scholarly journals The ecstasy and the agony; compression studies of 3,4-methylenedioxymethamphetamine (MDMA)

2015 ◽  
Vol 71 (1) ◽  
pp. 3-9 ◽  
Author(s):  
Lauren E. Connor ◽  
Amit Delori ◽  
Ian B. Hutchison ◽  
Niamh Nic Daeid ◽  
Oliver B. Sutcliffe ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Quality ◽  
Ambient Conditions ◽  
Positional Disorder ◽  
Class A ◽  
Hydrostatic Limit

MDMA (3,4-methylenedioxymethamphetamine) is a Class A substance that is usually found in a tableted form. It is only observed in one orthorhombic polymorph under ambient conditions. It shows slight positional disorder around the methlyenedioxy ring which persists during compression up to 6.66 GPa. The crystal quality deteriorates above 6.66 GPa where the hydrostatic limit of the pressure-transmitting medium is exceeded. The structure undergoes anisotropic compression with thea-axis compressing the greatest (12%cf.4 and 10% for theb- andc-axes, respectively). This is due to the pattern of the hydrogen bonding which acts like a spring and allows the compression along this direction.

Hydrogen bonding in liquid methanol at ambient conditions and at high pressure

2000 ◽  
Vol 98 (3) ◽  
pp. 125-134 ◽  
Author(s):  
T. Weitkamp, J. Neuefeind, H. E. Fisch
Keyword(s):  
High Pressure ◽  
Hydrogen Bonding ◽  
Ambient Conditions

Hydrogen bonding in liquid methanol at ambient conditions and at high pressure

2000 ◽  
Vol 98 (3) ◽  
pp. 125-134 ◽  
Author(s):  
T. WEITKAMP ◽  
J. NEUEFEIND ◽  
H. E. FISCHER ◽  
M. D. ZEIDLER
Keyword(s):  
High Pressure ◽  
Hydrogen Bonding ◽  
Ambient Conditions

Double zipper helical assembly of deoxyoligonucleotides: mutual templating and chiral imprinting to form hybrid DNA ensembles

2015 ◽  
Vol 51 (25) ◽  
pp. 5493-5496 ◽  
Author(s):  
Nagarjun Narayanaswamy ◽  
Gorle Suresh ◽  
U. Deva Priyakumar ◽  
T. Govindaraju
Keyword(s):  
Hydrogen Bonding ◽  
Ambient Conditions ◽  
Hydrogen Bonding Potential ◽  
Hybrid Dna

Herein, the conventional and unconventional hydrogen bonding potential of adenine in APA for double zipper helical assembly of deoxyoligonucleotides is demonstrated under ambient conditions.

scholarly journals Crystal structures of three complexes of zinc chloride with tri-tert-butylphosphane

2016 ◽  
Vol 72 (1) ◽  
pp. 35-39 ◽  
Author(s):  
Aaron D. Finke ◽  
Danielle L. Gray ◽  
Jeffrey S. Moore
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Zinc Chloride ◽  
Chloride Complex ◽  
Lewis Base ◽  
Ambient Conditions ◽  
Hydrogen Bonding Interactions ◽  
Complex Forms ◽  
Cl Atoms

Under anhydrous conditions and in the absence of a Lewis-base solvent, a zinc chloride complex with tri-tert-butylphosphane as the μ-bridged dimer is formed,viz.di-μ-chlorido-bis[chloridobis(tri-tert-butylphosphane)zinc], [ZnCl4(C12H27P)2], (1), which features a nearly square-shaped (ZnCl)2cyclic core and whose Cl atoms interact weakly with C—H groups on the phosphane ligand. In the presence of THF, monomeric dichlorido(tetrahydrofuran-κO)(tri-tert-butylphosphane-κP)zinc, [ZnCl2(C4H8O)(C12H27P)] or [P(tBu3)(THF)ZnCl2], (2), is formed. This slightly distorted tetrahedral Zn complex has weak C—H...Cl interactions between the Cl atoms and phosphane and THF C—H groups. Under ambient conditions, the hydrolysed complex tri-tert-butylphosphonium aquatrichloridozincate 1,2-dichloroethane monosolvate, (C12H28P)[ZnCl3(H2O)]·C2H4Cl2or [HPtBu3]+[(H2O)ZnCl3]−·C2H4Cl2, (3), is formed. This complex forms chains of [(H2O)ZnCl3]−anions from hydrogen-bonding interactions between the water H atoms and Cl atoms that propagate along thebaxis.

