Structure and Conformations of GABA-Transaminase Inhibitors. V. 4-[(2-Hydroxy-3,6-dimethylbenzyl)-methylamino]butanoic Acid Monohydrate

1988 ◽  
Vol 41 (10) ◽  
pp. 1607 ◽  
Author(s):  
PR Andrews ◽  
JM Gulbis ◽  
MN Iskander ◽  
MF Mackay ◽  
C Dipaola
Keyword(s):  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Intramolecular Hydrogen Bonding ◽  
Intermolecular Hydrogen Bonding ◽  
Butanoic Acid ◽  
Gaba Transaminase ◽  
Phenolic Oxygen ◽  
Dimensional Network ◽  
Intramolecular Hydrogen ◽  
Potential Inhibitors

As part of a program to define conformational detail of potential inhibitors based on the calculated transition state of GABA-T, we report the crystal structure of the title compound. Crystals were triclinic and belong to the space group Pī with a 10.110(1), b 9.358(1), c 13.933Ǻ, α 90.37(1), β 93.27(1), γ 88.12(1)? and Z 4. Refinement on 3505 data measured with Cu Kα radiation converged at R 0.052. The two independent inhibitor molecules are essentially identical in conformation detail and are in a dipolar form. There is no intramolecular hydrogen bonding between the GABA nitrogen and phenolic oxygen but extensive intermolecular hydrogen bonding links the molecules into a three-dimensional network in the crystal.

Structure and Conformations of Gaba-Transaminase Inhibitors. I. Multisubstrate Analogs

1986 ◽  
Vol 39 (10) ◽  
pp. 1559
Author(s):  
PR Andrews ◽  
V Cody ◽  
MN Iskander ◽  
AI Jeffrey ◽  
MF Mackay ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Transition State ◽  
Intramolecular Hydrogen Bonding ◽  
Side Chain ◽  
Gaba Transaminase ◽  
X Ray ◽  
Potential Energy Calculations ◽  
Phenolic Oxygen ◽  
Structural Differences ◽  
Intramolecular Hydrogen

Two multisubstrate analogues of the transition state in the reaction catalysed by the enzyme GABA- transaminase (E.C. 2.6.1.19), sulfonic acid pyridoxal dervative , C10H16N2O5S (1) and carboxylic acid pyridoxal derivative, C13H18N2O4 (2), have been characterized by X-ray analyses of crystals of (1). HCl , (1).H2O and (2). HCl . In each structure, the nitrogen on the side chain is the donor in intramolecular hydrogen bonding. However, it is only in (2). HCl that this interaction is with the phenolic oxygen as postulated in the proposed transition state of the reaction catalysed by GABA- transaminase . For both structures of (1), on the other hand, this interaction is with the oxygen of the ring hydroxymethyl substituent, and results in a seven- membered ring. Conformational analysis indicates that both modes of hydrogen bonding may be present in the pyridoxal derivatives, although no quantitative assessment is possible at the MINDO/3 or MNDO levels. Simple classical potential energy calculations indicate significant structural differences between the lowest energy conformations of these compounds and the calculated transition state. However, conformations which match the key features of the transition state are also relatively low in energy.

Crystal structures of two polymorphic forms of DOTAM-mono-acid dihydrate

2018 ◽  
Vol 74 (5) ◽  
pp. 542-547
Author(s):  
Paul Jurek ◽  
Garry E. Kiefer ◽  
Frank R. Fronczek
Keyword(s):  
Hydrogen Bonding ◽  
Intramolecular Hydrogen Bonding ◽  
Temperature Structure ◽  
Intermolecular Hydrogen Bonding ◽  
Space Group ◽  
Pendant Arm ◽  
Polymorphic Forms ◽  
Higher Temperature ◽  
Hydrogen Bonding Network ◽  
Intramolecular Hydrogen

