scholarly journals Conformation and supramolecular arrangement of 1,3:2,4-dibenzyli-dene-D-sorbitol in solution and in single crystals

2021 ◽  
Author(s):  
Fernán Berride ◽  
Victor M. Sánchez-Pedregal ◽  
Bruno Dacuña ◽  
Eurico Cabrita ◽  
Armando Navarro-Vázquez ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Nmr Spectroscopy ◽  
Van Der Waals Interactions ◽  
Side Chain ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Definitive Evidence ◽  
Phenyl Rings

The X-ray crystal structure of the gelator 1,3:2,4-dibenzylidene-D-sorbitol (DBS) is reported here. DBS is an important gelating molecule known for nearly 130 years, that has eluded crystallization until now. The crystal obtained presents an axial stacking of DBS molecules stabilized by both Van der Waals interactions and intermolecular hydrogen bonds of the side chain hydroxyl groups with either neighboring DBS or water molecules. The crystal structure shows definitive evidence for the frequently assumed “butterfly” type aggregation mode and experimentally proves the equatorial placement of the phenyl rings. The conformation of DBS has been analyzed in the crystal structure and compared with that determined in solution through NMR spectroscopy.

scholarly journals Crystal structure of the DNA sequence d(CGTGAATTCACG)2with DAPI

2017 ◽  
Vol 73 (9) ◽  
pp. 500-504 ◽  
Author(s):  
Hristina I. Sbirkova-Dimitrova ◽  
Boris Shivachev
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Minor Groove ◽  
Van Der Waals Interactions ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Base Pairs ◽  
X Ray ◽  
Dna Molecule ◽  
Dna Fragment

The structure of 4′,6-diamidine-2-phenylindole (DAPI) bound to the synthetic B-DNA oligonucleotide d(CGTGAATTCACG) has been solved in space groupP212121by single-crystal X-ray diffraction at a resolution of 2.2 Å. The structure is nearly isomorphous to that of the previously reported crystal structure of the oligonucleotide d(CGTGAATTCACG) alone. The adjustments in crystal packing between the native DNA molecule and the DNA–DAPI complex are described. DAPI lies in the narrow minor groove near the centre of the B-DNA fragment, positioned over the A–T base pairs. It is bound to the DNA by hydrogen-bonding and van der Waals interactions. Comparison of the two structures (with and without ligand) shows that DAPI inserts into the minor groove, displacing the ordered spine waters. Indeed, as DAPI is hydrophobic it confers this behaviour on the DNA and thus restricts the presence of water molecules.

1,2-Dimethyl-4-nitro-5-morpholinoimidazole and its hydrate: a case of a centrosymmetric–noncentrosymmetric ambiguity

2003 ◽  
Vol 59 (4) ◽  
pp. 487-491 ◽  
Author(s):  
Maciej Kubicki ◽  
Teresa Borowiak ◽  
Grzegorz Dutkiewicz ◽  
Stanisław Sobiak ◽  
Iwona Weidlich
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Van Der Waals Interactions ◽  
Water Molecules ◽  
Intermolecular Hydrogen Bonds ◽  
Strong Electron ◽  
Crystal Forms ◽  
Basic Character ◽  
Centrosymmetric Matrix ◽  
Water Hydrogen

The compound studied is 1,2-dimethyl-4-nitro-5-morpholinoimidazole (1) in its anhydrous (1) and hydrated [(1)·H2O] crystal forms. In spite of the strong electron-withdrawing effect of the nitro group, the unsubstituted N atom of the imidazole moiety retains its basic character and acts as an acceptor for intermolecular hydrogen bonds: either weak C—H...N bonds in (1) or strong O—H...N bonds, with the water molecules, in (1)·H2O. The packing in (1) is determined by weak C—H...N and C—H...O hydrogen bonds, van der Waals interactions and the stacking of imidazole fragments. The crystal structure of (1)·H2O is determined by strong O—H(water)...N3(imidazole) and O—H(water)...O(water) hydrogen bonds. This structure consists of a centrosymmetric `matrix' of imidazole derivative molecules and locally noncentrosymmetric arrays of hydrogen-bonded water molecules. Each of these arrays is strictly homodromic, i.e. it runs only in one direction: ...H—O...H—O...H—O... or ...O—H...O—H...O—H.... These homodromic domains are statistically distributed within the crystal.

scholarly journals Crystal structure of 3,14-dimethyl-2,6,13,17-tetraazoniatricyclo[16.4.0.07,12]docosane tetrachloride tetrahydrate from synchrotron X-ray data

2018 ◽  
Vol 74 (8) ◽  
pp. 1039-1041
Author(s):  
Dohyun Moon ◽  
Jong-Ha Choi
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Synchrotron Radiation ◽  
Three Dimensional ◽  
Water Molecules ◽  
Inversion Symmetry ◽  
Asymmetric Unit ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Dimensional Network

