościuszko-Panek ◽  
T. Ossowski ◽  
A. Konitz ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Space Groups ◽  
Cell Parameters

AbstractThe crystal structures of three diaza crowns-18, namely 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane (crown 1), 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diacetonitrile (crown 2) and N,N′-(1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyldi-2,1-ethanediyl)bis-[4-methyl-benzenesulfonamide] (crown 3) have the following space groups and unit cell parameters: crown 1(C

scholarly journals Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

2010 ◽  
Vol 66 (5) ◽  
pp. 544-558 ◽  
Author(s):  
Jacco van de Streek ◽  
Marcus A. Neumann
Keyword(s):  
Density Functional Theory ◽  
Crystal Structures ◽  
Density Functional ◽  
Unit Cell ◽  
Organic Crystal ◽  
Large Temperature ◽  
Unit Cell Parameters ◽  
Functional Theory ◽  
Cell Parameters ◽  
Experimental Crystal

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

Structural studies of ligands for the glycine binding site of the excitatory amino acid receptor complex: 2. 6-bromo-, 6-methyl-, and 6-styryl-1,8-ethano-4-hydro-2,3-quinoxalinedione

1994 ◽  
Vol 72 (10) ◽  
pp. 2028-2036 ◽  
Author(s):  
Maciej Kubicki ◽  
Teresa W. Kindopp ◽  
Mario V. Capparelli ◽  
Penelope W. Codding
Keyword(s):  
Hydrogen Bond ◽  
Binding Site ◽  
Crystal Structures ◽  
Excitatory Amino Acid ◽  
Glycine Receptor ◽  
Three Dimensional ◽  
Unit Cell ◽  
Geometric Constraints ◽  
Cell Parameters ◽  
Π Stacking

The crystal structures of three tricyclic quinoxalinedione derivatives, 6-bromo-1,8-ethano-4-hydro-2,3-quinoxalinedione (1), 6-methyl-1,8-ethano-4-hydro-2,3-quinoxalinedione hydrate (2), and 6-styryl-1,8-ethano-4-hydro-2,3-quinoxalinedione (3), are reported. For 1 and 2, the space groups are P21/n with the unit cell parameters for 1: a = 7.4003(5) Å, b = 8.5799(5) Å, c = 14.3127(9) Å, β = 90.639(6)°, and for 2: a = 7.0590(2) Å, b = 10.7483(3) Å, c = 13.9509(7) Å, β = 103.290(3)°. For 3, the space group is P21/c, with a = 19.3683(10) Å, b = 8.0962(16) Å, c = 19.5801(16) Å, β = 114.028(6)°. Compound 3 crystallizes with two molecules in the asymmetric part of the unit cell; in one of them the styryl group is disordered. The geometries of the 1,8-ethano-4-hydro-2,3-quinoxalinedione fragments are similar in all observations, with the differences mainly caused by the different nature of the substituents in the 6-position. Hydrogen bonds connect the molecules into three-dimensional networks. Head-to-tail π-stacking between molecules connected by a center of symmetry determines the packing modes in 1 and 2 but there is no π-stacking in the crystal structure of 3. The crystal structures of the three quinoxaline derivative ligands for the glycine receptor suggest a mode of recognition that involves an [Formula: see text]receptor hydrogen bond, a three-centre hydrogen bond to the neighboring carbonyl groups on the ligand, and π-stacking between ligand and receptor. This mode is consistent with the geometric constraints of the current binding site model but places greater emphasis on hydrogen-bond interactions.

Redefinition of satimolite

2018 ◽  
Vol 82 (5) ◽  
pp. 1033-1047 ◽  
Author(s):  
Igor V. Pekov ◽  
Natalia V. Zubkova ◽  
Dmitry A. Ksenofontov ◽  
Nikita V. Chukanov ◽  
Vasiliy O. Yapaskurt ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Rietveld Method ◽  
Three Dimensional ◽  
Direct Methods ◽  
Salt Dome ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Octahedral Clusters

ABSTRACTThe borate mineral satimolite, which was first described in 1969 and remained poorly-studied until now, has been re-investigated (electron microprobe analysis, single-crystal and powder X-ray diffraction studies, crystal-structure determination, infrared spectroscopy) and redefined based on the novel data obtained for the holotype material from the Satimola salt dome and a recently found sample from the Chelkar salt dome, both in North Caspian Region, Western Kazakhstan. The revised idealized formula of satimolite is KNa2(Al5Mg2)[B12O18(OH)12](OH)6Cl4·4H2O (Z = 3). The mineral is trigonal, space group R$\bar{3}$m, unit-cell parameters are: a = 15.1431(8), c = 14.4558(14) Å and V = 2870.8(4) Å3 (Satimola) and a = 15.1406(4), c = 14.3794(9) Å and V = 2854.7(2) Å3 (Chelkar). The crystal system and unit-cell parameters are quite different from those reported previously. The crystal structure of the sample from Chelkar was solved based on single-crystal data (direct methods, R = 0.0814) and the structure of the holotype from Satimola was refined on a powder sample by the Rietveld method (Rp = 0.0563, Rwp = 0.0761 and Rall = 0.0667). The structure of satimolite is unique for minerals. It contains 12-membered borate rings [B12O18(OH)12] in which BO3 triangles alternate with BO2(OH)2 tetrahedra sharing common vertices, and octahedral clusters [M7O6(OH)18] with M = Al5Mg2 in the ideal case, with sharing of corners between rings and clusters to form a three-dimensional heteropolyhedral framework. Each borate ring is connected with six octahedral clusters: three under the ring and three over the ring. Large ellipsoidal cages in the framework host Na and K cations, Cl anions and H2O molecules.