The structural chemistry of 2-[4,7,10-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecan-1-yl]acetic acid dihydrate, C16H31N7O5·2H2O, is described. The macrocyclic compound, also known by the abbreviation DOTAM-mono-acid, crystallized at room temperature and was isolated concomitantly as two polymorphic forms. The structures of both polymorphs were determined at 90 K. The first polymorph crystallized as a zwitterionic dihydrate [systematic name: 4,7,10-tris(carbamoylmethyl)-1-(carboxylatomethyl)-1,4,7,10-tetraazacyclododecan-1-ium dihydrate] in the space group P21/n, with Z′ = 1. The second polymorph crystallized as a zwitterionic dihydrate in the space group P21 at 90 K, with Z′ = 2. The two independent molecules are related by a local center. In each polymorph, the zwitterion is formed between the negatively-charged carboxylate group and the ring N atom that bears the acetate pendant arm. Extensive inter- and intramolecular hydrogen bonding exists in both polymorphic structures. In polymorph 1, an intermolecular hydrogen-bonding network propagating parallel to the a direction creates an infinite chain. A second hydrogen-bonding network is observed through a water molecule of hydration in the b direction. Polymorph 2 also has two intermolecular hydrogen-bonding networks. One propagates parallel to the a direction, while the other propagates in the [\overline{1}10] direction. Increasing the temperature of polymorph 2 yields the same structure at T = 180 K, but the pseudocenter becomes exact at 299 K. The higher-temperature structure has Z′ = 1 in the space group P21/c.

scholarly journals Crystal structures of chlorido[dihydroxybis(1-iminoethoxy)]arsanido-κ3 N,As,N′]platinum(II) and of a polymorph of chlorido[dihydroxybis(1-iminopropoxy)arsanido-κ3 N,As,N′]platinum(II)

2020 ◽  
Vol 76 (2) ◽  
pp. 180-185
Author(s):  
Nina R. Marogoa ◽  
D.V. Kama ◽  
Hendrik G. Visser ◽  
M. Schutte-Smith
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Donor Ligands ◽  
Intermolecular Hydrogen Bonding ◽  
Π Interactions ◽  
Hydrogen Bonding Interactions ◽  
Oxygen Donor ◽  
Dimensional Network

Each central platinum(II) atom in the crystal structures of chlorido[dihydroxybis(1-iminoethoxy)arsanido-κ3 N,As,N′]platinum(II), [Pt(C4H10AsN2O4)Cl] (1), and of chlorido[dihydroxybis(1-iminopropoxy)arsanido-κ3 N,As,N′]platinum(II), [Pt(C6H14AsN2O4)Cl] (2), is coordinated by two nitrogen donor atoms, a chlorido ligand and to arsenic, which, in turn, is coordinated by two oxygen donor ligands, two hydroxyl ligands and the platinum(II) atom. The square-planar and trigonal–bipyramidal coordination environments around platinum and arsenic, respectively, are significantly distorted with the largest outliers being 173.90 (13) and 106.98 (14)° for platinum and arsenic in (1), and 173.20 (14)° and 94.20 (9)° for (2), respectively. One intramolecular and four classical intermolecular hydrogen-bonding interactions are observed in the crystal structure of (1), which give rise to an infinite three-dimensional network. A similar situation (one intramolecular and four classical intermolecular hydrogen-bonding interactions) is observed in the crystal structure of (2). Various π-interactions are present in (1) between the platinum(II) atom and the centroid of one of the five-membered rings formed by Pt, As, C, N, O with a distance of 3.7225 (7) Å, and between the centroids of five-membered (Pt, As, C, N, O) rings of neighbouring molecules with distances of 3.7456 (4) and 3.7960 (6) Å. Likewise, weak π-interactions are observed in (2) between the platinum(II) atom and the centroid of one of the five-membered rings formed by Pt, As, C, N, O with a distance of 3.8213 (2) Å, as well as between the Cl atom and the centroid of a symmetry-related five-membered ring with a distance of 3.8252 (12) Å. Differences between (2) and the reported polymorph [Miodragović et al. (2013). Angew. Chem. Int. Ed. 52, 10749–10752] are discussed.

