Crystal structures and hydrogen bonding in the anhydrous tryptaminium salts of the isomeric (2,4-dichlorophenoxy)acetic and (3,5-dichlorophenoxy)acetic acids

The anhydrous salts of 2-(1H-indol-3-yl)ethanamine (tryptamine) with isomeric (2,4-dichlorophenoxy)acetic acid (2,4-D) and (3,5-dichlorophenoxy)acetic (3,5-D), both C10H13N2+·C8H5Cl2O3−[(I) and (II), respectively], have been determined and their one-dimensional hydrogen-bonded polymeric structures are described. In the crystal of (I), the aminium H atoms are involved in three separate inter-species N—H...O hydrogen-bonding interactions, two with carboxylate O-atom acceptors and the third in an asymmetric three-centre bidentate carboxylateO,O′chelate [graph setR12(4)]. The indole H atom forms an N—H...Ocarboxylatehydrogen bond, extending the chain structure along theb-axis direction. In (II), two of the three aminium H atoms are also involved in N—H...Ocarboxylatehydrogen bonds similar to (I) but with the third, a three-centre asymmetric interaction with carboxylate and phenoxy O atoms is found [graph setR12(5)]. The chain polymeric extension is also alongb. There are no π–π ring interactions in either of the structures. The aminium side-chain conformations differ significantly between the two structures, reflecting the conformational ambivalence of the tryptaminium cation, as found also in the benzoate salts.

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Crystal structure of ammonium (3,5-dichlorophenoxy)acetate hemihydrate

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989015016345 ◽

2015 ◽

Vol 71 (10) ◽

pp. o717-o718 ◽

Cited By ~ 2

Author(s):

Graham Smith

Keyword(s):

Crystal Structure ◽

Hydrogen Bonding ◽

Acetic Acid ◽

Water Molecule ◽

Rotation Axis ◽

Ammonium Cation ◽

Side Chain ◽

Hydrogen Bonding Interactions ◽

Hydrated Salt ◽

Dichlorophenoxy Acetic Acid

In the structure of the title hydrated salt, NH4+·C8H5Cl2O3−·0.5H2O, where the anion derives from (3,5-dichlorophenoxy)acetic acid, the ammonium cation is involved in extensive N—H...O hydrogen bonding with both carboxylate and ether O-atom acceptors giving sheet structures lying parallel to (100). The water molecule of solvation lies on a crystallographic twofold rotation axis and is involved in intra-sheet O—H...Ocarboxylatehydrogen-bonding interactions. In the anion, the oxoacetate side chain assumes anantiperiplanarconformation with the defining C—O—C—C torsion angle = −171.33 (15)°.

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The significance of the Cα substituent in the selective inhibition of matrix metalloproteinases 1 and 9

Biological Chemistry ◽

10.1515/bc.2011.165 ◽

2011 ◽

Vol 392 (11) ◽

Author(s):

Riyad Domingo ◽

Kelly Chibale ◽

Edward D. Sturrock

Keyword(s):

Hydrogen Bonding ◽

Matrix Metalloproteinases ◽

Active Sites ◽

Unsaturated Compound ◽

Selective Inhibition ◽

Acid Group ◽

Side Chain ◽

Carboxylic Acid Group ◽

Lead Compounds ◽

Hydrogen Bonding Interactions

Abstract Matrix metalloproteinases (MMPs) cleave and degrade most components of the extracellular matrix, and unregulated MMP activity has been correlated to cancer and metastasis. Hence there is a burgeoning need to develop inhibitors that bind selectively to structurally similar MMPs. The inhibition profiles of peptidomimetics containing Cα substituents at the α,β unsaturated carbon were evaluated against the recombinant forms of ADAM17, MMP1, and MMP9. The dicarboxylic acid D2 and hydroxamate C2 inhibited MMP9 but not MMP1. The unsaturated compound E2 displayed selective inhibition for MMP1, compared with the saturated precursor C2, with an IC50 value of 3.91 μm. The molecular basis for this selectivity was further investigated by the molecular docking of E2 and D2 into the active sites of MMP1 and MMP9. These data demonstrate hydrogen-bonding interactions between the carbonyl group of the Cα substituent of E2 and the side chain of Asn180 present in the active site of MMP1. Conversely, the docked MMP9-D2 structure shows hydrophobic and hydrogen bonding between the ligand’s morpholine substituent and second carboxylic acid group with Leu187 and an amide, respectively. This study suggests that substituents other than P1′ and P2′ may confer selectivity among MMPs and may aid in the search for novel lead compounds.

