scholarly journals Bifurcated Hydrogen Bonds and the Fold Switching of Lymphotactin

2020 ◽  
Author(s):  
Prabir Khatua ◽  
Alan J Ray ◽  
Ulrich H. E. Hansmann
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Replica Exchange ◽  
Biological Functions ◽  
Physiological Conditions ◽  
Hydrogen Bond Pattern

AbstractLymphotactin (Ltn) exists under physiological conditions in an equilibrium between two interconverting structures with distinct biological functions. Using Replica-Exchange-with-Tunneling we study the conversion between the two folds. Unlike previously proposed, we find that the fold switching does not require unfolding of Lymphotactin, but proceeds through a series of intermediates that remain partially structured. This process relies on two bifurcated hydrogen bonds that connect the β2 and β3 strands and eases the transition between the hydrogen bond pattern by which the central three-stranded β-sheet in the two forms differ.

Two tautomers in one crystal: 4(5)-nitro-5(4)-methoxyimidazole

2004 ◽  
Vol 60 (2) ◽  
pp. 191-196 ◽  
Author(s):  
Maciej Kubicki
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Imidazole Derivative ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Dimensional Network ◽  
Hydrogen Bond Pattern ◽  
Annular Tautomerism

The case of prototropic annular tautomerism in an imidazole derivative has been found. The crystal structure contains a 50:50 mixture of two tautomers: 4-nitro-5-methoxyimidazole and 5-nitro-4-methoxyimidazole. The X-ray experiment actually shows the superposition of these compounds; it appears as if the structure is centrosymmetric and the N—H hydrogen atoms are disordered over two ring N atoms. Owing to the hydrogen-bond pattern, the values of their site occupation factors have to be exactly equal to 1/2. The molecules are connected into a three-dimensional network by means of N—H...N and C—H...O hydrogen bonds.

A novel tubular hydrogen-bond pattern in a new diazaphosphole oxide: a combination of X-ray crystallography and theoretical study of hydrogen bonds

2017 ◽  
Vol 73 (7) ◽  
pp. 508-516 ◽  
Author(s):  
Fahimeh Sabbaghi ◽  
Mehrdad Pourayoubi ◽  
Abolghasem Farhadipour ◽  
Nazila Ghorbanian ◽  
Pavel V. Andreev
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Coupling Constant ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Hydrogen Bond Pattern ◽  
Orbital Analysis ◽  
Tubular Array ◽  
Hydrogen Bonded

In the structure of 2-(4-chloroanilino)-1,3,2λ4-diazaphosphol-2-one, C12H11ClN3OP, each molecule is connected with four neighbouring molecules through (N—H)2...O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R 3 3(12) and R 4 3(14) hydrogen-bond ring motifs, combined with a C(4) chain motif. The hole constructed in the tubular architecture includes a 12-atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N—H groups of the diazaphosphole ring, not co-operating in classical hydrogen bonding, takes part in an N—H...π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen-bond pattern. The energies of the N—H...O and N—H...π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen-bonded cluster of molecules as the input file for the chemical calculations. In the 1H NMR experiment, the nitrogen-bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the 2 J H–P coupling constant.

scholarly journals Migrating hydrogen in 2,4,6-triaminopyrimidinium(1+) x hydrogen trioxofluorophosphate(−) x monohydrate/2,4,6-triaminopyrimidinium(2+)1–x trioxofluorophosphate(2–)1–x monohydrate (0.0 < x < 0.73) with changing temperature

2017 ◽  
Vol 73 (6) ◽  
pp. 1114-1124
Author(s):  
Irena Matulková ◽  
Jan Fábry ◽  
Ivan Němec ◽  
Ivana Císařová ◽  
Přemysl Vaněk
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Double Layers ◽  
Scanning Calorimetry ◽  
Electron Ring ◽  
Density Maps ◽  
Hydrogen Bond Pattern ◽  
Bonding Properties ◽  
The Difference

