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1.  1-(2,3-Di­hydroxy­prop­yl)-4-{2-[4-(di­methyl­amino)­phen­yl]vin­yl}pyridinium chloride 
The title compound, C18H23N2O2 +·Cl−, crystallizes with two independent cations and anions per cell. Each cation has twofold rotational disorder about the linking vinyl groups but with unequal occupancies [0.963 (5):0.037 (5) and 0.860 (8):0.140 (8)]. The two independent cations are close to being related by an inversion centre but the data does not support the expected centrosymmetric space-group assignment. The conclusion is that the differing rotational disorder has lead to an overall non-centrosymmetric lattice. In the crystal, the mol­ecules pack in layers parallel to (133) and (-13-3), chain-linked with motif C 1 2(7) by the di­hydroxy­propyl O–H⋯Cl⋯H–O hydrogen bonds. Other lattice binding is provided by O—H⋯Cl, C—H⋯Cl and C—H⋯N inter­actions.
PMCID: PMC3914108  PMID: 24527014
2.  2-(3-Cyano-4-{3-[1-(2-hy­droxy­eth­yl)-3,3-dimethyl-1,3-di­hydro­indol-2-yl­idene]prop-2-en­yl}-5,5-dimethyl-5H-furan-2-yl­idene)malono­nitrile 
The title compound, C25H24N4O2, adopts a cisoid configuration and has twofold orientational disorder of the 2-hy­droxy­ethyl group. The mol­ecule is twisted from planarity so that the dihedral angle between the terminating indol-2-yl­idene and the furan-2-yl­idene moiety mean planes is 12.75 (7)°. Conformational disorder occurs at the indol-2-yl­idene N atom, which results in two orientations for the hy­droxy­ethyl group [occupancy ratio = 0.896 (2):0.104 (2)], and the hy­droxy O atom of the 2-hy­droxy­ethyl group is located over three sites [occupancy ratio = 0.548 (2):0.348 (2):0.104 (2)]. An intra­molecular C—H⋯O hydrogen bond involving the lowest occupancy hy­droxy O atom is observed. In the crystal, the mol­ecules pack in parallel dimeric sheets about centres of symmetry, utilizing O—H⋯N(cyano), C—H⋯N(cyano) and O—H⋯O hydrogen bonds, in two sets parallel to (02-1) and (021) planes.
PMCID: PMC3914086  PMID: 24526989
3.  2-{2-[5-(4-Cyano-5-di­cyano­methyl­idene-2,2-dimethyl-2,5-di­hydro­furan-3-yl)penta-2,4-dienyl­idene]-3,3-dimethyl-2,3-di­hydro-1H-indol-1-yl}ethyl 3,5-bis­(benz­yloxy)benzoate 
In the title mol­ecule, C48H42N4O5, a potential non-linear optical compound, the furan ring [r.m.s. deviation = 0.010 (1) Å] and the indolyl­idene ring system [r.m.s. deviation = 0.013 (2) Å] are inclined to one another by 18.52 (6)°. This is similar to the arrangement [16.51 (18)°] found for the N-hy­droxy­ethyl adduct of the title compound [Bhuiyan et al. (2011 ▶). Mol. Cryst. Liq. Cryst. 548, 1–12]. Replacing the hy­droxy­ethyl group with 3,5-di­benzyl­oxybenzoate has not resulted in a non-centrosymmetric lattice arrangement or significant changes to the basic mol­ecular structure. In the crystal, mol­ecules are linked via pairs of C—H⋯N hydrogen bonds, forming inversion dimers with an R 2 2(20) ring motif. The dimers are linked via C—H⋯O hydrogen bonds, forming C(17) chains along [010]. The chains are linked by further C—H⋯N hydrogen bonds, forming layers parallel to (001) and enclosing R 2 2(44) ring motifs. There are also C—H⋯π inter­actions present, stabilizing the inter­layer orientation of the pendant bis­(benz­yloxy)benzo­yloxy group.
PMCID: PMC3914075  PMID: 24526976
4.  1-(4-{[(1,3,3-Tri­methyl­indolin-2-yl­idene)meth­yl]diazen­yl}phen­yl)ethanone 
The title compound, C20H21N3O, has crystallographic mirror symmetry with all non-H atoms apart from the methyl C atom of the CMe2 group lying on the mirror plane. Mol­ecules are linked into planar sheets parallel to (010) by phen­yl–azo C—H⋯N and phen­yl–ethanone C—H⋯O inter­actions. Methyl C—H⋯π inter­actions provide crosslinking between the planes.