scholarly journals Synthesis, Crystal structure, Vibrational, Optical and Dielectric properties Of 2-(2-Aminoethyl)-1-methylpyrrolidinum chloride hexachlorobismuthate (III) monohydrate [C7H18N2]2ClBiCl6.H2O

2013 ◽  
Vol 9 (3) ◽  
pp. 2005-2022 ◽  
Author(s):  
Fayçal Ben Tahar ◽  
Chakib Hrizi ◽  
Slaheddine Chaabouni ◽  
Nassira Chniba-Boudjada ◽  
Nicolas Ratel Ramond ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dielectric Properties ◽  
Room Temperature ◽  
Three Dimensional ◽  
Free Water ◽  
Unit Cell ◽  
Water Molecules ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Vis Spectroscopy

Synthesis, crystal structure, vibrational and dielectric properties of [C7H18N2]2ClBiCl6.H2O are reported. The compound crystallizes at room temperature in the orthorhombic system, space group P212121, with the following unit cell parameters : a = 7.5500(6) Å, b = 18.3780(2) Å, c = 19.8980(13) Å, V = 2760.9(4) Å3 and four molecules per unit cell. The structure has been solved by three-dimensional Patterson synthesis and refined by least-squares analysis (R1 = 0.0463, wR2 = 0.0764). The crystal structure of the title compound, [C7H18N2]2ClBiCl6.H2O consists of 2-(2-Aminoethyl)-1-methylpyrrolidinium cations, [BiCl6]3- anions, Cl- anions and free water molecules. The Bi(III) cation is coordinated by six Cl- anions in slightly distorsed octahedral geometry. In the crystal, extensive intermolecular N-H…Cl hydrogen bonds occur. The charge-transfer (CT) interactions between 2-(2-Aminoethyl)-1-methylpyrrolidinium cation and the anionic hosts have been revealed by structural analysis and UV-vis spectroscopy. The dielectric properties have been investigated at temperature range from 100 to 300 K at various frequencies (1 KHz – 1 MHz). The evolution of dielectric constant as a function of temperature and frequency of pellet has been investigated in order to determine some related parameters.

The Crystal Structures of the Diastereoisomers (+)589-(Λ-δ-δ)-cis-Bis(ethylenediamine)dinitrocobalt(III)Hydrogen-D-tartrate Monohydrate and (-)589-(Λ-λ-λ)-cis-Bis(ethylenediamine)dinitrocobalt(III) Hydrogen-D-tartrate Dihydrate

1988 ◽  
Vol 41 (9) ◽  
pp. 1305 ◽  
Author(s):  
JM Frederiksen ◽  
E Horn ◽  
MR Snow ◽  
ERT Tiekink
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Layer Structure ◽  
Three Dimensional ◽  
Water Molecules ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Tartrate Anion

The crystal structures of the diastereoisomers formed between the hydrogen-D-tartrate anion and the cations (+)-(Λ-[Co(en)2(NO2)2]+ (1) and (-)-(Δ)-[Co(en)2(NO2)2]+ (2) have been determined by three-dimensional X-ray analysis. The crystal structures are comprised of octahedrally coordinated cobalt atoms, hydrogentartrate anions and water molecules interconnected by a complex hydrogen bonding network. In (1), columns of complex parallel to a 21 screw axis along a, are linked via hydrogen bonding contacts to a total of six chains of 'head-to-tail' hydrogentartrate strands. In contrast, in (2) the chains of hydrogentartrate anions associate with each other to form well defined 'walls' which sandwich hydrogen-bonded columns of complex cations such that the structure may be thought of as a layer structure of hydrogentartrate anions and complex cations. Crystals of both compounds are orthorhombic, space group P212121 with Z = 4, unit cell parameters for (1): a 7.670(1), b 12.160(1), c 18.028(1)Ǻ, V 1681.4 Ǻ3 and for (2): a 7.735(2), b 8.505(5), c 26.846(9) Ǻ, V 1766 1 Ǻ3. The structures were each refined by a full-matrix least-squares procedure to final R 0.026, Rw 0.027 for 1764 reflections with I ≥ 2.5σ(I) for (1) and R 0.065, Rw 0.073 for 1322 reflections for (2).

Molecular and Crystal Structure of Sildenafil Base

2012 ◽  
Vol 67 (5) ◽  
pp. 491-494 ◽  
Author(s):  
Dmitrijs Stepanovs ◽  
Anatoly Mishnev
Keyword(s):  
Crystal Structure ◽  
Erectile Dysfunction ◽  
Crystal Structures ◽  
Unit Cell ◽  
Sildenafil Citrate ◽  
Unit Cell Parameters ◽  
Monoclinic System ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Sildenafil citrate monohydrate, well known as Viagra®, is a drug for the treatment of erectile dysfunction. Here we present the X-ray crystal structure of the sildenafil base, C22H30N6O4S. The compound crystallizes in the monoclinic system, space group P21/c with the unit cell parameters a = 17:273(1), b=17:0710(8), c=8:3171(4) Å , b =99:326(2), Z = 4, V = 2420:0(3) Å3. A comparison with the known crystal structures of sildenafil citrate monohydrate and sildenafil saccharinate is also presented.

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