Structural studies of ligands for the glycine binding site of the excitatory amino acid receptor complex: 2. 6-bromo-, 6-methyl-, and 6-styryl-1,8-ethano-4-hydro-2,3-quinoxalinedione

1994 ◽  
Vol 72 (10) ◽  
pp. 2028-2036 ◽  
Author(s):  
Maciej Kubicki ◽  
Teresa W. Kindopp ◽  
Mario V. Capparelli ◽  
Penelope W. Codding
Keyword(s):  
Hydrogen Bond ◽  
Binding Site ◽  
Crystal Structures ◽  
Excitatory Amino Acid ◽  
Glycine Receptor ◽  
Three Dimensional ◽  
Unit Cell ◽  
Geometric Constraints ◽  
Cell Parameters ◽  
Π Stacking

The crystal structures of three tricyclic quinoxalinedione derivatives, 6-bromo-1,8-ethano-4-hydro-2,3-quinoxalinedione (1), 6-methyl-1,8-ethano-4-hydro-2,3-quinoxalinedione hydrate (2), and 6-styryl-1,8-ethano-4-hydro-2,3-quinoxalinedione (3), are reported. For 1 and 2, the space groups are P21/n with the unit cell parameters for 1: a = 7.4003(5) Å, b = 8.5799(5) Å, c = 14.3127(9) Å, β = 90.639(6)°, and for 2: a = 7.0590(2) Å, b = 10.7483(3) Å, c = 13.9509(7) Å, β = 103.290(3)°. For 3, the space group is P21/c, with a = 19.3683(10) Å, b = 8.0962(16) Å, c = 19.5801(16) Å, β = 114.028(6)°. Compound 3 crystallizes with two molecules in the asymmetric part of the unit cell; in one of them the styryl group is disordered. The geometries of the 1,8-ethano-4-hydro-2,3-quinoxalinedione fragments are similar in all observations, with the differences mainly caused by the different nature of the substituents in the 6-position. Hydrogen bonds connect the molecules into three-dimensional networks. Head-to-tail π-stacking between molecules connected by a center of symmetry determines the packing modes in 1 and 2 but there is no π-stacking in the crystal structure of 3. The crystal structures of the three quinoxaline derivative ligands for the glycine receptor suggest a mode of recognition that involves an [Formula: see text]receptor hydrogen bond, a three-centre hydrogen bond to the neighboring carbonyl groups on the ligand, and π-stacking between ligand and receptor. This mode is consistent with the geometric constraints of the current binding site model but places greater emphasis on hydrogen-bond interactions.

Interesting Solvent Area in Crystal Structures of Two Natural Ergot Alkaloids

2005 ◽  
Vol 70 (1) ◽  
pp. 41-50 ◽  
Author(s):  
Blanka Klepetářová ◽  
Jan Čejka ◽  
Bohumil Kratochvíl ◽  
Svetlana Pakhomova ◽  
Ivana Císařová ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Three Dimensional ◽  
Ergot Alkaloids ◽  
Unit Cell ◽  
Dimensional Structure ◽  
Chemical Similarity ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Benzene Solvate ◽  
Similarity Structures

The structures of ergotamine bis(benzene) solvate (1) and ergocristine bis(benzene) solvate (2) are reported. Both structures crystallise in theP212121space group with cell parameters:1,a= 14.2968(3) Å,b= 15.4700(2) Å,c= 17.8123(4) Å, andV= 3939.57(13) Å3;2,a= 11.8358(2) Å,b= 17.6469(3) Å,c= 19.7125(3) Å, andV= 4117.25(12) Å3. Unexpectedly, despite the chemical similarity, structures of1and2significantly differ not only in the unit cell parameters, but also in the packing. Whereas in1solvent cavities are separated, there is only one unusual continuous solvent area in2filled with benzene, forming independent three-dimensional structure.

scholarly journals Crystal-to-Crystal Transformation from K2[Co(C2O4)2(H2O)2]·4H2O to K2[Co(μ-C2O4)(C2O4)]

