Supramolecular assembling using synthons with NH—CO(S)—CS—NH and NH—CO—CO—NH functionalities: crystal structures of (S,S)-N,N′-monothiooxalyldileucine methyl ester and its dithio analogue

2004 ◽  
Vol 60 (1) ◽  
pp. 90-96 ◽  
Author(s):  
Biserka Kojić-Prodić ◽  
Berislav Perić ◽  
Zoran Štefanić ◽  
Anton Meden ◽  
Janja Makarević ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Methyl Ester ◽  
Crystal Structures ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
Bond Network ◽  
Bonding Systems

To compare the structural properties of oxalamide and thiooxalamide groups in the formation of hydrogen bonds suitable for supramolecular assemblies a series of retropeptides was studied. Some of them, having oxalamide bridges, are gelators of organic solvents and water. However, retropeptides with oxygen replaced by the sp 2 sulfur have not exhibited such properties. The crystal structures of the two title compounds are homostructural, i.e. they have similar packing arrangements. The monothio compound crystallizes in the orthorhombic space group P212121 with two molecules in the asymmetric unit arranged in a hydrogen-bond network with an approximate 41 axis along the crystallographic b axis. However, the dithio and dioxo analogues crystallize in the tetragonal space group P41 with similar packing patterns and hydrogen-bonding systems arranged in agreement with a crystallographic 41 axis. Thus, these two analogues are isostructural having closely related hydrogen-bonding patterns in spite of the different size and polarity of oxygen and sulfur which serve as the proton acceptors.

Tautomerism and hydrogen bonding in guaninium phosphite and guaninium phosphate salts

2007 ◽  
Vol 63 (3) ◽  
pp. 448-458 ◽  
Author(s):  
El-Eulmi Bendeif ◽  
Slimane Dahaoui ◽  
Nourredine Benali-Cherif ◽  
Claude Lecomte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Monoclinic Space Group ◽  
Data Sets ◽  
Hydrogen Bond Network ◽  
Space Group ◽  
X Ray ◽  
Bond Network ◽  
Phosphate Salts

The crystal structures of three similar guaninium salts, guaninium monohydrogenphosphite monohydrate, C5H6N5O+·H2O3P−·H2O, guaninium monohydrogenphosphite dihydrate, C5H6N5O+·H2O3P−·2H2O, and guaninium dihydrogenmonophosphate monohydrate, C5H6N5O+·H2O4P−·H2O, are described and compared. The crystal structures have been determined from accurate single-crystal X-ray data sets collected at 100 (2) K. The two phosphite salts are monoclinic, space group P21/c, with different packing and the monophosphate salt is also monoclinic, space group P21/n. An investigation of the hydrogen-bond network in these guaninium salts reveals the existence of two ketoamine tautomers, the N9H form and an N7H form.

scholarly journals (Acetonitrile-κN)aqua[N,N′-bis(pyridin-2-ylmethyl)ethane-1,2-diamine-κ4N,N′,N′′,N′′′]zinc(II) perchlorate

2017 ◽  
Vol 73 (10) ◽  
pp. 1568-1571
Author(s):  
Ugochukwu Okeke ◽  
Yilma Gultneh ◽  
Ray J. Butcher
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Structural Features ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Bond Network ◽  
Bifurcated Hydrogen Bond ◽  
Coordinated Water ◽  
Ionic Hydrogen Bonding

The structure of the title compound, [Zn(C14H18N4)(C2H3N)(H2O)](ClO4)2, contains a six-coordinate cation consisting of the tetradentate bispicen ligand, coordinated water, and coordinated acetonitrile, with the latter two ligands adopting acisconfiguration. There are two formula units in the asymmetric unit. Both cations show almost identical structural features with the bispicen ligand adopting the more commoncis-β conformation. One of the four perchlorate anions is disordered over two positions, with occupancies of 0.9090 (15) and 0.0910 (15). There is extensive inter-ionic hydrogen bonding between the perchlorate anions and O—H and N—H groups in the cations, including a bifurcated hydrogen bond between an N—H group and two O atoms of one perchlorate anion. As a result of this extended hydrogen-bond network, the ions are linked into a complex three-dimensional array.

