7-Cyclopropyl-2′-deoxytubercidin: a carbocyclic side-chain derivative of 7-deaza-2′-deoxyadenosine

2014 ◽  
Vol 70 (12) ◽  
pp. 1116-1120 ◽  
Author(s):  
Haozhe Yang ◽  
Simone Budow-Busse ◽  
Henning Eickmeier ◽  
Hans Reuter ◽  
Frank Seela
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Torsion Angle ◽  
Three Dimensional ◽  
Side Chain ◽  
Sugar Residue ◽  
Amino Groups ◽  
Bifurcated Hydrogen Bond ◽  
The Individual

The title compound {systematic name: 4-amino-5-cyclopropyl-7-(2-deoxy-β-D-erythro-pentofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine}, C14H18N4O3, exhibits anantiglycosylic bond conformation, with the torsion angle χ = −108.7 (2)°. The furanose group shows a twisted C1′-exosugar pucker (S-type), withP= 120.0 (2)° and τm= 40.4 (1)°. The orientation of the exocyclic C4′—C5′ bond is -ap(trans), with the torsion angle γ = −167.1 (2)°. The cyclopropyl substituent points away from the nucleobase (antiorientation). Within the three-dimensional extended crystal structure, the individual molecules are stacked and arranged into layers, which are highly ordered and stabilized by hydrogen bonding. The O atom of the exocyclic 5′-hydroxy group of the sugar residue acts as an acceptor, forming a bifurcated hydrogen bond to the amino groups of two different neighbouring molecules. By this means, four neighbouring molecules form a rhomboidal arrangement of two bifurcated hydrogen bonds involving two amino groups and two O5′ atoms of the sugar residues.

scholarly journals Crystal structure of diethyl 2-acetoxy-2-[3-(4-nitrophenyl)-3-oxo-1-phenylpropyl]malonate

2016 ◽  
Vol 72 (2) ◽  
pp. 257-260
Author(s):  
Nóra Veronika May ◽  
Gyula Tamás Gál ◽  
Zsolt Rapi ◽  
Péter Bakó
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Side Chain ◽  
Compound C ◽  
Side Chain Conformation ◽  
Graph Set ◽  
Aromatic Ring Interactions

In the racemic title compound, C24H25NO9, the dihedral angle between the planes of the two benzene-ring systems is 80.16 (6)°, while the side-chain conformation is stabilized by a methylene–carboxyl C—H...O hydrogen bond. Weak intermolecular C—H...O hydrogen bonds form inversion dimers [graph setR22(16)] which are linked into chains extending alonga. Further C—H...O hydrogen bonding extends the structure alongbthrough cyclicR22(10) motifs. Although no π–π aromatic ring interactions are present in the structure, C—H...π ring interactions acrosscgenerate an overall three-dimensional supramolecular structure.

scholarly journals Crystal structure of 2′-hydroxyacetophenone 4-methylthiosemicarbazide

2015 ◽  
Vol 71 (4) ◽  
pp. o244-o245
Author(s):  
Junita Jamsari ◽  
Nur Fatihah Abas ◽  
Thahira Begum S. A. Ravoof ◽  
Edward R. T. Tiekink
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Torsion Angle ◽  
Organic Molecule ◽  
Side Chain ◽  
Water Molecules ◽  
Ethyl Group

In the organic molecule of the title hydrate, C11H15N3OS·H2O, {systematic name: 3-ethyl-1-{(E)-[1-(2-hydroxyphenyl)ethylidene]amino}thiourea monohydrate}, a dihedral angle of 5.39 (2)° is formed between the hydroxybenzene ring and the non-H atoms comprising the side chain (r.m.s. deviation = 0.0625 Å), with the major deviation from planarity noted for the terminal ethyl group [the C—N—C—C torsion angle = −172.17 (13)°]. The N—H H atoms aresynand an intramolecular hydroxy–imine O—H...N hydrogen bond is noted. In the crystal, the N-bonded H atoms form hydrogen bonds to symmetry-related water molecules, and the latter form donor interactions with the hydroxy O atom and with a hydroxybenzene ring, forming a O—H...π interaction. The hydrogen bonding leads to supramolecular tubes aligned along thebaxis. The tubes are connected into layersviaC—H...O interactions, and these stack along thecaxis with no directional interactions between them.

scholarly journals Crystal structure of morpholin-4-ium cinnamate

2015 ◽  
Vol 71 (11) ◽  
pp. o850-o851 ◽  
Author(s):  
Graham Smith
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Cinnamic Acid ◽  
Torsion Angle ◽  
Chain Structure ◽  
Side Chain ◽  
Hydrogen Bonding Interaction ◽  
Bonding Interaction ◽  
A Chain

In the anhydrous salt formed from the reaction of morpholine with cinnamic acid, C4H10NO+·C9H7O2−, the acid side chain in thetrans-cinnamate anion is significantly rotated out of the benzene plane [C—C—C— C torsion angle = 158.54 (17)°]. In the crystal, one of the the aminium H atoms is involved in an asymmetric three-centre cation–anion N—H...(O,O′)R12(4) hydrogen-bonding interaction with the two carboxylate O-atom acceptors of the anion. The second aminium-H atom forms an inter-species N—H...Ocarboxylatehydrogen bond. The result of the hydrogen bonding is the formation of a chain structure extending along [100]. Chains are linked by C—H...O interactions, forming a supramolecular layer parallel to (01-1).