2021 ◽  
Vol 7 (6) ◽  
pp. 77
Author(s):  
Bin Zhang ◽  
Yan Zhang ◽  
Guangcai Chang ◽  
Zheming Wang ◽  
Daoben Zhu
Keyword(s):  
Hydrogen Bond ◽  
Physical Properties ◽  
Crystal Structures ◽  
Molecular Crystal ◽  
Trigonal Prism ◽  
Space Group ◽  
Cell Parameters ◽  
Oxalate Anion ◽  
Crystal Transformation ◽  
Antiferromagnetic Ordering

Crystal-to-crystal transformation is a path to obtain crystals with different crystal structures and physical properties. K2[Co(C2O4)2(H2O)2]·4H2O (1) is obtained from K2C2O4·2H2O, CoCl2·6H2O in H2O with a yield of 60%. It is crystallized in the triclinic with space group P1 and cell parameters: a = 7.684(1) Å, b = 9.011(1) Å, c = 10.874(1) Å, α = 72.151(2)°, β = 70.278(2)°, γ = 80.430(2)°, V = 670.0(1) Å3, Z = 2 at 100 K. 1 is composed of K+, mononuclear anion [Co(C2O4)2(H2O)22−] and H2O. Co2+ is coordinated by two bidentated oxalate anion and two H2O in an octahedron environment. There is a hydrogen bond between mononuclear anion [Co(C2O4)2(H2O)22−] and H2O. K2[Co(μ-C2O4)(C2O4)] (2) is obtained from 1 by dehydration. The cell parameters of 2 are a = 8.460(5) Å, b = 6.906 (4) Å, c = 14.657(8) Å, β = 93.11(1)°, V = 855.0(8) Å3 at 100 K, with space group in P2/c. It is composed of K+ and zigzag [Co(μ-C2O4)(C2O42−]n chain. Co2+ is coordinated by two bisbendentate oxalate and one bidentated oxalate anion in trigonal-prism. 1 is an antiferromagnetic molecular crystal. The antiferromagnetic ordering at 8.2 K is observed in 2.

scholarly journals New crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 in two conformations

2014 ◽  
Vol 70 (11) ◽  
pp. 1468-1471
Author(s):  
Trung Thanh Thach ◽  
Sangho Lee
Keyword(s):  
Crystal Structures ◽  
Adenylate Kinase ◽  
Bound States ◽  
Critical Role ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
Ligand Free ◽  
Adenylate Kinases

Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groupsP21andP1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space groupC2, with unit-cell parametersa= 73.5,b= 54.3,c= 62.7 Å, β = 118.8°. The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on Cαatoms of 1.4 Å. The new crystal of the complex with the two-substrate-mimicking inhibitorP1,P5-bis(adenosine-5′-)pentaphosphate (Ap5A) belonged to space groupP1, with unit-cell parametersa= 53.9,b= 62.3,c= 63.0 Å, α = 101.9, β = 112.6, γ = 89.9°. Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.

Iodo-nitroarenesulfonamides: interplay of hard and soft hydrogen bonds, I...O interactions and aromatic π...π stacking interactions

2001 ◽  
Vol 58 (1) ◽  
pp. 94-108 ◽  
Author(s):  
Craig J. Kelly ◽  
Janet M. S. Skakle ◽  
James L. Wardell ◽  
Solange M. S. V. Wardell ◽  
John N. Low ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Space Group ◽  
Rotation Axes ◽  
Π Stacking ◽  
Structural Database ◽  
A Chain

