Substituent position effect on the crystal structures of N-phenyl-2-phthalimidoethanesulfonamide derivatives

2018 ◽  
Vol 74 (1) ◽  
pp. 31-36
Author(s):  
Resul Sevinçek ◽  
Duygu Barut Celepci ◽  
Serap Köktaş Koca ◽  
Özlem Akgül ◽  
Muittin Aygün
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Biological Activities ◽  
Position Effect ◽  
Intermolecular Hydrogen Bond ◽  
X Ray ◽  
Space Groups ◽  
X Ray Crystallography ◽  
Hydrogen Bond Interactions ◽  
The Impact

In order to determine the impact of different substituents and their positions on intermolecular interactions and ultimately on the crystal packing, unsubstituted N-phenyl-2-phthalimidoethanesulfonamide, C16H14N2O4S, (I), and the N-(4-nitrophenyl)-, C16H13N3O6S, (II), N-(4-methoxyphenyl)-, C16H16N3O6S, (III), and N-(2-ethylphenyl)-, as the monohydrate, C18H18N2O4S·H2O, (IV), derivatives have been characterized by single-crystal X-ray crystallography. Sulfonamides (I) and (II) have triclinic crystal systems, while (III) and (IV) are monoclinic. Although the molecules differ from each other only with respect to small substituents and their positions, they crystallized in different space groups as a result of differing intra- and intermolecular hydrogen-bond interactions. The structures of (I), (II) and (III) are stabilized by intermolecular N—H...O and C—H...O hydrogen bonds, while that of (IV) is stabilized by intermolecular O—H...O and C—H...O hydrogen bonds. All four structures are of interest with respect to their biological activities and have been studied as part of a program to develop anticonvulsant drugs for the treatment of epilepsy.

Positional isomeric effect on the crystallization of chlorine-substitutedN-phenyl-2-phthalimidoethanesulfonamide derivatives

2015 ◽  
Vol 71 (9) ◽  
pp. 839-843 ◽  
Author(s):  
Serap Köktaş Koca ◽  
Resul Sevinçek ◽  
Özlem Akgül ◽  
Muhittin Aygün
Keyword(s):  
Hydrogen Bond ◽  
Biological Activities ◽  
Intermolecular Hydrogen Bond ◽  
Stacking Interactions ◽  
X Ray ◽  
Space Groups ◽  
X Ray Crystallography ◽  
Hydrogen Bond Interactions ◽  
Benzene Rings ◽  
Isomeric Effect

Theortho-,para- andmeta-chloro-substitutedN-chlorophenyl-2-phthalimidoethanesulfonamide derivatives, C16H13ClN2O4S, have been structurally characterized by single-crystal X-ray crystallography.N-(2-Chlorophenyl)-2-phthalimidoethanesulfonamide, (I), has orthorhombic (P212121) symmetry,N-(4-chlorophenyl)-2-phthalimidoethanesulfonamide, (II), has triclinic (P\overline{1}) symmetry andN-(3-chlorophenyl)-2-phthalimidoethanesulfonamide, (III), has monoclinic (P21/c) symmetry. The molecules of (I)–(III) are regioisomers which have crystallized in different space groups as a result of the differing intra- and intermolecular hydrogen-bond interactions which are present in each structure. Compounds (I) and (II) are stabilized by N—H...O and C—H...O hydrogen bonds, while (III) is stabilized by N—H...O, C—H...O and C—H...Cl hydrogen-bond interactions. The structure of (II) also displays π–π stacking interactions between the isoindole and benzene rings. All three structures are of interest with respect to their biological activities and have been studied as part of a programme to develop anticonvulsant drugs for the treatment of epilepsy.

scholarly journals Intermolecular Hydrogen and Halogen Bonds in Fluorinated Benzimidazoles