Emergent Supramolecular Assembly Properties of Recognition-Encoded Oligoesters

2019 ◽  
Author(s):  
Filip Szczypiński ◽  
Luca Gabrielli ◽  
Christopher Hunter
Keyword(s):  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Supramolecular Assembly ◽  
Functional Materials ◽  
Intramolecular Hydrogen Bonding ◽  
Dimensional Structure ◽  
Stem Loop ◽  
Recognition Sites ◽  
Hydrogen Bonding Interactions ◽  
Intramolecular Hydrogen

The sequences of oligomeric molecules equipped with interacting side-chains encode the three-dimensional structure, the supramolecular assembly properties, and ultimately function. In an attempt to replicate the duplex forming properties of nucleic acids, an oligoester containing an alternating sequence of hydrogen bonding donor (<b>D</b>) and acceptor (<b>A</b>) residues was synthesised. Characterisation of assembly properties of the <b>ADAD</b> oligomer revealed a supramolecular architecture that resembles the kissing stem-loops motif found in folded RNA. NMR dilution and melting experiments in chloroform and 1,1,2,2-tetrachloroethane show that intramolecular hydrogen bonding interactions between the terminal phenol and phosphine oxide recognition sites in the <b>ADAD</b> 4-mer leads to 1,4-folding. This folded stem-loop structure can be denatured to give the single strand by heating. At higher concentrations or lower temperatures, the stem-loop dimerises via intermolecular hydrogen bonding interactions between the two inner recognition sites, leading to a kissing stem-loops structure. The results suggest a rich supramolecular chemistry for these recognition-encoded oligoesters and lay strong foundations for the future development of new functional materials based on synthetic information molecules.

scholarly journals Crystal structure of di-μ-benzato-κ4O:O′-bis[aqua(benzato-κO)(benzato-κ2O,O′)(2,2′:6′,2′′-terpyridine-κ3N,N′,N′′)europium(III)]–benzoic acid (1/2)

2014 ◽  
Vol 70 (9) ◽  
pp. m328-m329
Author(s):  
Frankie White ◽  
Richard E. Sykora
Keyword(s):  
Hydrogen Bonding ◽  
Benzoic Acid ◽  
Intramolecular Hydrogen Bonding ◽  
Acid Group ◽  
Inversion Symmetry ◽  
Intermolecular Hydrogen Bonding ◽  
Crystalline Compound ◽  
Carboxylic Acid Group ◽  
Intramolecular Hydrogen ◽  
The Eu

The title compound, [Eu2(C7H5O2)6(C15H11N3)2(H2O)2]·2C7H6O2, is a co-crystalline compound containing a dinuclear EuIIIcoordination complex with inversion symmetry co-crystallized with benzoic acid in a 1:2 ratio. The Eu3+ions within the dimer are nine-coordinate, containing one tridentate terpyridine, one water, and four benzoate ions, two of which bridge the Eu3+ions. Of the four benzoate ligands coordinating to each Eu3+position, three distinct coordination modes [monodentate, bidentate–chelating, and bidentate–bridging (twice)] are observed. Within the crystal, there are two additional uncoordinating benzoic acid molecules per dinuclear complex. Within the dimer, the water bound to each Eu3+ion participates in intramolecular hydrogen bonding with a coordinating benzoate. Additionally, the carboxylic acid group on the benzoic acid participates in intermolecular hydrogen bonding with a benzoate ligand bound to the dimer complex.

scholarly journals Isovaline monohydrate

2013 ◽  
Vol 69 (12) ◽  
pp. o1829-o1830 ◽  
Author(s):  
Ray J. Butcher ◽  
Greg Brewer ◽  
Aaron S. Burton ◽  
Jason P. Dworkin
Keyword(s):  
Amino Acids ◽  
Hydrogen Bonding ◽  
Amino Acid ◽  
Three Dimensional ◽  
Living Systems ◽  
Intermolecular Hydrogen Bonding ◽  
Compound C ◽  
Hydrogen Bonding Interactions ◽  
Dimensional Network ◽  
Natural Amino Acids

