scholarly journals Crystal structure of the Y52F/Y73F double mutant of phospholipase A2: Increased hydrophobic interactions of the phenyl groups compensate for the disrupted hydrogen bonds of the tyrosines

1992 ◽  
Vol 1 (12) ◽  
pp. 1585-1594 ◽  
Author(s):  
Chandra Sekharudu ◽  
Boopathy Ramakrishnan ◽  
Baohua Huang ◽  
Ru-Tai Jiang ◽  
Cynthia M. Dupureur ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Phospholipase A2 ◽  
Double Mutant ◽  
Hydrophobic Interactions

scholarly journals Crystal structure ofmeso-3,3′-(1,4-phenylene)bis(2-phenyl-2,3,5,6-tetrahydro-4H-1,3-thiazin-4-one)

2018 ◽  
Vol 74 (10) ◽  
pp. 1497-1499
Author(s):  
Hemant P. Yennawar ◽  
Quentin J. Moyer ◽  
Lee J. Silverberg
Keyword(s):  
Crystal Structure ◽  
Carbon Atom ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Phenyl Ring ◽  
Hydrophobic Interactions ◽  
The Other ◽  
Asymmetric Unit ◽  
Phenyl Rings ◽  
Thiazine Ring

The crystal structure of the title compound –meso-C26H24N2O2S2with two stereocenters – has half the molecule in the asymmetric unit with the other half generated by a crystallographic center of inversion. The thiazine ring is in a conformation that is between half-chair and envelope [θ = 52.51 (17)°]. The phenyl ring on the 2-carbon atom of the thiazine ring is pseudo-axial. The central phenyl ring of the molecule is close to orthogonal to the phenyl rings on either side with an angle of 76.85 (11)° between those planes. In the crystal, pairwise, weak C—H...O hydrogen bonds between the central phenyl ring and the oxygen atoms of neighboring molecules result in continuous strips propagating along thea-axis direction. Hydrophobic interactions of the C—H...π type are also observed.

A Crystallographic Study of Bis[S-benzyl-5-bromo-2-oxoindolin-3-ylidenemethanehydrazonthioate] Disulfide Solvated with Dimethylsulfoxide

2012 ◽  
Vol 9 (2) ◽  
pp. 87
Author(s):  
Mohd Abdul Fatah Abdul Manan ◽  
M. Ibrahim M. Tahir ◽  
Karen A. Crouse ◽  
Fiona N.-F. How ◽  
David J. Watkin
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Solvent Molecule ◽  
Site Occupancy ◽  
Unit Cell Parameters ◽  
Intermolecular Hydrogen Bonds ◽  
Triclinic Space Group ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Thiol Form

The crystal structure of the title compound has been determined. The compound crystallized in the triclinic space group P -1, Z = 2, V = 1839 .42( 18) A3 and unit cell parameters a= 11. 0460( 6) A, b = 13 .3180(7) A, c=13. 7321 (8) A, a = 80.659(3 )0, b = 69 .800(3 )0 and g = 77 .007 (2)0 with one disordered dimethylsulfoxide solvent molecule with the sulfur and oxygen atoms are distributed over two sites; S101/S102 [site occupancy factors: 0.6035/0.3965] and 0130/0131 [site occupancy factor 0.3965/0.6035]. The C22-S2 l and C 19-S20 bond distances of 1. 779(7) A and 1. 788(8) A indicate that both of the molecules are connected by the disulfide bond [S20-S21 2.055(2) A] in its thiol form. The crystal structure reveals that both of the 5-bromoisatin moieties are trans with respect to the [S21-S20 and CI 9-Nl 8] and [S20-S21 and C22-N23] bonds whereas the benzyl group from the dithiocarbazate are in the cis configuration with respect to [S21-S20 and C19-S44] and [S20-S21 and C22-S36] bonds. The crystal structure is further stabilized by intermolecular hydrogen bonds of N9-H35···O16 formed between the two molecules and N28-H281 ···O130, N28-H281 ···O131 and C4 l-H4 l l ···O 131 with the solvent molecule.