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His224 Alters the R2 Drug Binding Site and Phe218 Influences the Catalytic Efficiency of the Metallo-β-Lactamase VIM-7

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02735-13 ◽

2014 ◽

Vol 58 (8) ◽

pp. 4826-4836 ◽

Cited By ~ 14

Author(s):

Hanna-Kirsti S. Leiros ◽

Susann Skagseth ◽

Kine Susann Waade Edvardsen ◽

Marit Sjo Lorentzen ◽

Gro Elin Kjæreng Bjerga ◽

...

Keyword(s):

Hydrogen Bonding ◽

Active Site ◽

Pathogenic Bacteria ◽

Catalytic Efficiency ◽

Drug Binding ◽

Side Chain ◽

Wild Type ◽

Drug Binding Site ◽

Chain Conformations ◽

Positively Charged

ABSTRACTMetallo-β-lactamases (MBLs) are the causative mechanism for resistance to β-lactams, including carbapenems, in many Gram-negative pathogenic bacteria. One important family of MBLs is the Verona integron-encoded MBLs (VIM). In this study, the importance of residues Asp120, Phe218, and His224 in the most divergent VIM variant, VIM-7, was investigated to better understand the roles of these residues in VIM enzymes through mutations, enzyme kinetics, crystal structures, thermostability, and docking experiments. The tVIM-7-D120A mutant with a tobacco etch virus (TEV) cleavage site was enzymatically inactive, and its structure showed the presence of only the Zn1 ion. The mutant was less thermostable, with a melting temperature (Tm) of 48.5°C, compared to 55.3°C for the wild-type tVIM-7. In the F218Y mutant, a hydrogen bonding cluster was established involving residues Asn70, Asp84, and Arg121. The tVIM-7-F218Y mutant had enhanced activity compared to wild-type tVIM-7, and a slightly higherTm(57.1°C) was observed, most likely due to the hydrogen bonding cluster. Furthermore, the introduction of two additional hydrogen bonds adjacent to the active site in the tVIM-7-H224Y mutant gave a higher thermostability (Tm, 62.9°C) and increased enzymatic activity compared to those of the wild-type tVIM-7. Docking of ceftazidime in to the active site of tVIM-7, tVIM-7-H224Y, and VIM-7-F218Y revealed that the side-chain conformations of residue 224 and Arg228 in the L3 loop and Tyr67 in the L1 loop all influence possible substrate binding conformations. In conclusion, the residue composition of the L3 loop, as shown with the single H224Y mutation, is important for activity particularly toward the positively charged cephalosporins like cefepime and ceftazidime.

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Crystal structure of 2,5-dimethylanilinium hydrogen maleate

Acta Crystallographica Section E Structure Reports Online ◽

10.1107/s160053681402282x ◽

2014 ◽

Vol 70 (11) ◽

pp. o1183-o1184 ◽

Cited By ~ 3

Author(s):

Maha Mathlouthi ◽

Daron E. Janzen ◽

Mohamed Rzaigui ◽

Wajda Smirani Sta

Keyword(s):

Crystal Structure ◽

Hydrogen Bond ◽

Hydrogen Bonding ◽

Ammonium Group ◽

Hydrogen Bonding Interactions ◽

Graph Set

The crystal structure of the title salt, C8H12N+·C4H3O4−, consists of a 2,5-dimethylanilinium cation and an hydrogen maleate anion. In the anion, a strong intramolecular O—H...O hydrogen bond is observed, leading to anS(7) graph-set motif. In the crystal, the cations and anions pack in alternating layers parallel to (001). The ammonium group undergoes intermolecular N—H...O hydrogen-bonding interactions with the O atoms of three different hydrogen maleate anions. This results in the formation of ribbons extending parallel to [010] with hydrogen-bonding motifs of the typesR44(12) andR44(18).