5-Ethynyl-2′-deoxycytidine: a DNA building block with a `clickable' side chain

2012 ◽  
Vol 68 (10) ◽  
pp. o395-o398 ◽  
Author(s):  
Frank Seela ◽  
Hui Mei ◽  
Hai Xiong ◽  
Simone Budow ◽  
Henning Eickmeier ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Building Block ◽  
Title Compound ◽  
Crystalline State ◽  
Three Dimensional ◽  
Side Chain ◽  
Sugar Residue ◽  
A Chain ◽  
Dimensional Crystal

The title compound [systematic name: 4-amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-5-ethynylpyrimidin-2(1H)-one], C11H13N3O4, shows two conformations in the crystalline state. The N-glycosylic bonds of both conformers adopt similar conformations, with χ = −149.2 (1)° for conformer (I-1) and −151.4 (1)° for conformer (I-2), both in theantirange. The sugar residue of (I-1) shows a C2′-endoenvelope conformation (2E,S-type), withP= 164.7 (1)° and τm= 36.9 (1)°, while (I-2) shows a major C3′-exosugar pucker (C3′-exo-C2′-endo,3T2,S-type), withP= 189.2 (1)° and τm= 33.3 (1)°. Both conformers participate in the formation of a layered three-dimensional crystal structure with a chain-like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.

scholarly journals Crystal structure and hydrogen bonding in the water-stabilized proton-transfer salt brucinium 4-aminophenylarsonate tetrahydrate

2016 ◽  
Vol 72 (5) ◽  
pp. 751-755 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Network Structure ◽  
Three Dimensional ◽  
Water Molecules ◽  
Arsanilic Acid ◽  
Dimensional Network

In the structure of the brucinium salt of 4-aminophenylarsonic acid (p-arsanilic acid), systematically 2,3-dimethoxy-10-oxostrychnidinium 4-aminophenylarsonate tetrahydrate, (C23H27N2O4)[As(C6H7N)O2(OH)]·4H2O, the brucinium cations form the characteristic undulating and overlapping head-to-tail layered brucine substructures packed along [010]. The arsanilate anions and the water molecules of solvation are accommodated between the layers and are linked to them through a primary cation N—H...O(anion) hydrogen bond, as well as through water O—H...O hydrogen bonds to brucinium and arsanilate ions as well as bridging water O-atom acceptors, giving an overall three-dimensional network structure.

A novel self-complementary three-dimensional inorganic network organized by H-bond dimers of inorganic chains — Synthesis and crystal structure of (C6H16N2)[Zn(HPO4)2]

2004 ◽  
Vol 82 (5) ◽  
pp. 616-621 ◽  
Author(s):  
Xian-Ming Zhang ◽  
Chan-Juan Bai ◽  
Yan-Li Zhang ◽  
Hai-Shun Wu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Synthesis And Crystal Structure ◽  
X Ray ◽  
Crystal Structural ◽  
Inorganic Framework ◽  
Phosphate Groups ◽  
Inorganic Network

A novel organic-templated zincophosphate, namely (C6H16N2)[Zn(HPO4)2], was hydrothermally synthesized and X-ray single-crystal structural analysis reveals that the anions [Zn(HPO4)2]2–, which have square-twisted chains containing corner-sharing four-rings of alternating ZnO4 and PO4 tetrahedra, are assemblied via self-complementary strong and symmetrical hydrogen-bonding R22(8) synthons between the phosphate groups into three-dimensional hydrogen bond frameworks featuring three-dimensional intersecting pseudochannels. The doubly protonated 2,5-dimethylpiperazinium cations are attached to the three-dimensional inorganic framework via N-H···O hydrogen bonds to strengthen the 3-D network.

scholarly journals Threefold helical assembly via hydroxy hydrogen bonds: the 2:1 co-crystal of bicyclo[3.3.0]octane-endo-3,endo-7-diol and bicyclo[3.3.0]octane-endo-3,exo-7-diol

2021 ◽  
Vol 77 (3) ◽  
pp. 270-276
Author(s):  
Isa Y. H. Chan ◽  
Mohan M. Bhadbhade ◽  
Roger Bishop
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Hydroxy Group ◽  
Network Structure ◽  
General Position ◽  
Three Dimensional ◽  
Screw Axis ◽  
Hydroxy Groups