The protonation of the ethylenediphosphinetetraacetate anion and the crystal structure of the bis (hydrogen bromide) of ethylenediphosphinetetraacetic acid

1981 ◽  
Vol 46 (12) ◽  
pp. 3063-3073 ◽  
Author(s):  
Jana Podlahová ◽  
Bohumil Kratochvíl ◽  
Vratislav Langer ◽  
Josef Šilha ◽  
Jaroslav Podlaha
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Structure Determination ◽  
Free Acid ◽  
Hydrogen Bromide ◽  
Carboxyl Groups ◽  
Spectroscopic Methods ◽  
X Ray ◽  
Partial Formation

The equilibria and mechanism of addition of protons to the ethylenediphosphinetetraacetate anion (L4-) were studied in solution by the UV, IR, 1H and 31P NMR spectroscopic methods. A total of six protons can be bonded to the anion. They are added stepwise, first with partial formation of zwitterions containing P-H bonds, which then dissociate with formation of the free acid, H4L, where all four protons are bonded in carboxyl groups. The formation of zwitterions is strongly dependent on the concentration. In the final stage, the acid bonds two additional protons to form the bis-phosphonium cation, H6L2+. A number of isostructural salts containing this cation, H4L.2 HX (X = Cl, Br, I), have been prepared. The X-ray crystal structure determination of the bromide confirmed the expected arrangement. The bromide crystals are monoclinic, a = 578.2, b = 1 425.0, c = 1 046.7 pm, β = 103.07° with a space group of P21/c, Z = 2. The final R factor was 0.059 based on 1 109 observed reflections. The structure consists of H6L2+ cations containing protons bonded to phosphorus atoms (P-H distance 134 pm) and of bromide anions, located in gaps which are also sufficiently large for I- anions in the isostructural iodide. The interbonding of phosphonium cations proceeds through hydrogen bonds, C-OH...O=C, in which the O...O distance is 275.3 pm.

Synthesis, Crystal Structure And Spectroscopic Studies Of A Mixed Ligand Copper (Ii) Complex: Trans-Bis(Succinimidato)-Bis(Benzylamino)Cu(Ii)

2006 ◽  
Vol 61 (8) ◽  
pp. 979-982 ◽  
Author(s):  
Murat Taş ◽  
Hanife Saraçoğlu ◽  
Hümeyra Bati ◽  
Nezihe Çalışkan ◽  
Orhan Büyükgüngör
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Spectroscopic Studies ◽  
Mixed Ligand ◽  
Interplanar Angle ◽  
Space Group ◽  
Square Planar

The molecules of the title compound, [Cu(C11H13N2O2)2], lie across centres of inversion in space group P21/c and are linked by intermolecular N-H···O and C-H···O hydrogen bonds. The central Cu atom has a slightly distorted square-planar coordination comprised of four N atoms. Cu-N bond distances are 1.975(2) and 2.020(2) Å . The interplanar angle between the phenyl and succinimidato ring is 87.34(10)°

Crystal structure of tofacitinib dihydrogen citrate (Xeljanz®), (C16H21N6O)(H2C6H5O7)

2021 ◽  
pp. 1-8
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Acid Group ◽  
Dimensional Network ◽  
Van Der Waals Contacts ◽  
Citrate Anion

The crystal structure of tofacitinib dihydrogen citrate (tofacitinib citrate) has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Tofacitinib dihydrogen citrate crystallizes in space group P212121 (#19) with a = 5.91113(1), b = 12.93131(3), c = 30.43499(7) Å, V = 2326.411(6) Å3, and Z = 4. The crystal structure consists of corrugated layers perpendicular to the c-axis. Within the layers, cation⋯anion and anion⋯anion hydrogen bonds link the fragments into a two-dimensional network parallel to the ab-plane. Between the layers, there are only van der Waals contacts. A terminal carboxylic acid group in the citrate anion forms a strong charge-assisted hydrogen bond to the ionized central carboxylate group. The other carboxylic acid acts as a donor to the carbonyl group of the cation. The citrate hydroxy group forms an intramolecular charge-assisted hydrogen bond to the ionized central carboxylate. Two protonated nitrogen atoms in the cation act as donors to the ionized central carboxylate of the anion. These hydrogen bonds form a ring with the graph set symbol R2,2(8). The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

Crystal structure of pomalidomide Form I, C13H11N3O4

2021 ◽  
pp. 1-6
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Double Layers ◽  
Carbonyl Groups ◽  
Hydrogen Atoms ◽  
Powder Diffraction File ◽  
Functional Theory ◽  
Amine Hydrogen

The crystal structure of pomalidomide Form I has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Pomalidomide Form I crystallizes in the space group P-1 (#2) with a = 7.04742(9), b = 7.89103(27), c = 11.3106(6) Å, α = 73.2499(13), β = 80.9198(9), γ = 88.5969(6)°, V = 594.618(8) Å3, and Z = 2. The crystal structure is characterized by the parallel stacking of planes parallel to the bc-plane. Hydrogen bonds link the molecules into double layers also parallel to the bc-plane. Each of the amine hydrogen atoms acts as a donor to a carbonyl group in an N–H⋯O hydrogen bond, but only two of the four carbonyl groups act as acceptors in such hydrogen bonds. Other carbonyl groups participate in C–H⋯O hydrogen bonds. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

scholarly journals The 2.5 A crystal structure of a dimeric phospholipase A2 from the venom of Crotalus atrox.