2014 ◽  
Vol 70 (a1) ◽  
pp. C643-C643
Author(s):  
Rosa M Claramunt ◽  
Marta Pérez-Torralba ◽  
M. Ángeles García ◽  
Concepción López ◽  
M. Carmen Torralba ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Weak Interactions ◽  
Bond Distance ◽  
Imidazole Ring ◽  
Halogen Bonds ◽  
Aromatic Rings ◽  
Molecular Plane ◽  
X Ray ◽  
X Ray Crystallography

After hydrogen bonds (HB) the most studied of related weak interactions are the halogen bonds (XB). The competition between these two interactions as well as their interplay to determine the crystal packing of organic derivatives is a subject of interest. Most the studies related to XB concerns the heaviest halogen atoms, I and Br, less Cl and much less F, because the interaction energy decreases in this order. [1,2] We present here our studies on the structure of five tetrafluorinated benzazoles by X-ray crystallography and solid-state NMR, a powerful synergic mixture of techniques. The compounds are 4,5,6,7-tetrafluoro-1H-benzimidazole (1), 4,5,6,7-tetrafluoro-2-(trifluoromethyl)-1H-benzimidazole (2), 4,5,6,7-tetrafluoro-1H-benzimidazole-2(3H)-one (3), 4,5,6,7-tetrafluoro-1-methyl-1H-benzimidazole-2(3H)-one (4), and 4,5,6,7-tetrafluoro-1,3-dimethyl-1H-benzimidazole-2(3H)-one (5). As a common general feature, these compounds are quite planar due to the presence of the two aromatic rings. The existence of the methyl groups as substituent in the nitrogen atoms does not modify the planarity of the molecule. The bond distances and angles are in agreement with the expected ones for this kind of compounds. The presence of the carbonyl group induces some electronic changes in the imidazole ring that is resembled in the lengthening of the C2N3 bond distance and in a higher deviation of C2 atom from the molecular plane. Moreover, all the compounds show one or more interactions by strong linear hydrogen bonds, which lead to the formation of chains that, in some cases, can exhibit additional interactions via pi-pi and/or F···F contacts spreading out the dimensionality of the structure in the crystal. [3] The distribution of the F···F contacts in compounds 1-5 is similar to those of the literature and includes for 4,5,6,7-tetrafluoro-1H-benzimidazole-2(3H)-one (3) one of the shortest F···F distances ever reported [2.596(3) Å]. Two polymorphs of compound 4 are identified.

A combined X-ray crystallography and theoretical study of N—H...OX (X is =P and —C) hydrogen bonds in two new structures with a (C—O)2(N)P(=Y) (Y is O and S) skeleton

2018 ◽  
Vol 74 (12) ◽  
pp. 1610-1621 ◽  
Author(s):  
Banafsheh Vahdani Alviri ◽  
Mehrdad Pourayoubi ◽  
Abolghasem Farhadipour ◽  
Marek Nečas ◽  
Valerio Bertolasi
Keyword(s):  
Hydrogen Bonds ◽  
Quantum Chemical ◽  
Software Package ◽  
Theoretical Study ◽  
Natural Bond Orbital ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
X Ray ◽  
X Ray Crystallography ◽  
Hydrogen Bonding Interactions

The crystal structures of N,N′-(cyclohexane-1,4-diyl)bis(O,O′-diphenylphosphoramide), C30H32N2O6P2 or (C6H5O)2P(O)(1-NH)(C6H10)(4-NH)P(O)(OC6H5)2, (I), and N,N′-(1,4-phenylene)bis(O,O′-dimethylthiophosphoramide), C10H18N2O4P2S2 or (CH3O)2P(S)(1-NH)(C6H4)(4-NH)P(S)(OCH3)2, (II), have been investigated. In the structure of (I), with an (O)2(N)P(O) skeleton, two symmetry-independent phosphoramide molecules are linked through N—H...O=P hydrogen bonds. In the structure of (II), with an (O)2(N)P(S) skeleton, the ester O atoms take part in N—H...O—C hydrogen bonds as acceptors; the P=S groups do not participate in hydrogen-bonding interactions. The strengths of these hydrogen bonds were evaluated, using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6-311G(d,p) level of theory. For this, LP(O) to σ*(NH) charge transfers were studied, according to the second-order perturbation theory in natural bond orbital (NBO) methodology, for a three-component cluster of hydrogen-bonded molecules for both structures, including all of the independent N—H...O hydrogen bonds observed in the crystal packing. The details of the intermolecular interactions were studied by Hirshfeld surface maps and two-dimensional fingerprint plots.