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Crystal structure of magnesium copper(II) bis[orthophosphate(V)] monohydrate

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989014026930 ◽

2015 ◽

Vol 71 (1) ◽

pp. 55-57 ◽

Cited By ~ 3

Author(s):

Jamal Khmiyas ◽

Abderrazzak Assani ◽

Mohamed Saadi ◽

Lahcen El Ammari

Keyword(s):

Crystal Structure ◽

Hydrogen Bonding ◽

Single Crystals ◽

Water Molecules ◽

Framework Structure ◽

Hydrothermal Conditions ◽

The Third ◽

Hydrogen Bonding Interactions

Single crystals of magnesium copper(II) bis[orthophosphate(V)] monohydrate, Mg1.65Cu1.35(PO4)2·H2O, were grown under hydrothermal conditions. The crystal structure is formed by three types of cationic sites and by two unique (PO4)3−anions. One site is occupied by Cu2+, the second site by Mg2+and the third site by a mixture of the two cations with an Mg2+:Cu2+occupancy ratio of 0.657 (3):0.343 (3). The structure is built up from more or less distorted [MgO6] and [(Mg/Cu)O5(H2O)] octahedra, [CuO5] square-pyramids and regular PO4tetrahedra, leading to a framework structure. Within this framework, two types of layers parallel to (-101) can be distinguished. The first layer is formed by [Cu2O8] dimers linked to PO4tetrahedraviacommon edges. The second, more corrugated layer results from the linkage between [(Cu/Mg)2O8(H2O)2] dimers and [MgO6] octahedra by common edges. The PO4units link the two types of layers, leaving space for channels parallel [101], into which the H atoms of the water molecules protrude. The latter are involved in O—H...O hydrogen-bonding interactions (one bifurcated) with framework O atoms across the channels.

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EFFECT OF SIDE-CHAIN STRUCTURE ON THE THIRD-ORDER NONLINEAR OPTICAL PROPERTIES OF ACRYLATE POLYMERS

Acta Polymerica Sinica ◽

10.3724/sp.j.1105.2006.00443 ◽

2006 ◽

Vol 006 (3) ◽

pp. 443-449

Author(s):

Min FANG ◽

Hongyao XU ◽

Shanyi GUANG ◽

BenZhong TANG ◽

Minhua JIANG

Keyword(s):

Optical Properties ◽

Nonlinear Optical ◽

Chain Structure ◽

Nonlinear Optical Properties ◽

Side Chain ◽

Third Order ◽

The Third ◽

Acrylate Polymers

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Crystal structure of bis{N′-[(E)-4-hydroxybenzylidene]pyridine-4-carbohydrazide-κN1}diiodidocadmium methanol disolvate

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989016019575 ◽

2017 ◽

Vol 73 (1) ◽

pp. 28-30 ◽

Cited By ~ 2

Author(s):

Farhad Akbari Afkhami ◽

Harald Krautscheid ◽

Zeliha Atioğlu ◽

Mehmet Akkurt

Keyword(s):

Hydrogen Bonding ◽

Rotation Axis ◽

Complex Molecule ◽

Three Dimensional ◽

Chain Structure ◽

Complex Molecules ◽

Hydrogen Bonding Interactions ◽

Dimensional Network ◽

Ethanol Solvate ◽

A Chain

In the title compound, [Cd(C13H11IN3O2)2]·2CH3OH, which crystallizes withZ= 4 in the space groupPbcn, the CdIIatom is located on a twofold rotation axis and coordinated by two I−anions and two N atoms from the pyridine rings of the twoN′-[(E)-4-hydroxybenzylidene]pyridine-4-carbohydrazide ligands. The geometry around the CdIIatom is distorted tetrahedral, with bond angles in the range 94.92 (11)–124.29 (2)°. The iodide anions undergo intermolecular hydrogen-bonding contacts with the C—H groups of the organic ligands of an adjacent complex molecule, generating a chain structure along thebaxis. Furthermore, an extensive series of O—H...O, N—H...O and C—H...O hydrogen-bonding interactions involving both the complex molecules and the ethanol solvate molecules generate a three-dimensional network.