The data of the title structure of 2,4,6-triaminopyrimidinium(1+) x hydrogen trioxofluorophosphate(1−) x monohydrate/2,4,6-triaminopyrimidinium(2+)1−x trioxofluorophosphate(2−)1−x monohydrate (0.0 < x < 0.73), with the sum formula C4H11FN5O4P, were collected in 10 K intervals between 290 and 150 K, as well as at 100 K. The most interesting feature is the presence of a moderate though still strong O—H...N/O...H—N hydrogen bond. Its bridging H atom was found to be disordered over two positions in the temperature interval 290–220 K, with the larger occupation towards the O atom. The occupation in the latter position decreased with decreasing temperature, though not monotonously. At 210 K and below, the difference electron-density maps showed just one maximum which was closer to the N atom. Though difference scanning calorimetry (DSC) revealed no anomaly in the interval 303–93 K, the dependence of the length of the unit-cell axes b and c on temperature showed a kink in the slope at about 190 K. The N...O distance of the mentioned hydrogen bond or the occupational parameter of the electron density of the disordered H atom indicate less pronounced anomalies for the temperatures 270 and 230 K. The cation and the anion, as well as the water molecules, form layers which are parallel to (10\overline{1}) and which are interconnected by O—H...N (in the interval 290–220 K), N—H...O and O—H...O hydrogen bonds of moderate strength. The layers are arranged into centrosymmetric double layers in which the F atoms are directed outwards. The layers are interconnected by water–acid O—H...O hydrogen bonds, weak N—H...F interactions and π-electron ring...π-electron ring interactions. The dependence of P—F bond lengths on bonding properties of the trioxofluorophosphate or hydrogen trioxofluorophosphate anions is discussed. It has been recognized that a carbon-bonded F atom avoids participation in a hydrogen-bond pattern; however, this property seems to be also common to fluorine bonded to P, As and S, especially if an oxygen ligand is also present in a molecule. The deposited material contains an overview of the determined structures with trioxofluorophosphate or hydrogen trioxofluorophosphate anions.

Mixed crystals of 2-carbamoylguanidinium with hydrogen fluorophosphonate and hydrogen phosphite in the ratios 1:0, 0.76 (2):0.24 (2) and 0.115 (7):0.885 (7)

2012 ◽  
Vol 68 (2) ◽  
pp. o76-o83 ◽  
Author(s):  
Jan Fábry ◽  
Michaela Fridrichová ◽  
Michal Dušek ◽  
Karla Fejfarová ◽  
Radmila Krupková
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Mixed Crystals ◽  
Hydrogen Phosphite ◽  
Hydrogen Bond Pattern ◽  
Mixed Salts ◽  
First Time

The title compounds, 2-carbamoylguanidinium hydrogen fluorophosphonate, C2H7N4O+·HFO3P−, (I), 2-carbamoylguanidinium–hydrogen fluorophosphonate–hydrogen phosphite (1/0.76/0.24), C2H7N4O+·0.76HFO3P−·0.24H2O3P−, (II), and 2-carbamoylguanidinium–hydrogen fluorophosphonate–hydrogen phosphite (1/0.115/0.885), C2H7N4O+·0.115HFO3P−·0.885H2O3P−, (III), are isostructural with guanylurea hydrogen phosphite, C2H7N4O+·H2O3P−[Fridrichová, Němec, Císařová & Němec (2010).CrystEngComm,12, 2054–2056]. They constitute structures where the hydrogen phosphite anion has been fully or partially replaced by hydrogen fluorophosphonate. The title structures are the fourth example of isostructural compounds which differ by the presence of hydrogen fluorophosphonate and hydrogen phosphite or fluorophosphonate and phosphite anions. Moreover, the present study reports structures with these mixed anions for the first time. In the reported mixed salts, the P and O atoms of either anion overlap almost exactly, as can be judged by comparison of their equivalent isotropic displacement parameters, while the P—F and P—H directions are almost parallel. There are strong O—H...O hydrogen bonds between the anions, as well as strong N—H...O hydrogen bonds between the 2-carbamoylguanidinium cations in the title structures. Altogether they form a three-dimensional hydrogen-bond pattern. Interestingly, rare N—H...F interactions are also present in the title structures. Another exceptional feature concerns the P—O(H) distances, which are about as long as the P—F distance. The dependence of P—F distances on the longest P—O distances in FO3P2−or HFO3P−is presented. The greater content of hydrogen phosphite in the mixed crystals causes a larger deformation of the cations from planarity.

scholarly journals Crystal structure of 3-hydroxy-2-(4-hydroxy-3-methoxyphenylmethyl)-5,5-dimethylcyclohex-2-enone

2018 ◽  
Vol 74 (6) ◽  
pp. 796-798 ◽  
Author(s):  
Agnese Stikute ◽  
Karina Skestere ◽  
Inese Mierina ◽  
Anatoly Mishnev ◽  
Mara Jure
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Membered Ring ◽  
Partially Saturated ◽  
Compound C ◽  
Starting Compound ◽  
Dimensional Network ◽  
Hydrogen Bond Pattern ◽  
Sheet Structure

In the title compound, C16H20O4, a new starting compound for the synthesis of various heterocycles, the partially saturated six-membered ring adopts a sofa conformation. An intramolecular O—H...O hydrogen bond is observed in the guaiacol residue. In the crystal, molecules are assembled into a sheet structure parallel to the ab plane via O—H...O hydrogen bonds. The hydrogen-bond pattern is described by an R 4 4(28) graph-set motif. The sheets are further linked by C—H...O hydrogen bonds into a three-dimensional network.