Halides of Macrocyclic Silver(II) Complexes: Crystal Structures with Hydrogen Bond Network and Reaction Kinetics of the Decomposition

2021 ◽  
pp. 120431
Author(s):  
Akinori Honda ◽  
Shunta Kakihara ◽  
Shuhei Ichimura ◽  
Kazuaki Tomono ◽  
Mina Matsushita ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Reaction Kinetics ◽  
Crystal Structures ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Kinetics Of

Na1.5Rb0.5PO3F·H2O: synthesis, properties, and stepwise reconstruction of the hydrogen bond network

2021 ◽  
Author(s):  
Xin-Rui Yang ◽  
Xin Liu ◽  
Zujian Wang ◽  
Xuebin Deng ◽  
He-Jie Lu ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Optical Materials ◽  
Nonlinear Optical ◽  
Nonlinear Optical Materials ◽  
Hydrogen Bond Network ◽  
Space Group ◽  
Synthesis Properties ◽  
Deep Ultraviolet ◽  
Bond Network

Deep-ultraviolet (DUV) nonlinear optical materials have attracted intense attentions recently. Herein, we report a new DUV transparent (< 200 nm) noncentrosymmetric Na1.5Rb0.5PO3F·H2O crystallizing in the Pmn21 space group. This compound...

Synthesis, crystal structures and chemical bonding of RE5−xLixGe4(RE = Nd, Sm and Gd;x≃ 1) with the orthorhombic Gd5Si4type

2012 ◽  
Vol 69 (1) ◽  
pp. 1-4 ◽  
Author(s):  
Nian-Tzu Suen ◽  
Tae-Soo You ◽  
Svilen Bobev
Keyword(s):  
Rare Earth ◽  
Single Crystal ◽  
Crystal Structures ◽  
Chemical Bonding ◽  
Electronic Structures ◽  
Small Deviation ◽  
Structure Type ◽  
Asymmetric Unit ◽  
Orthorhombic Space Group ◽  
Space Group

The syntheses and single-crystal and electronic structures of three new ternary lithium rare earth germanides, RE5−xLixGe4(RE = Nd, Sm and Gd;x≃ 1), namely tetrasamarium lithium tetragermanide (Sm3.97Li1.03Ge4), tetraneodymium lithium tetragermanide (Nd3.97Li1.03Ge4) and tetragadolinium lithium tetragermanide (Gd3.96Li1.03Ge4), are reported. All three compounds crystallize in the orthorhombic space groupPnmaand adopt the Gd5Si4structure type (Pearson codeoP36). There are six atoms in the asymmetric unit: Li1 in Wyckoff site 4c, RE1 in 8d, RE2 in 8d, Ge1 in 8d, Ge2 in 4cand Ge3 in 4c. One of the RE sites,i.e.RE2, is statistically occupied by RE and Li atoms, accounting for the small deviation from ideal RE4LiGe4stoichiometry.

scholarly journals Crystal Structures of the Ferrous Dioxygen Complex of Wild-type Cytochrome P450eryF and Its Mutants, A245S and A245T

2005 ◽  
Vol 280 (23) ◽  
pp. 22102-22107 ◽  
Author(s):  
Shingo Nagano ◽  
Jill R. Cupp-Vickery ◽  
Thomas L. Poulos
Keyword(s):  
Hydrogen Bond ◽  
Water Molecule ◽  
Crystal Structures ◽  
Proton Donor ◽  
Initial Structure ◽  
Hydrogen Bond Network ◽  
Wild Type ◽  
In The Wild ◽  
Site Water ◽  
Bond Network

Cytochrome P450eryF (CYP107A) from Saccaropolyspora ertherea catalyzes the hydroxylation of 6-deoxyerythronolide B, one of the early steps in the biosynthesis of erythromycin. P450eryF has an alanine rather than the conserved threonine that participates in the activation of dioxygen (O2) in most other P450s. The initial structure of P450eryF (Cupp-Vickery, J. R., Han, O., Hutchinson, C. R., and Poulos, T. L. (1996) Nat. Struct. Biol. 3, 632–637) suggests that the substrate 5-OH replaces the missing threonine OH group and holds a key active site water molecule in position to donate protons to the iron-linked dioxygen, a critical step for the monooxygenase reaction. To probe the proton delivery system in P450eryF, we have solved crystal structures of ferrous wild-type and mutant (Fe2+) dioxygen-bound complexes. The catalytic water molecule that was postulated to provide protons to dioxygen is absent, although the substrate 5-OH group donates a hydrogen bond to the iron-linked dioxygen. The hydrogen bond network observed in the wild-type ferrous dioxygen complex, water 63-Glu360-Ser246-water 53-Ala241 carbonyl in the I-helix cleft, is proposed as the proton transfer pathway. Consistent with this view, the hydrogen bond network in the O2·A245S and O2 ·A245T mutants, which have decreased or no enzyme activity, was perturbed or disrupted, respectively. The mutant Thr245 side chain also perturbs the hydrogen bond between the substrate 5-OH and dioxygen ligand. Contrary to the previously proposed mechanism, these results support the direct involvement of the substrate in O2 activation but raise questions on the role water plays as a direct proton donor to the iron-linked dioxygen.