The title compound, C5H11NO2·H2O, is an isomer of the α-amino acid valine that crystallizes from water in its zwitterion form as a monohydrate. It is not one of the 20 proteinogenic amino acids that are used in living systems and differs from the natural amino acids in that it has no α-H atom. The compound exhibits hydrogen bonding between the water molecule and the carboxylate O atoms and an amine H atom. In addition, there are intermolecular hydrogen-bonding interactions between the carboxylate O atoms and amine H atoms. In the crystal, these extensive N—H...O and O—H...O hydrogen bonds lead to the formation of a three-dimensional network.

Determination of the structure of p-methylbenzamidinium formate monohydrate

1988 ◽  
Vol 53 (12) ◽  
pp. 3131-3137
Author(s):  
Bohumil Kratochvíl ◽  
Jan Ondráček ◽  
Jindřich Hašek ◽  
László Csordás
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
Hydrogen Atoms ◽  
Intermolecular Hydrogen Bonds ◽  
Dimensional Network ◽  
Intramolecular Hydrogen

The molecular and crystal structure of p-methylbenzamidinium formate monohydrate, C9H14N2O3, was solved by direct methods. The positions of all the atoms were localized and the structure was refined anisotropically. The final value of the R factor equalled 0·043 for 1 150 observed reflections (I > 1·96σ(I)). The substance crystallizes in the P21/c monoclinic space group with lattice parameters a = 1 038·9(4), b = 1 146·1(5), c = 912·4(3) pm, β = 94·77(3)0, Z = 4. The molecule contains an amidinium-carboxylate bond, formed by two intramolecular hydrogen bridges of the N-H···O type. Intermolecular hydrogen bonds are formed by the side hydrogen atoms of the amidine and the hydrogen atoms of the water molecule and are of the N-H···O and O-H···O types; they form a three-dimensional network in the crystal structure. In this, the structure of p-methylbenzamidinium formate monohydrate differs from the related structures of benzamidinium pyruvate and benzamidinium bromoacetate, characterized by infinite intermolecular chains formed through hydrogen bonding.

Hydrogen Bonding of 2-Tetrazenes, 2. Synthesis and Structural Studies of Hydroxyalkyl-Substituted 2-Tetrazenes

2002 ◽  
Vol 57 (4) ◽  
pp. 365-376 ◽  
Author(s):  
Bernd Porath ◽  
Paul Rademacher ◽  
Roland Boese ◽  
Dieter Bläser
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Steric Interaction ◽  
Stable Conformer ◽  
H Nmr ◽  
Dimensional Network ◽  
Group 3 ◽  
Nmr Methods ◽  
Intramolecular Hydrogen

Five hydroxyethyl-2-tetrazenes (1 - 5) and their methyl ethers (6 - 10) have been synthesized and hydrogen bonding in these compounds has been investigated by theoretical and spectroscopic (IR, 1H NMR, 15N NMR) methods. The structure of 1,1,4,4-tetrakis(2-hydroxyethyl)- 2-tetrazene (4) was determined byX-ray diffraction analysis. Several conformationswith intramolecular hydrogen bonds were investigated by ab initio B3LYP as well as semiempirical SCF calculations. In all cases, conformers with OH- - -N hydrogen bonds with azo nitrogen atoms as acceptors (conformers A, B, C) are found as most stable. Incompounds with small or flexible N1- and N4-substituents R besides the hydroxyethyl group (3, 4), hydrogen bonds forming six-membered rings, with the R groups taking syn positions at the N1-N2 and N3-N4 bonds (conformer A), are preferred over those with seven-membered rings and R taking anti positions (conformer B). Steric interaction in the other compounds (1, 2, 5) leads to destabilization of conformers A and conformers B become more stable. A special case is presented by compound 4 which has only hydroxyethyl substituents on the 2-tetrazene unit. In the most stable conformer (4C) there are two OH- - -O and one OH- - -N hydrogen bonds. By IR solution measurements intra- and intermolecular hydrogen bonds could be distinguished. Association shifts Δδ measured by 1H NMR spectroscopy, indicate that the investigated compounds exhibit comparable association properties with intermolecular association clearly prevailing. 15N NMR spectra of compounds 1 - 10 in two solvents have been measured if solubility was sufficient. The data indicate that all nitrogen atoms of 1 - 5 participate in H bonding. In the crystalline state, molecules 4 adopt a conformation without intramolecular H bonds (4D) and are associated by intermolecular OH- - -O hydrogen bonds that form a three-dimensional network. An untypical decomposition pattern was discovered for benzyl derivatives 5 and 10.

