2,3,5′,6,6′,7-Hexamethoxy-3′H,10H-spiro[anthracene-9,1′-isobenzofuran]-3′,10-dione

2007 ◽  
Vol 63 (11) ◽  
pp. o4390-o4391 ◽  
Author(s):  
Marlon R. Lutz ◽  
Matthias Zeller ◽  
Daniel P. Becker
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Cell Volume ◽  
Unit Cell Volume ◽  
Unit Cell ◽  
Spiro Compound ◽  
Π Interactions ◽  
Rigid Molecule ◽  
Title Molecule ◽  
Solvent Molecules

The title molecule, C27H24O9, was formed via a transannular electrophilic addition of a putative cyclotriveratrylene triketone and is made up of an anthrone and an isobenzofuranone ring that are connected via one C atom to form a spiro compound. The anthracene and isobenzofuranone ring systems of the spiro compound are both essentially planar and perpendicular to each other, with an angle of 89.90 (2)° between them. The rigid molecule crystallizes with large voids of 598.7 Å3, or 21.5% of the unit-cell volume, that are partially filled with unmodelled disordered solvent molecules. The voids stretch as infinite channels along the [101] direction. The packing of the structure is partially stabilized by a range of weak C—H...O hydrogen bonds and also by C—H...π interactions. No significant π–π interactions are present in the crystal structure.

scholarly journals 1,1′,3,3′-Tetramesitylquinobis(imidazole)-2,2′-dithione

IUCrData ◽  
2019 ◽  
Vol 4 (9) ◽  
Author(s):  
Jayaraman Selvakumar ◽  
Kuppuswamy Arumugam
Keyword(s):  
Crystal Structure ◽  
Molecular Weight ◽  
Solid State ◽  
Structural Analysis ◽  
Hydrogen Bonds ◽  
Cell Volume ◽  
Title Compound ◽  
Unit Cell Volume ◽  
Density Peaks ◽  
Solvent Molecules

The solid-state structural analysis of the title compound [systematic name: 5,11-disulfanylidene-4,6,10,12-tetrakis(2,4,6-trimethylphenyl)-4,6,10,12-tetraazatricyclo[7.3.0.03,7]dodeca-1(9),3(7)-diene-2,8-dione], C44H44N4O2S2 [+solvent], reveals that the molecule crystallizes in a highly symmetric cubic space group so that one quarter of the molecule is crystallographically unique, the molecule lying on special positions (two mirror planes, two twofold axes and a center of inversion). The crystal structure exhibits large cavities of 193 Å3 accounting for 7.3% of the total unit-cell volume. These cavities contain residual density peaks but it was not possible to unambiguously identify the solvent therein. The contribution of the disordered solvent molecules to the scattering was removed using a solvent mask and is not included in the reported molecular weight. No classical hydrogen bonds are observed between the main molecules.

scholarly journals Polder maps: improving OMIT maps by excluding bulk solvent

2017 ◽  
Vol 73 (2) ◽  
pp. 148-157 ◽  
Author(s):  
Dorothee Liebschner ◽  
Pavel V. Afonine ◽  
Nigel W. Moriarty ◽  
Billy K. Poon ◽  
Oleg V. Sobolev ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cell Volume ◽  
Electron Density ◽  
Unit Cell Volume ◽  
Model Building ◽  
Unit Cell ◽  
Structure Factors ◽  
Structure Solution ◽  
Solvent Model ◽  
Solvent Molecules

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. The tools described in this manuscript have been implemented and are available inPHENIX.

scholarly journals Crystal structure of 2,5-bis(4-methylpyridin-2-yl)pyrazine chloroform disolvate

2014 ◽  
Vol 70 (9) ◽  
pp. o893-o894 ◽  
Author(s):  
Laurette Schmitt ◽  
Helen Stoeckli-Evans
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Symmetry Code ◽  
Inversion Symmetry ◽  
Pyrazine Ring ◽  
Π Interactions ◽  
Heterocyclic Molecule ◽  
Centroid Distance ◽  
Title Molecule ◽  
Solvent Molecules