scholarly journals Streptomyces albus G serine β-lactamase. Probing of the catalytic mechanism via molecular modelling of mutant enzymes

1992 ◽  
Vol 282 (1) ◽  
pp. 189-195 ◽  
Author(s):  
J Lamotte-Brasseur ◽  
F Jacob-Dubuisson ◽  
G Dive ◽  
J M Frère ◽  
J M Ghuysen
Keyword(s):  
Hydrogen Bonding ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Site Directed Mutagenesis ◽  
Network Configuration ◽  
Beta Lactam ◽  
Beta Lactamases ◽  
Class A ◽  
Streptomyces Albus ◽  
Hydrogen Bonding Network

In previous studies, several amino acids of the active site of class A beta-lactamases have been modified by site-directed mutagenesis. On the basis of the catalytic mechanism proposed for the Streptomyces albus G beta-lactamase [Lamotte-Brasseur, Dive, Dideberg, Charlier, Frère & Ghuysen (1991) Biochem. J. 279, 213-221], the influence that these mutations exert on the hydrogen-bonding network of the active site has been analysed by molecular mechanics. The results satisfactorily explain the effects of the mutations on the kinetic parameters of the enzyme's activity towards a set of substrates. The present study also shows that, upon binding a properly structured beta-lactam compound, the impaired cavity of a mutant enzyme can readopt a functional hydrogen-bonding-network configuration.

Avoiding problems with hydrogen misplacement in reporting crystal structures

2013 ◽  
Vol 69 (8) ◽  
pp. 808-810 ◽  
Author(s):  
Ivan Bernal ◽  
Steven F. Watkins
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Quality Data ◽  
Computing Systems ◽  
High Quality Data ◽  
Positional Disorder ◽  
Donor Acceptor ◽  
Close Contacts

Intermolecular hydrogen bonding is an integral part of many crystal structures. Hydrogen bonding sometimes results in one-, two- or three-dimensional supramolecular assemblies, a common feature of which is positional disorder of H atoms related to space-group symmetry. Yet some reported structures fail to include all possible donor–acceptor close contacts, or to seek H-atom electron densities associated with apparentD—H...Atrios, while some H-atom positions violate principles of chemistry or crystal physics. Modern diffraction equipment and sophisticated computing systems provide high-quality data; thus, failure to characterize and report fully an accurate, complete and physically correct hydrogen-bonding model should not be acceptable. We illustrate the relevant issues with three published examples in the hope of slowing the proliferation of these problems, with the scientifically desirable goal of improving the accuracy of crystallographic models while also providing improved search keys for information retrieval.

scholarly journals Crystal structure of 5,15-dihexyl-5,15-dihydrobenzo[2,1-b:4,3-c′]dicarbazole hexane 0.375-solvate

2018 ◽  
Vol 74 (11) ◽  
pp. 1605-1608
Author(s):  
Dingchao Zhang ◽  
Longqiang Shi ◽  
Zhi Liu ◽  
Li Li ◽  
Zhenhao Hu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Solvent Molecule ◽  
Dihedral Angles ◽  
Monoclinic Space Group ◽  
Positional Disorder ◽  
Left Handed ◽  
Compound C ◽  
Hydrogen Bonding Interactions ◽  
The Right

The title compound, C38H40N2·0.375C6H14, crystallizes in the monoclinic space group P21/c and has a host–guest structure with the helicene molecules forming a porous structure and molecules of hexane inserted into the holes. The dihedral angles between the two carbazole sections of the right- and left-handed helicenes are 27.44 (3) and 25.63 (3)°, respectively. There are no classical π–π interactions or hydrogen-bonding interactions present between adjacent molecules in the crystal structure. The hexane solvent molecule shows positional disorder.