scholarly journals Crystal structure and hydrogen bonding inN-(1-deoxy-β-D-fructopyranos-1-yl)-2-aminoisobutyric acid

2018 ◽  
Vol 74 (1) ◽  
pp. 72-77 ◽  
Author(s):  
Valeri V. Mossine ◽  
Charles L. Barnes ◽  
Thomas P. Mawhinney
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Three Dimensional ◽  
Chair Conformation ◽  
Sugar Amino Acids ◽  
Aminoisobutyric Acid ◽  
Dimensional Network ◽  
Fructose 2 ◽  
Intramolecular Hydrogen

The title compound, alternatively called D-fructose-2-aminoisobutyric acid (FruAib), C10H19NO7, (I), crystallizes exclusively in the β-pyranose form, with two conformationally non-equivalent molecules [(IA) and (IB)] in the asymmetric unit. In solution, FruAib establishes an equilibrium, with 75.6% of the population consisting of β-pyranose, 10.4% β-furanose, 10.1% α-furanose, 3.0% α-pyranose and <0.7% the acyclic forms. The carbohydrate ring in (I) has the normal2C5chair conformation and the amino acid portion is in the zwitterion form. Bond lengths and valence angles compare well with the average values from related pyranose structures. All carboxyl, hydroxy and ammonium groups are involved in hydrogen bonding and form a three-dimensional network of infinite chains that are connected through homodromic rings and short chains. Intramolecular hydrogen bonds bridge the amino acid and sugar portions in both molecules. A comparative Hirshfeld surfaces analysis of FruAib and four other sugar–amino acids suggests an increasing role of intramolecular heteroatom interactions in crystal structures with an increasing proportion of C—H bonds.

Emergent Supramolecular Assembly Properties of Recognition-Encoded Oligoesters

2019 ◽  
Author(s):  
Filip Szczypiński ◽  
Luca Gabrielli ◽  
Christopher Hunter
Keyword(s):  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Supramolecular Assembly ◽  
Functional Materials ◽  
Intramolecular Hydrogen Bonding ◽  
Dimensional Structure ◽  
Stem Loop ◽  
Recognition Sites ◽  
Hydrogen Bonding Interactions ◽  
Intramolecular Hydrogen

The sequences of oligomeric molecules equipped with interacting side-chains encode the three-dimensional structure, the supramolecular assembly properties, and ultimately function. In an attempt to replicate the duplex forming properties of nucleic acids, an oligoester containing an alternating sequence of hydrogen bonding donor (<b>D</b>) and acceptor (<b>A</b>) residues was synthesised. Characterisation of assembly properties of the <b>ADAD</b> oligomer revealed a supramolecular architecture that resembles the kissing stem-loops motif found in folded RNA. NMR dilution and melting experiments in chloroform and 1,1,2,2-tetrachloroethane show that intramolecular hydrogen bonding interactions between the terminal phenol and phosphine oxide recognition sites in the <b>ADAD</b> 4-mer leads to 1,4-folding. This folded stem-loop structure can be denatured to give the single strand by heating. At higher concentrations or lower temperatures, the stem-loop dimerises via intermolecular hydrogen bonding interactions between the two inner recognition sites, leading to a kissing stem-loops structure. The results suggest a rich supramolecular chemistry for these recognition-encoded oligoesters and lay strong foundations for the future development of new functional materials based on synthetic information molecules.

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