PMCID: PMC3790374  PMID: 24098196
5.  2-(3-Cyano-4-methyl-5,5-diphenyl-5H-furan-2-yl­idene)malono­nitrile 
The title compound, C21H13N3O, crystallizes with two independent molecules with similar conformations per asymmetric unit. The dihydrofuran rings are essentially planar with maximum deviations of 0.017 (1) and 0.006 (1) Å for the O atoms. The dihedral angles between the di­hydro­furan ring and the attached phenyl rings are 79.90 (6) and 82.07 (6)° in one mol­ecule and 79.36 (6) and 72.26 (6)° in the other. In the crystal, the molecules are linked by weak C—H⋯π and C—H⋯N inter­actions similar to those in other closely related crystals. The replacement of appended methyl by phenyl groups has not significantly affected the dihydrofuran ring structure or the crystal packing interactions.
PMCID: PMC3884449  PMID: 24427012
6.  4-Methyl-5-(4-nitro­benzyl­idene)-2-oxo-2,5-di­hydro-1H-pyrrole-3-carbo­nitrile 
Mol­ecules of the potential non-linear optical title compound, C13H9N3O3, form dimeric stacks of mol­ecules along the a axis cross-linked around inversion centers by N—H⋯O hydrogen bonds and weak (phen­yl)C—H⋯O inter­molecular inter­actions, forming a ‘collaboration’ of R 2 2(8) and R 2 2(16) ring motifs. The mol­ecules are then further linked by weak C—H⋯O and C—H⋯N inter­actions into sheets parallel to (121).
PMCID: PMC3770419  PMID: 24046704
7.  Acet­oxy-γ-valerolactone 
Levulinyl cellulose esters have been produced as an effective renewable binder for architectural coatings. The title compound, C7H10O4 (systematic name: 2-methyl-5-oxo­tetra­hydro­furan-2-yl acetate), assigned as the esterifying species, was isolated and crystallized to confirm the structure. In the crystal, the mol­ecules pack in layers parallel to (102) utilizing weak C—H⋯O inter­actions.
PMCID: PMC3685093  PMID: 23795112
8.  Bis(2-carb­oxy-N-{[1-(2-hy­droxy­eth­yl)-3,3-dimethyl­indolin-2-yl­idene]methyl­imino}­anilinium) sulfate monohydrate 
The asymmetric unit of the title compound, 2C20H22N3O3 +·SO4 2−·H2O, contains four cations, two sulfate anions and two lattice water mol­ecules. One of the four cations shows a different conformation of the hy­droxy­ethyl group; the remaining three are all essentially superimposable. Two cations exhibit two-site orientational disorder [ratios = 0.524 (5):0.476 (5) and 0.616 (6):0.384 (6)] of the last two atoms of their hy­droxy­ethyl groups, and one water mol­ecule is disordered over two positions in a 0.634 (13):0.366 (13) ratio. Each imine H atom is intra­molecularly in contact with the adjacent carboxyl O atom, forming an S(6) motif, while all the carb­oxy­lic acid H atoms are hydrogen bonded to O atoms of the sulfate anions. Other notable hydrogen-bond inter­actions involve (methyl­ene, phenyl and imine chain) C—H⋯O (sulfate and carbox­yl) and O—H⋯O(water) contacts, making up a comprehensive three-dimensional network involving D 2 2(n), with n = 4–6 and 15–16, and C 2 2(17) classical hydrogen-bond motifs. The crystal investigated was twinned by pseudomerohedry with a twin component ratio of 0.4745 (12):0.5255 (12).
PMCID: PMC3588437  PMID: 23476537
9.  2-(Acet­oxy­meth­yl)benzoic acid 
The title compound, C10H10O4, crystallizes with the well-known carb­oxy­lic acid dimer-forming R 2 2(8) hydrogen-bond motif. Chains approximately parallel to (-1-12) are then built through C(methyl­ene,phen­yl)–H⋯O(carbon­yl) inter­actions [C(6) and C(8) motifs] with one (meth­yl)C—H⋯π inter­action providing inter­planar binding. The weakness of the latter inter­action is consistent with the difficulty experienced in obtaining suitable single crystals.