Synthesis and structural study of five new phosphoric triamides: interplay between classical and non-classical intermolecular interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Bahar Bakhshipour ◽  
Atekeh Tarahhomi ◽  
Arie van der Lee
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Phosphoric Triamide ◽  
Ft Ir ◽  
Phosphoric Triamides

Abstract Phosphoric triamides are attractive to investigate because of their extensive applications in various fields, especially in medicine. Five new phosphoric triamides with the main parts [N]P(O)[NH]2 and [C(O)NH]P(O)[N]2 have been structurally analyzed by single crystal MoKα/synchrotron-based X-ray diffraction and characterized by spectroscopic methods (FT-IR and 1H, 13C, 31P NMR). Compounds crystallize in orthorhombic (1 with space group Pnma) and monoclinic (2 (P21/a), 3 (C2/c), 4 (P21/n) and 5 (P21/c)) crystal systems. The asymmetric unit of all structures consists of one phosphoric triamide molecule, except for 1 with one half of molecule. X-ray crystallography data reveal that the molecular architectures constructed by classical N—H … O hydrogen bonds are as 1D linear (building the R 2 1 ( 6 ) ${R}\_{2}^{1}(6)$ , C(4) and R 2 2 ( 10 ) / R 2 1 ( 6 ) ${R}\_{2}^{2}(10)/{R}\_{2}^{1}(6)$ motifs, respectively, for 1–3) or dimeric (the R 2 2 ( 8 ) ${R}\_{2}^{2}(8)$ ring motif for 4 and 5). A detailed investigation of the intermolecular interactions using Hirshfeld surface (HS) analysis illustrates that the H … H, O … H/H … O and C … H/H … C contacts for all compounds, and Cl … H/H … Cl and F … H/H … F contacts for 3–5, are the most significant contributors to the crystal packing. Moreover, based on the calculated enrichment ratios (E), the O … H/H … O contacts including the classical N—H … O hydrogen bonds for all structures are considered as favoured contacts.

C−H- - -O Hydrogen Bonds in β-Sheetlike Networks:  Combined X-ray Crystallography and High-Pressure Infrared Study

2003 ◽  
Vol 125 (40) ◽  
pp. 12358-12364 ◽  
Author(s):  
Kwang Ming Lee ◽  
Hai-Chou Chang ◽  
Jyh-Chiang Jiang ◽  
Jack C. C. Chen ◽  
Hsiang-En Kao ◽  
...  
Keyword(s):  
High Pressure ◽  
Hydrogen Bonds ◽  
Infrared Study ◽  
X Ray ◽  
X Ray Crystallography

Configurational and conformational studies on condensation products of biogenic amines with 2,5-anhydro-D-mannose

1985 ◽  
Vol 63 (11) ◽  
pp. 2915-2921 ◽  
Author(s):  
Ian M. Piper ◽  
David B. MacLean ◽  
Romolo Faggiani ◽  
Colin J. L. Lock ◽  
Walter A. Szarek
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Direct Methods ◽  
Conformational Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Twist Conformation ◽  
Cell Dimensions ◽  
Internal Hydrogen Bond