Synthesis and characterization of a cadmium(II)–organic supramolecular coordination compound based on the multifunctional 2-amino-5-sulfobenzoic acid ligand

2016 ◽  
Vol 72 (12) ◽  
pp. 939-946 ◽  
Author(s):  
Gan-Yin Yuan ◽  
Lei Zhang ◽  
Meng-Jie Wang ◽  
Kou-Lin Zhang
Keyword(s):  
Hydrogen Bonding ◽  
Solid State ◽  
Coordination Compound ◽  
Coordination Compounds ◽  
Structural Characteristics ◽  
Three Dimensional ◽  
Distorted Octahedral Geometry ◽  
Two Dimensional ◽  
Ambient Conditions ◽  
Supramolecular Coordination

Much attention has been paid by chemists to the construction of supramolecular coordination compounds based on the multifunctional ligand 5-sulfosalicylic acid (H3SSA) due to the structural and biological interest of these compounds. However, no coordination compounds have been reported for the multifunctional amino-substituted sulfobenzoate ligand 2-amino-5-sulfobenzoic acid (H2asba). We expected that H2asba could be a suitable building block for the assembly of supramolecular networks due to its interesting structural characteristics. The reaction of cadmium(II) nitrate with H2asba in the presence of the auxiliary flexible dipyridylamide ligandN,N′-bis[(pyridin-4-yl)methyl]oxamide (4bpme) under ambient conditions formed a new mixed-ligand coordination compound, namely bis(3-amino-4-carboxybenzenesulfonato-κO1)diaquabis{N,N′-bis[(pyridin-4-yl)methyl]oxamide-κN}cadmium(II)–N,N′-bis[(pyridin-4-yl)methyl]oxamide–water (1/1/4), [Cd(C7H6NO5S)2(C14H14N4O2)2(H2O)2]·C14H14N4O2·4H2O, (1), which was characterized by single-crystal and powder X-ray diffraction analysis (PXRD), FT–IR spectroscopy, thermogravimetric analysis (TG), and UV–Vis and photoluminescence spectroscopic analyses in the solid state. The central CdIIatom in (1) occupies a special position on a centre of inversion and exhibits a slightly distorted octahedral geometry, being coordinated by two N atoms from two monodentate 4bpme ligands, four O atoms from two monodentate 4-amino-3-carboxybenzenesulfonate (Hasba−) ligands and two coordinated water molecules. Interestingly, complex (1) further extends into a threefold polycatenated 0D→2D (0D is zero-dimensional and 2D is two-dimensional) interpenetrated supramolecular two-dimensional (4,4) layer through intermolecular hydrogen bonding. The interlayer hydrogen bonding further links adjacent threefold polycatenated two-dimensional layers into a three-dimensional network. The optical properties of complex (1) indicate that it may be used as a potential indirect band gap semiconductor material. Complex (1) exhibits an irreversible dehydration–rehydration behaviour. The fluorescence properties have also been investigated in the solid state at room temperature.

The tropolone–isobutylamine complex: a hydrogen-bonded troponoid without dominant π–π interactions

2016 ◽  
Vol 72 (10) ◽  
pp. 730-737
Author(s):  
Zachary N. Vealey ◽  
Brandon Q. Mercado ◽  
Patrick H. Vaccaro
Keyword(s):  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Density Functional ◽  
Synergistic Effects ◽  
Structural Parameters ◽  
Intermolecular Forces ◽  
Crystalline Lattice ◽  
Organic Salt ◽  
Ambient Conditions ◽  
Π Interactions