The crystal structure of the title salt, C20H44N4 4+·4Cl−·4H2O, has been determined using synchrotron radiation at 220 K. The structure determination reveals that protonation has occurred at all four amine N atoms. The asymmetric unit contains one half-cation (completed by crystallographic inversion symmetry), two chloride anions and two water molecules. There are two molecules in the unit cell. The Cl− anions and hydrate molecules are involved in hydrogen bonding. The crystal structure is stabilized by intermolecular hydrogen bonds involving the macrocycle N—H groups and water O—H groups as donors and the O atoms of the water molecules and the Cl− anions as acceptors, giving rise to a three-dimensional network.

scholarly journals Crystal structure of 3,14-diethyl-2,6,13,17-tetraazoniatricyclo[16.4.0.07,12]docosane tetrachloride tetrahydrate from synchrotron X-ray data

2021 ◽  
Vol 77 (2) ◽  
pp. 213-216
Author(s):  
Dohyun Moon ◽  
Jong-Ha Choi
Keyword(s):  
Crystal Structure ◽  
Synchrotron Radiation ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Water Molecules ◽  
Inversion Symmetry ◽  
Asymmetric Unit ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Dimensional Network

The crystal structure of the hydrated title salt, C22H48N4 4+·4Cl−·4H2O (C22H48N4 = H4 L = 3,14-diethyl-2,6,13,17-tetraazoniatricyclo[16.4.0.07,12]docosane), has been determined using synchrotron radiation at 220 K. The structure determination reveals that protonation has occurred at all four amine N atoms. The asymmetric unit comprises one half of the macrocyclic cation (completed by crystallographic inversion symmetry), two chloride anions and two water molecules. The macrocyclic ring of the tetracation adopts an exodentate (3,4,3,4)-D conformation. The crystal structure is stabilized by intermolecular hydrogen bonds involving the macrocycle N—H groups and water O—H groups as donors, and the O atoms of the water molecules and chloride anions as acceptors, giving rise to a three-dimensional network.

scholarly journals Crystal structure of bis[cis-(1,4,8,11-tetraazacyclotetradecane-κ4N)bis(thiocyanato-κN)chromium(III)] dichromate monohydrate from synchrotron X-ray diffraction data

2017 ◽  
Vol 73 (1) ◽  
pp. 72-75 ◽  
Author(s):  
Dohyun Moon ◽  
Masahiro Takase ◽  
Takashiro Akitsu ◽  
Jong-Ha Choi
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Complex Salt ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
Rotation Symmetry ◽  
X Ray ◽  
Dimensional Network ◽  
Distorted Octahedral

The structure of the complex salt,cis-[Cr(NCS)2(cyclam)]2[Cr2O7]·H2O (cyclam = 1,4,8,11-tetraazacyclotetradecane, C10H24N4), has been determined from synchrotron data. The asymmetric unit comprises of one [Cr(NCS)2(cyclam)]+cation, one half of a Cr2O72−anion (completed by inversion symmetry) and one half of a water molecule (completed by twofold rotation symmetry). The CrIIIion is coordinated by the four cyclam N atoms and by two N atoms ofcis-arranged thiocyanate anions, displaying a distorted octahedral coordination sphere. The Cr—N(cyclam) bond lengths are in the range 2.080 (2) to 2.097 (2) Å while the average Cr—N(NCS) bond length is 1.985 (4) Å. The macrocyclic cyclam moiety adopts thecis-V conformation. The bridging O atom of the dichromate anion is disordered around an inversion centre, leading to a bending of the Cr—O—Cr bridging angle [157.7 (3)°]; the anion has a staggered conformation. The crystal structure is stabilized by intermolecular hydrogen bonds involving the cyclam N—H groups and water O—H groups as donor groups, and the O atoms of the Cr2O72−anion and water molecules as acceptor groups, giving rise to a three-dimensional network.

scholarly journals Crystal structure of bis[(oxalato-κ2O1,O2)(1,4,8,11-tetraazacyclotetradecane-κ4N)chromium(III)] dichromate octahydrate from synchrotron X-ray data

2017 ◽  
Vol 73 (3) ◽  
pp. 403-406 ◽  
Author(s):  
Dohyun Moon ◽  
Jong-Ha Choi
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Distorted Octahedral Geometry ◽  
Water Molecules ◽  
Asymmetric Unit ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Dimensional Network ◽  
Oxalate Ligand ◽  
Distorted Octahedral

The asymmetric unit of the title compound, [Cr(C2O4)(C10H24N4)]2[Cr2O7]·8H2O (C10H24N4= 1,4,8,11-tetraazacyclotetradecane, cyclam; C2O4= oxalate, ox) contains one [Cr(ox)(cyclam)]+cation, one half of a dichromate anion that lies about an inversion centre so that the bridging O atom is equally disordered over two positions, and four water molecules. The terminal O atoms of the dichromate anion are also disordered over two positions with a refined occupancy ratio 0.586 (6):0.414 (6). The CrIIIion is coordinated by the four N atoms of the cyclam ligand and one bidentate oxalato ligand in acisarrangement, resulting in a distorted octahedral geometry. The Cr—N(cyclam) bond lengths are in the range 2.069 (2)–2.086 (2) Å, while the average Cr—O(ox) bond length is 1.936 Å. The macrocyclic cyclam moiety adopts thecis-V conformation. The dichromate anion has a staggered conformation. The crystal structure is stabilized by intermolecular hydrogen bonds involving the cyclam N—H groups and water O—H groups as donors, and the O atoms of oxalate ligand, water molecules and the Cr2O72−anion as acceptors, giving rise to a three-dimensional network.