PMCID: PMC3569790  PMID: 23424536
10.  2-[4-(2-{5-tert-Butyl-2-chloro-3-[2-(3-pentyl-1,3-benzothia­zol-2-yl­idene)ethyl­idene]cyclo­hex-1-en­yl}ethen­yl)-3-cyano-5,5-dimethyl­furan-2-yl­idene]malono­nitrile 
In the title mol­ecule, C36H39ClN4OS, the non-aromatic part of the cyclo­hex-1-enyl ring and the attached tert-butyl group are disordered over two conformations with occupancy ratios of 0.52 (3):0.48 (3) and 0.53 (3):0.47 (3), respectively. The polyene chain single- and double-bond dimensions contrast with a closely related compound [Bouit et al. (2007 ▶). Chem. Mater. 19, 5325–5335] with an approximate 19° twist between donor and acceptor ends of the mol­ecule, related to the additional intra­molecular C—H⋯S inter­action. In the title compound, the mol­ecules pack into dimeric units about centres of symmetry utilizing weak C—H⋯N(cyano) and C—H⋯O attractive inter­actions, building both chain and ring motifs about the centres [R 2 2(8) and R 2 2(9)]. Adjacent dimeric sets then form a herringbone configuration.
PMCID: PMC3588378  PMID: 23476383
11.  (E)-5-[3-Cyano-2-(dicyano­methyl­ene)-1-oxaspiro­[4.5]dec-3-en-4-yl]-3-(1-methyl-1,4-dihydro­pyridin-4-yl­idene)pent-4-en-1-yl 3,5-bis­(benz­yloxy)benzoate 
In the title compound, C45H40N4O5, the cyclo­hexane entity on the (3-cyano-2,5-dihydro­furan-2-yl­idene)propane­dinitrile group, which replaces the usual dimethyl substituents, has not perturbed the delocalization geometry significantly. Weak inter­molecular inter­actions, viz. C—H⋯N(cyano), C—H⋯O(ether), C—H⋯π and π–π [between the aromatic rings with the shortest centroid–centroid distance of 3.603 (3) Å], consolidate the crystal packing, which exhibits voids of 57 Å3.
PMCID: PMC3588224  PMID: 23476366
12.  2-{3-Cyano-4-[2-(4-diethylamino-2-hy­droxyphenyl)ethenyl]-5,5-dimethyl-2,5-dihydrofuran-2-ylidene}malononitrile acetone 0.25-solvate 
In the title compound, C22H22N4O2·0.25C3H6O, the disordered acetone mol­ecule lies with partial occupancy about the 2 axis. The mol­ecule of the malononitrile derivative is essentially planar excluding the methyl groups, with the largest deviation from the mean plane through the non-H atoms being 0.1955 (13) Å. Two rotamers with different orientations of the benzene ring are observed in the ratio of 0.919 (2):0.081 (2), and as a result the OH group is disordered over two sets of sites. In the crystal, the mol­ecules form ribbons along (101) utilizing a strong O—H⋯N(cyano) hydrogen bond. Inter­leaving of the nearly planar ribbons is provided by the twofold disordered acetone molecule through C—H⋯O inter­actions.
PMCID: PMC3470352  PMID: 23125765
13.  tert-Butyl (2R,4aR,5aR,11aS,12R,12aR)-8-[bis­(tert-but­oxycarbon­yl)amino]-12-hydroxy-2-meth­oxy-2,10-dioxo-4,4a,5a,6,9,10,11,11a,12,12a-deca­hydro-2H-1,3,5-trioxa-6,7,9,11-tetra­aza-2λ5-phosphatetra­cene-6-carboxyl­ate methanol monosolvate monohydrate 
The title compound, C26H40N5O13P·CH3OH·H2O, crystallizes with one water and one methanol mol­ecule providing important crystal-binding inter­actions. The compound has the unusual feature of having two but­oxy­carbonyl groups bound to one N atom. The conventional attractive hydrogen bonds involving hy­droxy, amine and water donors include bifurcations at both donors and acceptors with novel R 1 2(6) and R 2 1(6) motifs. These are supplemented by C—H⋯O inter­actions between adjacent mol­ecules forming chain and R 2 2(10) ring motifs.
PMCID: PMC3394038  PMID: 22798903
14.  (4R,5S)-4-Hy­droxy­meth­yl-5-[(methyl­sulfanyl)­meth­yl]-1,3-oxazolidin-2-one 
The title compound, C6H11NO3S, crystallizes utilizing a three-dimensional set of O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds. The 1,3-oxazolidin-2-one ring adopts an envelope conformation with the C atom bearing the hy­droxy­methyl group as the flap.