Molecules of N-(4′-iodophenylsulfonyl)-4-nitroaniline, 4-O2NC6H4NHSO2C6H4I-4′ (1), are linked by three-centre I...O2N interactions into chains and these chains are linked into a three-dimensional framework by C—H...O hydrogen bonds. In the isomeric N-(4′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4NHSO2C6H4NO2-4′ (2), the chains generated by the I...O2N interactions are again linked into a three-dimensional framework by C—H...O hydrogen bonds. Molecules of N,N-bis(3′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4N(SO2C6H4NO2-3′)2 (3), lie across twofold rotation axes in space group C2/c and they are linked into chains by paired I...O=S interactions: these chains are linked into sheets by a C—H...O hydrogen bond, and the sheets are linked into a three-dimensional framework by aromatic π...π stacking interactions. In N-(4′-iodophenylsulfonyl)-3-nitroaniline, 3-O2NC6H4NHSO2C6H4I-4′ (4), there are R^2_2(8) rings formed by hard N—H...O=S hydrogen bonds and R^2_2(24) rings formed by two-centre I...nitro interactions, which together generate a chain of fused rings: the combination of a C—H...O hydrogen bond and aromatic π...π stacking interactions links the chains into sheets. Molecules of N-(4′-iodophenylsulfonyl)-4-methyl-2-nitroaniline, 4-CH3-2-O2NC6H3NHSO2C6H4I-4′ (5), are linked by N—H...O=S and C—H...O(nitro) hydrogen bonds into a chain containing alternating R^2_2(8) and R^2_2(10) rings, but there are no I...O interactions of either type. There are two molecules in the asymmetric unit of N-(4′-iodophenylsulfonyl)-2-nitroaniline, 2-O2NC6H4NHSO2C6H4I-4′ (6), and the combination of an I...O=S interaction and a hard N—H...O(nitro) hydrogen bond links the two types of molecule to form a cyclic, centrosymmetric four-component aggregate. C—H...O hydrogen bonds link these four-molecule aggregates to form a molecular ladder. Comparisons are made with structures retrieved from the Cambridge Structural Database.

The structures of marialite (Me6) and meionite (Me93) in space groups P42/n and I4/m, and the absence of phase transitions in the scapolite series

2011 ◽  
Vol 26 (2) ◽  
pp. 119-125 ◽  
Author(s):  
Sytle M. Antao ◽  
Ishmael Hassan
Keyword(s):  
Phase Transitions ◽  
High Resolution ◽  
Crystal Structures ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Space Groups ◽  
Cell Parameters ◽  
The Mean

The crystal structures of marialite (Me6) from Badakhshan, Afghanistan and meionite (Me93) from Mt. Vesuvius, Italy were obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinements. Their structures were refined in space groups I4/m and P42/n, and similar results were obtained. The Me6 sample has a formula Ca0.24Na3.37K0.24[Al3.16Si8.84O24]Cl0.84(CO3)0.15, and its unit-cell parameters are a=12.047555(7), c=7.563210(6) Å, and V=1097.751(1) Å3. The average ⟨T1-O⟩ distances are 1.599(1) Å in I4/m and 1.600(2) Å in P42/n, indicating that the T1 site contains only Si atoms. In P42/n, the average distances of ⟨T2-O⟩=1.655(2) and ⟨T3-O⟩=1.664(2) Å are distinct and are not equal to each other. However, the mean ⟨T2,3-O⟩=1.659(2) Å in P42/n and is identical to the ⟨T2′-O⟩=1.659(1) Å in I4/m. The ⟨M-O⟩ [7]=2.754(1) Å (M site is coordinated to seven framework O atoms) and M-A=2.914(1) Å; these distances are identical in both space groups. The Me93 sample has a formula of Na0.29Ca3.76[Al5.54Si6.46O24]Cl0.05(SO4)0.02(CO3)0.93, and its unit-cell parameters are a=12.19882(1), c=7.576954(8) Å, and V=1127.535(2) Å3. A similar examination of the Me93 sample also shows that both space groups give similar results; however, the C–O distance is more reasonable in P42/n than in I4/m. Refining the scapolite structure near Me0 or Me100 in I4/m forces the T2 and T3 sites (both with multiplicity 8 in P42/n) to be equivalent and form the T2′ site (with multiplicity 16 in I4/m), but ⟨T2-O⟩ is not equal to ⟨T3-O⟩ in P42/n. Using different space groups for different regions across the series implies phase transitions, which do not occur in the scapolite series.