Erdalkaliquadratate, VI [1] SrC4 O4 · 3H2O, Typ III / Alkaline-earth Squarates, VI [1] SrC4O4 ·3H2O, Type III

1988 ◽  
Vol 43 (1) ◽  
pp. 99-103 ◽  
Author(s):  
Christian Robl
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Alkaline Earth ◽  
Crystal Structure Analysis ◽  
Water Molecules ◽  
Type I ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Type Iii ◽  
Close Relationship

AbstractSrC4O4 ·3 H2O, type III. was obtained in an aqueous silica gel besides crystals of SrC4O4-3 H20. type I. X-ray crystal structure analysis showed close relationship to BaC4O4-3H20. but no isotypism. Sr2+ is coord|inated by four water molecules and four oxygen atoms of the squarate dianion. The connection of Sr2+ with C4O42- leads to layers. The geometry of C4O42- is typical for delocalized π-systems. The Osquarate atoms are not equally bound to Sr2+. One Osquaralc atom (0(4)) is bound to two Sr2+, two (O(1). O(2)) are bound to one Sr2+, respectively, and the fourth Osquaratc atom (0(3)) shows no bonding contact to Sr2+. These differences are compensated for by intermolecular hydrogen bonds which involve O(3) three times, O( I) and O(2) once each, but not O(4).

scholarly journals A New Decavanadate with Organic Cation: Synthesis, Crystal Structure, and Hirshfeld Surface Analysis

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Rawia Nasri ◽  
Regaya Ksiksi ◽  
Mohsen Graia ◽  
Mohamed Faouzi Zid
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Room Temperature ◽  
Organic Cation ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Van Der Waals Interactions ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
X Ray

A new 2,6-bis aminomethyl piperidine decavanadate hydrate, (C7N3H20)2V10O28.4.21H2O, was synthesized by slow evaporation of a solution at room temperature. The molecular structure was investigated by single-crystal X-ray diffraction. In the crystal structure, the layers of decavanadate groups, organic cations, and water molecules are arranged parallel to the (010) plane. Also, the prepared compound has been analysed by FTIR spectroscopy and scanning electron microscopy (SEM). The crystal structure of the title compound is stabilized by hydrogen bonds and van der Waals interactions. The cohesion of the structure is ensured by O-H…O and N-H…O hydrogen bonds. The three-dimensional Hirshfeld surface (3D-HS) and the relative two-dimensional fingerprint plots (2D-FPs) of (C7N3H20)2V10O28.4.21H2O compound revealed that the structure is dominated by O…H/H…O (70.8%) and H…H (18.5%) contacts.

Crystal structure of mupirocin form I, C26H44O9

2016 ◽  
Vol 31 (2) ◽  
pp. 118-125
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Density Functional ◽  
Three Dimensional ◽  
Van Der Waals Interactions ◽  
Hydroxyl Groups ◽  
Powder Diffraction Data ◽  
Powder Diffraction File ◽  
X Ray ◽  
Bond Network

The crystal structure of mupirocin Form I has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Mupirocin Form I crystallizes in space group P21 (#4) with a = 12.562 81(16), b = 5.103 63(4), c = 21.713 34(29) Å, β = 100.932(1)°, V = 1366.91(2) Å3, and Z = 2. Although the three hydroxyl groups and the carboxylic acid participate in a three-dimensional hydrogen bond network, the crystal energy appears to be dominated by van der Waals interactions. The Rietveld-refined and density functional optimized structures differ significantly. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™.

scholarly journals Crystal structure of pimecrolimus Form B, C43H68ClNO11

2021 ◽  
Vol 36 (1) ◽  
pp. 35-42
Author(s):  
Shivang Bhaskar ◽  
Joseph T. Golab ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Density Functional ◽  
Van Der Waals Interactions ◽  
Powder Diffraction File ◽  
X Ray ◽  
Weak Intermolecular Interactions ◽  
Significant Difference ◽  
Atomic Coordinates ◽  
Solid State Conformation

The crystal structure of pimecrolimus Form B has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Pimecrolimus crystallizes in the space group P21 (#4) with a = 15.28864(7), b = 13.31111(4), c = 10.95529(5) Å, β = 96.1542(3)°, V = 2216.649(9) Å3, and Z = 2. Although there are an intramolecular six-ring hydrogen bond and some larger chain and ring patterns, the crystal structure is dominated by van der Waals interactions. There is a significant difference between the conformation of the Rietveld-refined and the DFT-optimized structures in one portion of the macrocyclic ring. Although weak, intermolecular interactions are apparently important in determining the solid-state conformation. The powder pattern is included in the Powder Diffraction File™ (PDF®) as entry 00-066-1619. This study provides the atomic coordinates to be added to the PDF entry.

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