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Crystal structures and hydrogen bonding in the morpholinium salts of four phenoxyacetic acid analogues

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989015019842 ◽

2015 ◽

Vol 71 (11) ◽

pp. 1392-1396 ◽

Cited By ~ 4

Author(s):

Graham Smith ◽

Daniel E. Lynch

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonding ◽

Ion Pairs ◽

Phenoxyacetic Acid ◽

Dimensional Chain ◽

Hydrogen Bonding Interaction ◽

One Dimensional ◽

Bonding Interaction ◽

Graph Set ◽

Dichlorophenoxy Acetic Acid

The anhydrous salts morpholinium (tetrahydro-2-H-1,4-oxazin-4-ium) phenoxyacetate, C4H10NO+·C8H7O3−, (I), morpholinium (4-fluorophenoxy)acetate, C4H10NO+·C8H6 FO3−, (II), and isomeric morpholinium (3,5-dichlorophenoxy)acetate (3,5-D), (III), and morpholinium (2,4-dichlorophenoxy)acetic acid (2,4-D), C4H10NO+·C8H5Cl2O3−, (IV), have been determined and their hydrogen-bonded structures are described. In the crystals of (I), (III) and (IV), one of the the aminium H atoms is involved in a three-centre asymmetric cation–anion N—H...O,O′R12(4) hydrogen-bonding interaction with the two carboxyl O-atom acceptors of the anion. With the structure of (II), the primary N—H...O interaction is linear. In the structures of (I), (II) and (III), the second N—H...Ocarboxylhydrogen bond generates one-dimensional chain structures extending in all cases along [100]. With (IV), the ion pairs are linked though inversion-related N—H...O hydrogen bonds [graph setR42(8)], giving a cyclic heterotetrameric structure.

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Synthesis and crystal structure of poly[(3-amino-1,2,4-triazole)(μ3-1H-benzimidazole-5,6-dicarboxylato)cobalt(II)]

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989021005867 ◽

2021 ◽

Vol 77 (7) ◽

pp. 714-717

Author(s):

Chen Zhao ◽

Yi Li ◽

Jin-Sheng Xiao ◽

Peng-Dan Zhang ◽

Xue-Qian Wu ◽

...

Keyword(s):

Crystal Structure ◽

Hydrogen Bonding ◽

Three Dimensional ◽

Chain Structure ◽

Asymmetric Unit ◽

Straight Chain ◽

Tetrahedral Geometry ◽

Synthesis And Crystal Structure ◽

One Dimensional ◽

Hydrogen Bonding Interactions

The asymmetric unit of the title coordination polymer, [Co(C9H4N2O4)(C2H4N4)] n or [Co(L 1)(L 2)] n , consists of one crystallographically independent Co2+ centre, one L 1 2− ligand and one L 2 ligand (L 1 = 1H-benzimidazole-5,6-dicarboxylic acid, L 2 = 3-amino-1,2,4-triazole). The Co2+ centre is coordinated by two carboxylato-O atoms from two independent L 1 2− ligands and two nitrogen atoms from L 2 and another L 1 ligand. Thus, the metal center adopts a four-coordinate mode, forming a tetrahedral geometry. Interestingly, through the combination of two L 1 2−, two L 2 ligands and two Co2+ ions, a basic repeating unit is constructed, resulting in the formation of a one-dimensional straight chain structure. These chains are further expanded to the final three-dimensional framework via N—H...O hydrogen-bonding interactions.

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