The heterocyclic molecule in the title solvate, C16H14N4·2CHCl3, possesses inversion symmetry, with the inversion centre situated at the centre of the pyrazine ring. The outer pyridine rings are inclined to the central pyrazine ring by 4.89 (9)°. The compound crystallized as a chloroform disolvate with the solvent molecules linked to the title molecule by C—H...N hydrogen bonds. In the crystal, molecules are further linked by π–π interactions involving the pyrazine and pyridine rings of neighbouring molecules [inter-centroid distance = 3.5629 (12) Å; symmetry code:x,y + 1,z + 1].

scholarly journals Crystal structure of 4-azidomethyl-6-isopropyl-2H-chromen-2-one

2015 ◽  
Vol 71 (4) ◽  
pp. o227-o228 ◽  
Author(s):  
M. S. Krishnamurthy ◽  
Noor Shahina Begum ◽  
D. Shamala ◽  
K. Shivashankar
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Ring System ◽  
Maximum Deviation ◽  
Two Dimensional ◽  
Π Interactions ◽  
Dimensional Network ◽  
Title Molecule

In the title molecule, C13H13N3O2, the benzopyran ring system is essentially planar, with a maximum deviation of 0.017 (1) Å. In the crystal, weak C—H...O hydrogen bonds link molecules into ladders along [010]. In addition, π–π interactions between inversion-related molecules, with centroid–centroid distances in the range 3.679 (2)–3.876 (2) Å, complete a two-dimensional network parallel to (001).

scholarly journals 3-[1-(3-Hydroxybenzyl)-1H-benzimidazol-2-yl]phenol

2009 ◽  
Vol 65 (6) ◽  
pp. o1374-o1375 ◽  
Author(s):  
Naser Eltaher Eltayeb ◽  
Siang Guan Teoh ◽  
Hoong-Kun Fun ◽  
Samuel Robinson Jebas ◽  
Rohana Adnan
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Dihedral Angles ◽  
Π Interactions ◽  
Benzene Rings ◽  
Title Molecule

In the title molecule, C20H16N2O2, the benzimidazole mean plane forms dihedral angles of 56.55 (3) and 81.65 (4)° with the two benzene rings. In the crystal structure, intermolecular O—H...O and O—H...N hydrogen bonds link the molecules into layers parallel to the (101) plane. The crystal packing also exhibits weak intermolecular C—H...O and C—H...π interactions.

scholarly journals Crystal structure of 1,1′-[selanediylbis(4,1-phenylene)]bis(2-chloroethan-1-one)

2015 ◽  
Vol 71 (12) ◽  
pp. o935-o936 ◽  
Author(s):  
Hazem Bouraoui ◽  
Ali Boudjada ◽  
Noudjoud Hamdouni ◽  
Youcef Mechehoud ◽  
Jean Meinnel
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Three Dimensional ◽  
Torsion Angles ◽  
Axis Direction ◽  
Π Interactions ◽  
Dimensional Network ◽  
Benzene Rings ◽  
Title Molecule

In the title molecule, C16H12Cl2O2Se, the C—Se—C angle is 100.05 (14)°, with the dihedral angle between the planes of the benzene rings being 69.92 (17)°. The average endocyclic angles (Se—Car—Car; ar = aromatic) facing the Se atom are 120.0 (3) and 119.4 (3)°. The Se atom is essentially coplanar with the benzene rings, with Se—Car—Car—Cartorsion angles of −179.2 (3) and −179.7 (3)°. In the crystal, molecules are linkedviaC—H...O hydrogen bonds forming chains propagating along thea-axis direction. The chains are linkedviaC—H...π interactions, forming a three-dimensional network.

scholarly journals Ethyl α-L-sorboside

IUCrData ◽  
2020 ◽  
Vol 5 (12) ◽  
Author(s):  
Natsumi Nagayama ◽  
Norito Taniguchi ◽  
Mao Matsumoto ◽  
Kei Takeshita ◽  
Tomohiko Ishii
Keyword(s):  
Hydrogen Bonds ◽  
Cell Volume ◽  
Unit Cell Volume ◽  
Three Dimensional ◽  
Unit Cell ◽  
Rare Sugar ◽  
Dimensional Network

Ethyl L-sorboside, C8H16O6, was prepared from the rare sugar L-sorbose, C6H12O6, and crystallized. It was confirmed that ethyl L-sorboside formed α-pyranose with a 2 C 5 conformation. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming a three-dimensional network. The unit-cell volume of the title ethyl α-L-sorboside is 940.63 Å3 (Z = 4), which is about 194.69 Å3 (26.1%) bigger than that of L-sorbose [745.94 Å3 (Z = 4)].