Reduction of bicyclo[3.3.0]octane-3,7-dione yields a mixture of the endo-3,endo-7-diol and endo-3, exo-7-diol (C8H14O2) isomers (5 and 6). These form (5)2·(6) co-crystals in the monoclinic P21/n space group (with Z = 6, Z′ = 1.5) rather than undergoing separation by means of fractional recrystallization or column chromatography. The molecule of 5 occupies a general position, whereas the molecule of 6 is disordered over two orientations across a centre of symmetry with occupancies of 0.463 (2) and 0.037 (2). Individual diol hydroxy groups associate around a pseudo-threefold screw axis by means of hydrogen bonding. The second hydroxy group of each diol behaves in a similar manner, generating a three-dimensional hydrogen-bonded network structure. This hydrogen-bond connectivity is identical to that present in three known helical tubuland diol–hydroquinone co-crystals, and the new crystal structure is even more similar to two homologous aliphatic diol co-crystals.

scholarly journals (Acetonitrile-κN)aqua[N,N′-bis(pyridin-2-ylmethyl)ethane-1,2-diamine-κ4N,N′,N′′,N′′′]zinc(II) perchlorate

2017 ◽  
Vol 73 (10) ◽  
pp. 1568-1571
Author(s):  
Ugochukwu Okeke ◽  
Yilma Gultneh ◽  
Ray J. Butcher
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Structural Features ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Bond Network ◽  
Bifurcated Hydrogen Bond ◽  
Coordinated Water ◽  
Ionic Hydrogen Bonding

The structure of the title compound, [Zn(C14H18N4)(C2H3N)(H2O)](ClO4)2, contains a six-coordinate cation consisting of the tetradentate bispicen ligand, coordinated water, and coordinated acetonitrile, with the latter two ligands adopting acisconfiguration. There are two formula units in the asymmetric unit. Both cations show almost identical structural features with the bispicen ligand adopting the more commoncis-β conformation. One of the four perchlorate anions is disordered over two positions, with occupancies of 0.9090 (15) and 0.0910 (15). There is extensive inter-ionic hydrogen bonding between the perchlorate anions and O—H and N—H groups in the cations, including a bifurcated hydrogen bond between an N—H group and two O atoms of one perchlorate anion. As a result of this extended hydrogen-bond network, the ions are linked into a complex three-dimensional array.

1,7-Dideaza-2′-deoxy-6-nitronebularine: a pyrrolo[2,3-b]pyridine nucleoside with an intramolecular hydrogen bond stabilizing thesynconformation

2013 ◽  
Vol 69 (8) ◽  
pp. 892-895
Author(s):  
Haozhe Yang ◽  
Simone Budow ◽  
Henning Eickmeier ◽  
Hans Reuter ◽  
Frank Seela
Keyword(s):  
Hydrogen Bond ◽  
Intramolecular Hydrogen Bond ◽  
Torsion Angle ◽  
Pyridine Ring ◽  
Pyrrole Ring ◽  
Three Dimensional ◽  
Sugar Residue ◽  
Adjacent Layer ◽  
Dimensional Network ◽  
Intramolecular Hydrogen

The title compound [systematic name: 1-(2-deoxy-β-D-erythro-pentofuranosyl)-4-nitro-1H-pyrrolo[2,3-b]pyridine], C12H13N3O5, forms an intramolecular hydrogen bond between the pyridine N atom as acceptor and the 5′-hydroxy group of the sugar residue as donor. Consequently, the N-glycosylic bond exhibits asynconformation, with a χ torsion angle of 61.6 (2)°, and the pentofuranosyl residue adopts a C2′-endoenvelope conformation (2E,S-type), withP= 162.1 (1)° and τm= 36.2 (1)°. The orientation of the exocyclic C4′—C5′ bond is +sc(gauche,gauche), with a torsion angle γ = 49.1 (2)°. The title nucleoside forms an ordered and stacked three-dimensional network. The pyrrole ring of one layer faces the pyridine ring of an adjacent layer. Additionally, intermolecular O—H...O and C—H...O hydrogen bonds stabilize the crystal structure.

scholarly journals 6-[(2-Methylphenyl)sulfanyl]-5-propylpyrimidine-2,4(1H,3H)-dione

2014 ◽  
Vol 70 (7) ◽  
pp. o768-o769 ◽  
Author(s):  
Nadia G. Haress ◽  
Hazem A. Ghabbour ◽  
Ali A. El-Emam ◽  
C. S. Chidan Kumar ◽  
Hoong-Kun Fun
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Torsion Angle ◽  
Three Dimensional ◽  
Dione Derivative ◽  
Dimensional Network ◽  
A Chain ◽  
Ring Motif

In the title pyrimidine-2,4-dione derivative, C14H16N2O2S, the dihedral angle between the six-membered rings is 77.81 (10)°. The molecule is twisted about the Cp—S (p = pyrimidine) bond, with a C—S—C—N torsion angle of −59.01 (17)°. An intramolecular C—H...S hydrogen bond generates anS(5) ring motif. In the crystal, bifurcated acceptor N—H...O and C—H...O hydrogen bonds generate inversion-related dimers incorporatingR21(9) andR22(8) loops. These dimers are connected into a chain extending along thea-axis direction by a second pair of inversion-related N—H...O hydrogen bonds, forming anotherR22(8) loop. The crystal structure is further stabilized by weak intermolecular C—H...π interactions, generating a three-dimensional network.

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