The products of a Pictet–Spengler condensation of tryptamine and of histamine with 2,5-anhydro-D-mannose have been studied by X-ray crystallography to establish their absolute configuration. 1(S)-(α-D-Arabinofuranosyl)-1,2,3,4-tetrahydro-β-carboline (1), C16H20N20O4, is monoclinic, P21 (No. 4), with cell dimensions a = 13.091(4), b = 5.365(1), c = 11.323(3) Å, β = 115.78(2)°, and Z = 2. 4-(α-D-Arabinofuranosyl)imidazo[4,5-c]-4,5,6,7-tetrahydropyridine (3), C11H17N3O4, is orthorhombic, P212121 (No. 19), with cell dimensions a = 8.118(2), b = 13.715(4), c = 10.963(3) Å, and Z = 4. The structures were determined by direct methods and refined to R1 = 0.0514, R2 = 0.0642 for 3210 reflections in the case of 1, and to R1 = 0.0312, R2 = 0.0335 for 1569 reflections in the case of 3. Bond lengths and angles within both molecules are normal and agree well with those observed in related structures. In 3 the base and sugar adopt a syn arrangement, which is maintained by an internal hydrogen bond between O(2′) and N(3). The sugar adopts a normal 2T3 twist conformation. The sugar has the opposite anti arrangement in the β-carboline 1 and the conformation of the sugar is unusual; it is close to an envelope conformation with O(4′) being the atom out of the plane. This conformation is caused by a strong intermolecular hydrogen bond from O(5′) in a symmetry-related molecule to O(4′). Both compounds are held together in the crystal by extensive hydrogen-bonding networks. The conformations of the compounds in solution have been investigated by 1H nmr spectroscopy, and the results obtained were compared with those obtained by X-ray crystallography for 1 and 3.

Systhesis, Characterization and Spectroscopic Properties of (2E,6E)-2,6-Bis(2,3,4-tri-methoxy-benzylidene)cyclohexanone

2011 ◽  
Vol 396-398 ◽  
pp. 2338-2341
Author(s):  
Xing Chuan Wei ◽  
Zhi Li Liu ◽  
Kun Zhang ◽  
Zhi Yun Du ◽  
Xi Zheng
Keyword(s):  
Crystal Structure ◽  
Acetic Acid ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Spectroscopic Properties ◽  
Spectral Studies ◽  
Double Bonds ◽  
X Ray ◽  
Π Interactions ◽  
X Ray Crystallography

In this paper, (2E,6E)-2,6-Bis(2,3,4-tri-methoxy -benzylidene)cyclohexanone (omitted as tmbcho) (1) was obtained by the reaction of acetic acid, tetrahydrofuran, cyclohexanone and 2,3,4-tri-methoxy-benzaldehyde. Three non-classic hydrogen bonds were observed in the compound. X-ray crystallography shows that the crystal structure is stabilized by intermolecular C-H•••π interactions and it contains plenty of conjugated double bonds. The title compound was characterized by UV-vis and fluorescent spectral studies.

A Zinc(II)-Silver(I) Bimetallic Coordination Polymer Assembled Through Argentophilic and π-π Interactions, f[Zn(phen)2(H2O) {Ag(CN)2g][Ag(CN)2]·MeOH}n (phen=1,10-Phenanthroline)

2013 ◽  
Vol 68 (2) ◽  
pp. 161-167 ◽  
Author(s):  
Muhammad Monim-ul-Mehbooba ◽  
Muhammad Ramzan ◽  
Tobias Rüffe ◽  
Heinrich Lang ◽  
Shafqat Naddem ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thermal Analysis ◽  
Ir Spectroscopy ◽  
Coordination Polymer ◽  
Hydrogen Bonds ◽  
X Ray ◽  
Π Interactions ◽  
X Ray Crystallography ◽  
3D Network ◽  
Argentophilic Interactions

A cyanido-bridged Zn(II)-Ag(I) bimetallic coordination polymer, {[Zn(phen)2(H2O){Ag(CN)2}] [Ag(CN)2]·MeOH}n (1), was prepared using ZnCl2, 1,10-phenanthroline (phen) and K[Ag(CN)2] and characterized by IR spectroscopy, thermal analysis and X-ray crystallography. The crystal structure of 1 consists of dinuclear [Zn(phen)2(H2O){Ag(CN)2}]+ cations, [Ag(CN)2]- anions and a methanol molecule. The non-coordinated [Ag(CN)2]- anions are linked to the [Zn(phen)2(H2O){Ag(CN)2}]+ complex cations through argentophilic interactions leading to the formation of chains. The chains are connected by hydrogen bonds and π-π interactions to give a 3D network.