Tropolone long has served as a model system for unraveling the ubiquitous phenomena of proton transfer and hydrogen bonding. This molecule, which juxtaposes ketonic, hydroxylic, and aromatic functionalities in a framework of minimal complexity, also has provided a versatile platform for investigating the synergism among competing intermolecular forces, including those generated by hydrogen bonding and aryl coupling. Small members of the troponoid family typically produce crystals that are stabilized strongly by pervasive π–π, C—H...π, or ion–π interactions. The organic salt (TrOH·iBA) formed by a facile proton-transfer reaction between tropolone (TrOH) and isobutylamine (iBA), namely isobutylammonium 7-oxocyclohepta-1,3,5-trien-1-olate, C4H12N+·C7H5O2−, has been investigated by X-ray crystallography, with complementary quantum-chemical and statistical-database analyses serving to elucidate the nature of attendant intermolecular interactions and their synergistic effects upon lattice-packing phenomena. The crystal structure deduced from low-temperature diffraction measurements displays extensive hydrogen-bonding networks, yet shows little evidence of the aryl forces (viz.π–π, C—H...π, and ion–π interactions) that typically dominate this class of compounds. Density functional calculations performed with and without the imposition of periodic boundary conditions (the latter entailing isolated subunits) documented the specificity and directionality of noncovalent interactions occurring between the proton-donating and proton-accepting sites of TrOH and iBA, as well as the absence of aromatic coupling mediated by the seven-membered ring of TrOH. A statistical comparison of the structural parameters extracted for key hydrogen-bond linkages to those reported for 44 previously known crystals that support similar binding motifs revealed TrOH·iBA to possess the shortest donor–acceptor distances of any troponoid-based complex, combined with unambiguous signatures of enhanced proton-delocalization processes that putatively stabilize the corresponding crystalline lattice and facilitate its surprisingly rapid formation under ambient conditions.

scholarly journals Probing the Mechanism of Inactivation of the FOX-4 Cephamycinase by Avibactam

2018 ◽  
Vol 62 (5) ◽  
pp. e02371-17 ◽  
Author(s):  
Michiyoshi Nukaga ◽  
Krisztina M. Papp-Wallace ◽  
Tyuji Hoshino ◽  
Scott T. Lefurgy ◽  
Christopher R. Bethel ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Single Amino Acid ◽  
Content Type ◽  
Class A ◽  
Hydrogen Bonding Interactions ◽  
Extended Spectrum ◽  
Inhibitor Combination ◽  
Lactamase Inhibitor ◽  
Inhibition Analysis

ABSTRACTCeftazidime-avibactam is a “second-generation” β-lactam–β-lactamase inhibitor combination that is effective againstEnterobacteriaceaeexpressing class A extended-spectrum β-lactamases, class A carbapenemases, and/or class C cephalosporinases. Knowledge of the interactions of avibactam, a diazabicyclooctane with different β-lactamases, is required to anticipate future resistance threats. FOX family β-lactamases possess unique hydrolytic properties with a broadened substrate profile to include cephamycins, partly as a result of an isoleucine at position 346, instead of the conserved asparagine found in most AmpCs. Interestingly, a single amino acid substitution at N346 in theCitrobacterAmpC is implicated in resistance to the aztreonam-avibactam combination. In order to understand how diverse active-site topologies affect avibactam inhibition, we tested a panel of clinicalEnterobacteriaceaeisolates producingblaFOXusing ceftazidime-avibactam, determined the biochemical parameters for inhibition using the FOX-4 variant, and probed the atomic structure of avibactam with FOX-4. Avibactam restored susceptibility to ceftazidime for most isolates producingblaFOX; two isolates, one expressingblaFOX-4and the other producingblaFOX-5, displayed an MIC of 16 μg/ml for the combination. FOX-4 possessed ak2/Kvalue of 1,800 ± 100 M−1· s−1and an off rate (koff) of 0.0013 ± 0.0003 s−1. Mass spectrometry showed that the FOX-4–avibactam complex did not undergo chemical modification for 24 h. Analysis of the crystal structure of FOX-4 with avibactam at a 1.5-Å resolution revealed a unique characteristic of this AmpC β-lactamase. Unlike in thePseudomonas-derived cephalosporinase 1 (PDC-1)–avibactam crystal structure, interactions (e.g., hydrogen bonding) between avibactam and position I346 in FOX-4 are not evident. Furthermore, another residue is not observed to be close enough to compensate for the loss of these critical hydrogen-bonding interactions. This observation supports findings from the inhibition analysis of FOX-4; FOX-4 possessed the highestKd(dissociation constant) value (1,600 nM) for avibactam compared to other AmpCs (7 to 660 nM). Medicinal chemists must consider the properties of extended-spectrum AmpCs, such as the FOX β-lactamases, for the design of future diazabicyclooctanes.

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