PMCID: PMC3393898  PMID: 22798763
15.  1d-1-O-tert-Butyl­diphenyl­silyl-2,3,6-O-tris­(meth­oxy­methyl­ene)-myo-inositol 4,5-bis­(dibenzyl­phosphate) 
The title compound [systematic name: tetra­benzyl (1R,2R,3S,4R,5R,6S)-4-(tert-butyl­diphenyl­sil­yloxy)-3,5,6-tris­(meth­oxy­meth­oxy)cyclo­hexane-1,2-diyl bis­phosphate], C56H68O15P2Si, was isolated as an inter­mediate in the preparation of a phosphatidylinositol phosphate for biological studies. In the crystal, the mol­ecules are connected via one methyl­ene C—H⋯π and two weak phen­yl–ether C—H⋯O inter­actions. One benz­yloxy group is disordered over two overlapping positions with an occupancy ratio of 0.649 (7):0.351 (7).
PMCID: PMC3297945  PMID: 22412748
16.  (9H-Fluoren-9-yl)methyl N-{(2R,3R,4S)-4-hy­droxy-2-[(2S,5R)-2-isopropyl-5-methyl­cyclo­hex­yloxy]-5-oxooxolan-3-yl}carbamate propan-2-ol 0.334-solvate 
The title compound, C29H35NO6.0.334C3H8O, a novel chiral N-(fluoren-9-yl­methyl­oxyxcarbon­yl) precursor, crystallizes with two independent carbamate (M) mol­ecules and propan-2-ol solvent mol­ecules in the unit cell. Its crystal structure has been determined from barely adequate data obtained from a multi-fragment needle crystal. In the crystal, N—H⋯O hydrogen bonds link M mol­ecules related by translation along the a axis into two independent chains. The ordered solvent mol­ecule, having a partial occupancy of 0.334, is attached to one independent M mol­ecule through O—H⋯O hydrogen bonds. The crystal packing exhibits weak inter­molecular C—H⋯O inter­actions and voids of 270 Å3 filled with randomly disordered solvent mol­ecules which were handled using the SQUEEZE methodology.
PMCID: PMC3275078  PMID: 22347023
17.  C—H⋯π packing inter­actions in 2-[5,5-bis­(4-benzyl­oxyphen­yl)-3-cyano-4-methyl-2,5-dihydro­furan-2-yl­idene]malononitrile 
The title mol­ecule, C35H25N3O3, packs utilizing C—H⋯π attractive inter­actions causing the identical 4-benzyl­oxyphenyl groups to pack with different conformational angles. This difference is consistent with the variable inter­planar dihedral angles found in closely related structures.
PMCID: PMC3247440  PMID: 22220058
18.  2-(3-Cyano-4-{7-[1-(2-hy­droxy­eth­yl)-3,3-dimethyl­indolin-2-yl­idene]hepta-1,3,5-trien­yl}-5,5-dimethyl-2,5-dihydro­furan-2-yl­idene)malononitrile 
The title compound, C29H28N4O2, excluding the hydroxyethyl and methyl groups, is slightly twisted from planarity so that the terminating indol-2-yl­idene and furan-2-yl­idene moiety planes subtend a dihedral angle of 6.27 (8)°. A small inwards fold in the polymethine atom chain is consistent with centrosymmetric dimer formation via O—H⋯N(cyano) hydrogen bonds. In the crystal, the mol­ecules pack in layers approximately parallel to the (10) plane via pairs of O—H⋯N and C—H⋯N(cyano) inter­actions.
PMCID: PMC3247422  PMID: 22220040
19.  (4aR,6aS,10aR,10bS)-7,7,10a-Trimethyl-1,4,4a,5,6,6a,7,8,9,10,10a,10b-dodecahydro-2H-naphtho­[2,1-c]pyran (Pyamber) 
The crystal structure of the title compound, C16H28O, features C—H⋯O hydrogen bonds making C(6) zigzag chains along one 21 screw axis. Within the limits of the data collection affected by crystal quality, the Hooft parameter gave correct indications of the known molecular chirality based on the single O atom anomalous dispersion in contrast to the indeterminate Flack value. Synthetic steps starting from manool are reported.
PMCID: PMC3247605  PMID: 22219910
20.  Methyl 6-azido-6-de­oxy-α-d-galactoside 
The structure of the title compound, C7H13N3O5, was solved using data from a multiple fragment crystal. The galactoside ring adopts a 4 C 1 chair conformation. In the crystal, the molecules are linked by strong O—H⋯O hydrogen bonds, which build linkages around the screw axis of the cell in a similar way to the iodo analogue. These C-5 and C-6 packing motifs expand to R 2 2(10), C 2 2(7) and C 2 2 2(8) motifs, as found in closely related compounds.