Theoretical aspects of the enhancement of metal binding affinity by intramolecular hydrogen bonding and modulating pKavalues

2017 ◽  
Vol 41 (24) ◽  
pp. 15110-15119 ◽  
Author(s):  
Ahmad Motahari ◽  
Alireza Fattahi
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Binding Affinity ◽  
Metal Binding ◽  
Intramolecular Hydrogen Bonding ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
The Stability ◽  
Intramolecular Hydrogen

The stability balance shows that the hydrogen bond network and modulation of pKavalues can enhance the metal binding affinity.

A Comparison of the Enamino Carbonyl Conjugation Efficiency for Hydrogen Bonding Formation in Pyridone and Dihydropyridone Systems

2000 ◽  
Vol 55 (1) ◽  
pp. 5-11 ◽  
Author(s):  
Teresa Borowiak ◽  
Irena Wolska ◽  
Artur Korzański ◽  
Wolfgang Milius ◽  
Wolfgang Schnick ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Steric Hindrance ◽  
Crystal Packing ◽  
Intermolecular Hydrogen Bond ◽  
Asymmetric Unit ◽  
Intermolecular Hydrogen Bonds

The crystal structures of two compounds containing enaminone heterodiene systems and forming intermolecular hydrogen bonds N-H·O are reported: 1) 3-ethoxycarbonyl-2-methyl-4-pyridone (hereafter ETPY) and 2) 3-ethoxycarbonyl-2-phenyl-6-methoxycarbonyl-5,6-di-hydro-4-pyridone (hereafter EPPY). The crystal packing is controlled by intermolecular hydro­ gen bonds N-H·O = C connecting the heteroconjugated enaminone groups in infinite chains. In ETPY crystals the intermolecular hydrogen bond involves the heterodienic pathway with the highest π-delocalization that is effective for a very short N·O distance of 2.701(9) Å (average from two molecules in the asymmetric unit). Probably due to the steric hindrance, the hydrogen bond in EPPY is formed following the heterodienic pathway that involves the ester C = O group, although π-delocalization along this pathway is less than that along the pyridone-part pathway resulting in a longer N·O distance of 2.886(3) Å

L-2-Aminobutyric acid: two fully ordered polymorphs with Z′ = 4

2010 ◽  
Vol 66 (2) ◽  
pp. 253-259 ◽  
Author(s):  
Carl Henrik Görbitz
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Diffraction Data ◽  
Aminobutyric Acid ◽  
Side Chain ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Space Groups ◽  
Bond Network

The crystal structure of L-2-aminobutyric acid, an L-alanine analogue with an ethyl rather than a methyl side chain, has proved elusive owing to problems growing diffraction quality crystals. Good diffraction data have now been obtained for two polymorphs, in space groups P21 and I2, revealing surprisingly complex, yet fully ordered crystalline arrangements with Z′ = 4. The closely related structures are divided into hydrophilic and hydrophobic layers, the latter being the thinnest ever found for an amino acid (other than α-glycine). The hydrophobic layers furthermore contain conspicuous pseudo-centers-of-symmetry, leading to overall centrosymmetric intensity statistics. Uniquely, the four molecules in the asymmetric unit can be divided into two pairs that each forms an independent hydrogen-bond network.

L-Leucylglycine 0.67-hydrate and [(4S)-2,2-dimethyl-4-(2-methylpropyl)-5-oxoimidazolidin-3-ium-1-yl]acetate

2012 ◽  
Vol 68 (12) ◽  
pp. o498-o501 ◽  
Author(s):  
Tamiko Kiyotani ◽  
Yoko Sugawara
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Carbonyl Group ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Amino Groups ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Bond Network

Crystals of L-leucylglycine (L-Leu–Gly) 0.67-hydrate, C8H16N2O3·0.67H2O, (I), were obtained from an aqueous solution. There are three symmetrically independent dipeptide zwitterionic molecules in (I) and they are parallel to one another. The hydrogen-bond network composed of carboxylate and amino groups and water molecules extends parallel to theabplane. Hydrophilic regions composed of main chains and hydrophobic regions composed of the isobutyl groups of the leucyl residues are aligned alternately along thecaxis. An imidazolidinone derivative was obtained from L-Leu–Gly and acetone,viz.[(4S)-2,2-dimethyl-4-(2-methylpropyl)-5-oxoimidazolidin-3-ium-1-yl]acetate, C11H20N2O3, (II), and was crystallized from a methanol–acetone solution of L-Leu–Gly. The unit-cell parameters coincide with those reported previously for L-Leu–Gly dihydrate revealing that the previously reported values should be assigned to the structure of (II). One of the imidazolidine N atoms is protonated and the ring is nearly planar, except for the protonated N atom. Protonated N atoms and deprotonated carboxy groups of neighbouring molecules form hydrogen-bonded chains. The ring carbonyl group is not involved in hydrogen bonding.

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