scholarly journals Isomers and polymorphs of (E,E)-1,4-bis(nitrophenyl)-2,3-diaza-1,3-butadienes

2006 ◽  
Vol 62 (4) ◽  
pp. 666-675 ◽  
Author(s):  
Christopher Glidewell ◽  
John N. Low ◽  
Janet M. S. Skakle ◽  
James L. Wardell
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Stacking Interactions ◽  
Space Group ◽  
Stacking Interaction ◽  
Space Groups ◽  
Π Stacking ◽  
Π Stacking Interaction ◽  
Polymorphic Forms

The structures of five of the possible six isomers of (E,E)-1,4-bis(nitrophenyl)-2,3-diaza-1,3-butadiene are reported, including two polymorphs of one of the isomers. (E,E)-1,4-Bis(2-nitrophenyl)-2,3-diaza-1,3-butadiene, C14H10N4O4 (I), crystallizes in two polymorphic forms (Ia) and (Ib) in which the molecules lie across centres of inversion in space groups P21/n and P21/c, respectively: the molecules in (Ia) and (Ib) are linked into chains by aromatic π...π stacking interactions and C—H...π(arene) hydrogen bonds, respectively. Molecules of (E,E)-1-(2-nitrophenyl)-4-(3-nitrophenyl)-2,3-diaza-1,3-butadiene (II) are linked into sheets by two independent C—H...O hydrogen bonds. The molecules of (E,E)-1,4-bis(3-nitrophenyl)-2,3-diaza-1,3-butadiene (III) lie across inversion centres in the space group P21/n, and a combination of a C—H...O hydrogen bond and a π...π stacking interaction links the molecules into sheets. A total of four independent C—H...O hydrogen bonds link the molecules of (E,E)-1-(3-nitrophenyl)-4-(4-nitrophenyl)-2,3-diaza-1,3-butadiene (IV) into sheets. In (E,E)-1,4-bis(4-nitrophenyl)-2,3-diaza-1,3-butadiene (V) the molecules, which lie across centres of inversion in the space group P21/n, are linked by just two independent C—H...O hydrogen bonds into a three-dimensional framework.

Crystal structure of three diaza-crowns-18

1997 ◽  
Vol 212 (5) ◽  
Author(s):  
P. Dokurno ◽  
R. Trokowski ◽  
B. Kościuszko-Panek ◽  
T. Ossowski ◽  
A. Konitz ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Space Groups ◽  
Cell Parameters

AbstractThe crystal structures of three diaza crowns-18, namely 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane (crown 1), 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diacetonitrile (crown 2) and N,N′-(1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyldi-2,1-ethanediyl)bis-[4-methyl-benzenesulfonamide] (crown 3) have the following space groups and unit cell parameters: crown 1(C

scholarly journals N-[2-(2-Hydroxyethoxy)phenethyl]phthalimide

2012 ◽  
Vol 68 (6) ◽  
pp. o1636-o1636
Author(s):  
Er-Qun Yang ◽  
Jun-Tao Zhang ◽  
Xiao-Ping Cao ◽  
Jin-Zhong Gu
Keyword(s):  
Hydrogen Bond ◽  
Network Structure ◽  
Title Compound ◽  
Three Dimensional ◽  
Stacking Interactions ◽  
Compound C ◽  
Π Stacking ◽  
Dimensional Network ◽  
Benzene Rings

The title compound, C18H17NO4, was obtained accidentally through acid-catalysed aromatization of a phthalimide-substituted 2-(1-hydroxyethyl)cyclohex-2-enone. It exhibits an intramolecular O—H...Oc (c = carbonyl) hydrogen bond and forms a three-dimensional network structure via π–π stacking interactions between adjacent benzene rings (phthalimide-to-phenylene and phthalimide-to-phthalimide), with centroid–centroid distances of 3.8262 (6) and 3.6245 (5) Å.