PMCID: PMC3212328  PMID: 22090985
21.  4-tert-Butyl-2-[2-(1,3,3-trimethyl­indolin-2-yl­idene)ethyl­idene]cyclo­hexa­none 
The title mol­ecule, C23H31NO, has two alternative cyclo­hexa­none configurations at the 4-position in a ratio of 0.663 (3):0.337 (3). The plane of the five-membered planar ring in the indolin-2-yl­idene subtends an angle of 2.19 (7)° with its fused aromatic ring, an angle of 16.24 (8)° with the plane of the major cyclo­hexa­none configuration and an angle of 8.54 (15)° with the bridging planar ethyl­idene C atoms. These last atoms subtend an angle of 8.37 (16)° with the mean plane through the major cyclo­hexa­none configuration. The mol­ecules pack approximately parallel to the (01) plane via C—H⋯π and C—H⋯O inter­actions.
PMCID: PMC3089154  PMID: 21754509
22.  A synchrotron radiation study of the one-dimensional complex of sodium with (1S)-N-carboxyl­ato-1-(9-deaza­adenin-9-yl)-1,4-dide­oxy-1,4-imino-d-ribitol, a member of the ’immucillin’ family 
The sodium salt of [immucillin-A–CO2H]− (Imm-A), namely catena-poly[[[triaqua­disodium(I)](μ-aqua)[μ-(1S)-N-car­box­yl­ato-1-(9-deaza­adenin-9-yl)-1,4-dide­oxy-1,4-imino-d-ribi­tol][triaqua­disodium(I)][μ-(1S)-N-carboxyl­ato-1-(9-deaza­aden­in-9-yl)-1,4-dide­oxy-1,4-imino-d-ribitol]] tetra­hydrate], {[Na2(C12H13N4O6)2(H2O)7]·4H2O}n, (I), forms a polymeric chain via Na+—O inter­actions involving the carboxyl­ate and keto O atoms of two independent Imm-A mol­ecules. Extensive N,O—H⋯O hydrogen bonding utilizing all water H atoms, including four waters of crystallization, provides crystal packing. The structural definition of this novel compound was made possible through the use of synchrotron radiation utilizing a minute fragment (volume ∼2.4 × 10−5 mm−3) on a beamline optimized for protein data collection. A summary of intra-ring conformations for immucillin structures indicates considerable flexibility while retaining similar intra-ring orientations.
PMCID: PMC2855577  PMID: 20203397
23.  2-{[(Biphenyl-2-yl)diazen­yl]methyl­idene}-1,3,3-trimethyl­indoline 
The title mol­ecule, C24H23N3, shows some delocalization of charge based on the small [8.0 (2)°] angle between the indolin-2-yl­idene ring system and the link methyl­diazene C2N2 atom plane. A further twist of 17.2 (3)° is subtended between the C2N2 plane and its attached benzene ring. The dihedral angle between the biphenyl rings is 47.96(14)°. In the crystal, the mol­ecules pack via C—H⋯π attractive inter­actions.
PMCID: PMC3099795  PMID: 21754168
24.  Methyl 6-de­oxy-6-iodo-α-d-galactoside 
In the crystal of the title compound, C7H13IO5, the molecules are linked by O—H⋯O hydrogen bonds, which build linkages around one screw axis of the cell. These C(5) and C(6) packing motifs expand to R 2 2(10) and C2 2(11) motifs and are similar to those found for closely related compounds. The galactoside ring has a 1 C 4 chair conformation.
PMCID: PMC3007047  PMID: 21587941
25.  7-(5-Methyl­sulfanyl-β-d-erythrofuran­osyl)-7H-pyrrolo­[2,3-d]pyrimidin-4-amine monohydrate (MT-tubercidin·H2O) 
The title compound, C12H16N4O3S·H2O, which has potential as a possible anti­malarial drug, was studied when small deviations in melting points, for two differently aged preparations, were observed. The unexpected existence of a water mol­ecule of crystallization is considered to be the cause of this variation. The 7H-pyrrolo­[2,3-d]pyrimidine unit is very slightly puckered with a total puckering amplitude of 0.035 (2) Å; its mean plane makes an angle of 88.40 (12)° with the mean plane through the ribofuranosyl unit. In the crystal, the mol­ecules are bound by strong O—H⋯N and N—H⋯O hydrogen bonds, utilizing all available protons and linking mainly through the water of crystallization.
PMCID: PMC3006811  PMID: 21587912

Results 1-25 (41)