1981 ◽  
Vol 256 (16) ◽  
pp. 8602-8607
Author(s):  
C. Keith ◽  
D.S. Feldman ◽  
S. Deganello ◽  
J. Glick ◽  
K.B. Ward ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Phospholipase A2 ◽  
Crotalus Atrox

scholarly journals Organotin(IV) selenate derivatives – Crystal structure of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n

2021 ◽  
Vol 44 (1) ◽  
pp. 213-217
Author(s):  
Waly Diallo ◽  
Hélène Cattey ◽  
Laurent Plasseraud
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Point Of View ◽  
Intermolecular Hydrogen Bonds

Abstract Crystallization of [(Ph3Sn)2SeO4] ⋅ 1.5H2O in methanol leads to the formation of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n (1) which constitutes a new specimen of organotin(IV) selenate derivatives. In the solid state, complex 1 is arranged in polymeric zig-zag chains, composed of alternating Ph3Sn and SeO4 groups. In addition, pendant Ph3Sn ⋅ CH3OH moieties are branched along chains according to a syndiotactic organization and via Sn-O-Se connections. From a supramolecular point of view, intermolecular hydrogen bonds established between the selenate groups (uncoordinated oxygen) and the hydroxyl functions (CH3OH) of the pendant groups link the chains together.

scholarly journals Crystal structure of atazanavir, C38H52N6O7

2020 ◽  
Vol 35 (2) ◽  
pp. 129-135
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Carbonyl Oxygen ◽  
Hydroxyl Group ◽  
Amide Nitrogen ◽  
Classical Hydrogen Bond ◽  
Intramolecular Hydrogen ◽  
Atazanavir Sulfate

The crystal structure of atazanavir has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Atazanavir crystallizes in space group P21 (#4) with a = 15.33545(7), b = 5.90396(3), c = 21.56949(13) Å, β = 96.2923(4)°, V = 1941.134(11) Å3, and Z = 2. Despite being labeled as “atazanavir sulfate”, the commercial reagent sample consisted of atazanavir free base. The structure consists of an array of extended-conformation molecules parallel to the ac-plane. Although the atazanavir molecule contains only four classical hydrogen bond donors, hydrogen bonding is, surprisingly, important to the crystal energy. Both intra- and intermolecular hydrogen bonds are significant. The hydroxyl group forms bifurcated intramolecular hydrogen bonds to a carbonyl oxygen atom and an amide nitrogen. Several amide nitrogens act as donors to the hydroxyl group and carbonyl oxygen atoms. An amide nitrogen acts as a donor to another amide nitrogen. Several methyl, methylene, methyne, and phenyl hydrogens participate in hydrogen bonds to carbonyl oxygens, an amide nitrogen, and the pyridine nitrogen. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1426.

Crystal structure of oxybutynin hydrochloride hemihydrate, C22H32NO3Cl(H2O)0.5

2019 ◽  
Vol 34 (1) ◽  
pp. 50-58
Author(s):  
James A. Kaduk ◽  
Nicholas C. Boaz ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Hydroxyl Group ◽  
Layered Crystal ◽  
Powder Diffraction File ◽  
X Ray ◽  
Layered Crystal Structure ◽  
Oxybutynin Hydrochloride

The crystal structure of oxybutynin hydrochloride hemihydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Oxybutynin hydrochloride hemihydrate crystallizes in space group I2/a (#15) with a = 14.57266(8), b = 8.18550(6), c = 37.16842(26) Å, β = 91.8708(4)°, V = 4421.25(7) Å3, and Z = 8. The compound exhibits X-ray-induced photoreduction of the triple bond. Prominent in the layered crystal structure is the N–H⋅⋅⋅Cl hydrogen bond between the cation and anion, as well as O–H⋅⋅⋅Cl hydrogen bonds from the water molecule and hydroxyl group of the oxybutynin cation. C–H⋅⋅⋅Cl hydrogen bonds also contribute to the crystal energy, and help determine the conformation of the cation. The powder pattern is included in the Powder Diffraction File™ as entry 00-068-1305.

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