scholarly journals Crystal structures of two 6-(2-hydroxybenzoyl)-5H-thiazolo[3,2-a]pyrimidin-5-ones

2015 ◽  
Vol 71 (7) ◽  
pp. 766-771
Author(s):  
Ligia R. Gomes ◽  
John Nicolson Low ◽  
Fernando Cagide ◽  
Fernanda Borges
Keyword(s):  
Hydrogen Bond ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Dihedral Angles ◽  
Stacking Interactions ◽  
Mechanism Of Formation ◽  
Π Stacking ◽  
Heterocyclic Moiety

The title compounds, 6-(2-hydroxybenzyl)-5H-thiazolo[3,2-a]pyrimidin-5-one, C13H8N2O3S, (1), and 6-(2-hydroxybenzyl)-3-methyl-5H-thiazolo[3,2-a]pyrimidin-5-one, C14H10N2O3S, (2), were synthesized when a chromone-3-carboxylic acid, activated with (benzotriazol-1-yloxy)tripyrrolidinylphosphonium hexafluoridophosphate (PyBOP), was reacted with a primary heteromamine. Instead of the expected amidation, the unusual title thiazolopyrimidine-5-one derivatives were obtained serendipitously and a mechanism of formation is proposed. Both compounds present an intramolecular O—H...O hydrogen bond, which generates anS(6) ring. The dihedral angles between the heterocyclic moiety and the 2-hydroxybenzoyl ring are 55.22 (5) and 46.83 (6)° for (1) and (2), respectively. In the crystals, the molecules are linked by weak C—H...O hydrogen bonds and π–π stacking interactions.

Hydrogen-bond patterns in 1,4-dihydro-2,3-quinoxalinediones: ligands for the glycine modulatory site on the NMDA receptor

1996 ◽  
Vol 52 (3) ◽  
pp. 487-499 ◽  
Author(s):  
M. Kubicki ◽  
T. W. Kindopp ◽  
M. V. Capparelli ◽  
P. W. Codding
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Binding Site ◽  
Three Dimensional ◽  
Hydrogen Bonding Pattern ◽  
Wide Range ◽  
Show Evidence ◽  
Additional Hydrogen Bond ◽  
Hydrogen Bond Patterns ◽  
Solvent Molecules

The crystal structures of five 1,4-dihydro-2,3-quinoxalinediones, antagonists of the NMDA modulatory glycine binding site on the excitary amino acid (EAA) receptor complex, have been determined: (I) 6,7-dinitro-1,4-dihydro-2,3-quinoxalinedione (DNQX); (II) 5,7-dinitro-1,4-dihydro-2,3-quinoxalinedione (MNQX); (III) 6-nitro-1,4-dihydro-2,3-quinoxalinedione hydrate; (IV) 6,7-dichloro-1,4-dihydro-2,3-quinoxalinedione; (V) 5,7-dichloro-1,4-dihydro-2,3-quinoxalinedione dimethylformamide. The crystal structure of the most active compound (II) contains a unique intramolecular N—H...O(NO2) hydrogen bond, which may be important for activity, as semiempirical calculations show that this bond is stable over a wide range of dihedral angles between the planes of the molecule and of the nitro group. In the other compounds the intermolecular hydrogen bonds connect molecules into three-dimensional networks. In compounds (I), (III) and (IV) head-to-tail: π-stacking is found between molecules connected by a center of symmetry. The geometries of the hydrogen-bonded —NH—C=O fragments show evidence of π-cooperativity or resonance-assisted hydrogen bonding. Graph-set analysis of the hydrogen-bond patterns of quinoxalinedione derivatives shows a tendency to form two types of hydrogen-bonding motifs: a centrosymmetric dimeric ring and an infinite chain. Even though this pattern may be modified by the presence of additional hydrogen-bond acceptors and/or donors, as well as by solvent molecules, general similarities have been found. Comparison of all quinoxalinedione structures suggests that the hydrogen-bonding pattern necessary for the biological activity at the glycine binding site contains one donor and two acceptors.

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