scholarly journals Crystal structure of bis{1-[(E)-(2-methoxyphenyl)diazenyl]naphthalen-2-olato-κ3O,N2,O′}copper(II) containing an unknown solvate

2015 ◽  
Vol 71 (11) ◽  
pp. m207-m208 ◽  
Author(s):  
Souheyla Chetioui ◽  
Noudjoud Hamdouni ◽  
Djamil-Azzeddine Rouag ◽  
Salah Eddine Bouaoud ◽  
Hocine Merazig
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Title Complex ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Coordination Environment ◽  
Independent Molecules ◽  
Solvent Molecules

The title complex, [Cu(C17H13N2O2)2], crystallizes with two independent molecules in the asymmetric unit. Each CuIIatom has a distorted ocahedral coordination environment defined by two N atoms and four O atoms from two tridentate 1-[(E)-(2-methoxyphenyl)diazenyl]naphthalen-2-olate ligands. In the crystal, the two molecules are linkedviaweak C—H...O hydrogen bonds which in turn stack parallel to [010]. A region of disordered electron density, most probably disordered methanol solvent molecules, was corrected for using the SQUEEZE routine inPLATON[Spek (2015).Acta Cryst.C71, 9–18]. Their formula mass and unit-cell characteristics were not taken into account during refinement.

scholarly journals 7,7′,8,8′-Tetramethoxy-4,4′-dimethyl-3,5′-bichromene-2,2′-dione

2009 ◽  
Vol 65 (6) ◽  
pp. o1322-o1323 ◽  
Author(s):  
Hoong-Kun Fun ◽  
Samuel Robinson Jebas ◽  
Mehtab Parveen ◽  
Zakia Khanam ◽  
Raza Murad Ghalib
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
The Other ◽  
Torsion Angles ◽  
Π Interactions ◽  
Methoxy Groups ◽  
Additional Stabilization ◽  
The Mean ◽  
Title Molecule

In the title molecule, C24H22O8, the mean planes of the two coumarin units are inclined to each other at a dihedral angle of 79.93 (3)°. The attached methoxy groups form torsion angles of 7.65 (19) and 78.36 (14)° with respect to one coumarin unit, and angles of 9.01 (16) and 99.08 (11)° with respect to the other coumarin unit. In the crystal structure, weak intermolecular C—H...O hydrogen bonds connect pairs of molecules to form dimers, generatingR22(16) andR22(18) rings; the dimers are linked by further weak intermolecular C—H...O hydrogen bonds, forming extended chains. Additional stabilization is provided by weak C—H...π interactions.

scholarly journals (E)-7-[(4-Nitrophenyl)diazenyl]-3a-(p-tolyl)-2,3,3a,4-tetrahydro-1H-benzo[d]pyrrolo[1,2-a]imidazol-1-one 0.58-dimethyl sulfoxide 0.42-acetonitrile solvate: crystal structure, Hirshfeld analysis and DFT estimation of the energy of intermolecular interactions

2017 ◽  
Vol 73 (10) ◽  
pp. 1590-1594
Author(s):  
Vyacheslav S. Grinev ◽  
Natalya V. Babkina ◽  
Alevtina Yu. Yegorova
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Dimethyl Sulfoxide ◽  
Molecular Surface ◽  
Π Interactions ◽  
Compound C ◽  
Energy Of Intermolecular Interactions ◽  
Hirshfeld Analysis ◽  
Intermolecular Contacts ◽  
Solvent Molecules

In the crystal structure of the title compound, C23H19N5O3·0.58C2H6OS·0.42C2H3N, prepared by the azo coupling of the 4-nitrophenyldiazonium salt with 3a-(p-tolyl)-2,3,3a,4-tetrahydro-1H-benzo[d]pyrrolo[1,2-a]imidazol-1-one, the azo molecules are linked by N—H...O hydrogen bonds into chains along thea-axis direction, and by the π–π interaction into [101] chains. The dimethyl sulfoxide and acetonitrile solvent molecules occupy the same positions, with populations of 0.585 (3) and 0.415 (3), respectively. These molecules take part in C—H...O(N) and C—H...π contacts. The energy of the π–π interactions was estimated using DFT calculations. The Hirshfeld molecular surface analysis revealed the positions of the most important intermolecular contacts, such as hydrogen bonds and π–π interactions.

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