scholarly journals 1-[N-Methyl-N-(Phenyl)amino]-3- (4-Methylphenyl)Thiourea

Molbank ◽  
10.3390/m1052 ◽  
2019 ◽  
Vol 2019 (1) ◽  
pp. M1052 ◽  
Author(s):  
Chien Yeo ◽  
Edward Tiekink
Keyword(s):  
Hydrogen Bond ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Elemental Analysis ◽  
Title Compound ◽  
Molecular Conformation ◽  
Phenyl Hydrazine ◽  
X Ray ◽  
X Ray Crystallography

The title compound, 1-[N-methyl-N-(phenyl)amino]-3-(4-methylphenyl)thiourea (1), was synthesized by the reaction of 1-methyl-1-phenyl hydrazine and 4-tolyl isothiocyanate, and was characterized by spectroscopy (1H and 13C{1H} NMR, IR, and UV), elemental analysis as well as by single crystal X-ray crystallography. In the solid state, the molecule exists as the thioamide tautomer and features an anti-disposition of the thioamide–N–H atoms; an intramolecular N–H⋯N hydrogen bond is noted. The molecular conformation resembles that of the letter L. In the molecular packing, thioamide-N1–H⋯S1(thione) hydrogen bonds lead to centrosymmetric eight-membered {⋯HNCS}2 synthons. The dimers are assembled into a supramolecular layer in the bc-plane by phenyl- and methyl-C–H⋯π(phenyl) interactions.

scholarly journals A hybrid approach reveals the allosteric regulation of GTP cyclohydrolase I

2020 ◽  
Vol 117 (50) ◽  
pp. 31838-31849
Author(s):  
Rebecca Ebenhoch ◽  
Simone Prinz ◽  
Susann Kaltwasser ◽  
Deryck J. Mills ◽  
Robert Meinecke ◽  
...  
Keyword(s):  
Crystal Packing ◽  
Substrate Binding ◽  
Regulatory Protein ◽  
Allosteric Regulation ◽  
Hybrid Approach ◽  
Site Directed Mutagenesis ◽  
Gtp Cyclohydrolase I ◽  
Gtp Cyclohydrolase ◽  
X Ray ◽  
X Ray Crystallography

Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP to dihydroneopterin triphosphate (H2NTP), the initiating step in the biosynthesis of tetrahydrobiopterin (BH4). Besides other roles, BH4 functions as cofactor in neurotransmitter biosynthesis. The BH4 biosynthetic pathway and GCH1 have been identified as promising targets to treat pain disorders in patients. The function of mammalian GCH1s is regulated by a metabolic sensing mechanism involving a regulator protein, GCH1 feedback regulatory protein (GFRP). GFRP binds to GCH1 to form inhibited or activated complexes dependent on availability of cofactor ligands, BH4 and phenylalanine, respectively. We determined high-resolution structures of human GCH1−GFRP complexes by cryoelectron microscopy (cryo-EM). Cryo-EM revealed structural flexibility of specific and relevant surface lining loops, which previously was not detected by X-ray crystallography due to crystal packing effects. Further, we studied allosteric regulation of isolated GCH1 by X-ray crystallography. Using the combined structural information, we are able to obtain a comprehensive picture of the mechanism of allosteric regulation. Local rearrangements in the allosteric pocket upon BH4 binding result in drastic changes in the quaternary structure of the enzyme, leading to a more compact, tense form of the inhibited protein, and translocate to the active site, leading to an open, more flexible structure of its surroundings. Inhibition of the enzymatic activity is not a result of hindrance of substrate binding, but rather a consequence of accelerated substrate binding kinetics as shown by saturation transfer difference NMR (STD-NMR) and site-directed mutagenesis. We propose a dissociation rate controlled mechanism of allosteric, noncompetitive inhibition.

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