Hydrogen bonds in N-(3-chloro-2-benzo[b]thienocarbonyl)- and N-(2-benzo[b]thienocarbonyl)-N'-monosubstituted thioureas

1987 ◽  
Vol 52 (11) ◽  
pp. 2673-2679 ◽  
Author(s):  
Oľga Hritzová ◽  
Peter Kutschy ◽  
Ján Imrich ◽  
Thomas Schöffmann
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Strong Hydrogen Bond ◽  
Cyclic Form ◽  
Thiourea Derivatives

N-(3-Chloro-2-benzo[b]thienocarbonyl)-N'-monosubstituted thiourea derivatives undergo photocyclizations with lower yields than those obtained from analogous N',N'-disubstituted derivatives. This decreased reactivity is caused by the existence of a six-membered cyclic form with the very strong hydrogen bond NH···O=C. The possibility of formation of various conformers has been found with N-(2-benzo[b]thienocarbonyl)-N'-monosubstituted thiourea derivatives as a consequence of the rotation around the C(2)-C(O) connecting line.

Crystal structure of tofacitinib dihydrogen citrate (Xeljanz®), (C16H21N6O)(H2C6H5O7)

2021 ◽  
pp. 1-8
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Acid Group ◽  
Dimensional Network ◽  
Van Der Waals Contacts ◽  
Citrate Anion

The crystal structure of tofacitinib dihydrogen citrate (tofacitinib citrate) has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Tofacitinib dihydrogen citrate crystallizes in space group P212121 (#19) with a = 5.91113(1), b = 12.93131(3), c = 30.43499(7) Å, V = 2326.411(6) Å3, and Z = 4. The crystal structure consists of corrugated layers perpendicular to the c-axis. Within the layers, cation⋯anion and anion⋯anion hydrogen bonds link the fragments into a two-dimensional network parallel to the ab-plane. Between the layers, there are only van der Waals contacts. A terminal carboxylic acid group in the citrate anion forms a strong charge-assisted hydrogen bond to the ionized central carboxylate group. The other carboxylic acid acts as a donor to the carbonyl group of the cation. The citrate hydroxy group forms an intramolecular charge-assisted hydrogen bond to the ionized central carboxylate. Two protonated nitrogen atoms in the cation act as donors to the ionized central carboxylate of the anion. These hydrogen bonds form a ring with the graph set symbol R2,2(8). The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

6,9-Dibromo-2a,10b-diphenyl-2a,5,10,10b-tetrahydro-2H,3H-2,3,4a,10a-tetraazabenzo[g]cyclopenta[cd]azulene-1,4-dione monohydrate

2006 ◽  
Vol 62 (5) ◽  
pp. o1754-o1755
Author(s):  
Neng-Fang She ◽  
Sheng-Li Hu ◽  
Hui-Zhen Guo ◽  
An-Xin Wu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Supramolecular Structure ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Compound C ◽  
Bifurcated Hydrogen Bond

The title compound, C24H18Br2N4O2·H2O, forms a supramolecular structure via N—H...O, O—H...O and C—H...O hydrogen bonds. In the crystal structure, the water molecule serves as a bifurcated hydrogen-bond acceptor and as a hydrogen-bond donor.

Synthesis and Structural Characterisation of New Bifunctional o-Hydroxyacetophenones – Potential Linker Molecules for Coordinative Framework Construction

2013 ◽  
Vol 68 (3) ◽  
pp. 214-222 ◽  
Author(s):  
Jörg Hübscher ◽  
Michael Günthel ◽  
Robert Rosin ◽  
Wilhelm Seichter ◽  
Florian Mertens ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
X Ray ◽  
Structural Characterisation ◽  
Crystallographic Study ◽  
Copper Coordination ◽  
Resonance Assisted Hydrogen Bond ◽  
Intramolecular Hydrogen ◽  
Fitting In ◽  
Linker Molecules

Two new linker-type molecules 1a and 1b composed of o-hydroxyacetophenone coordinative groups attached to linear ethynylene or 1,4-phenylenediethynylene spacer units have been synthesised and structurally characterised. An X-ray crystallographic study for both compounds has shown structures with strong intramolecular hydrogen bonds fitting in the model of ‘Intramolecular Resonance Assisted Hydrogen Bond (IRHAB)’. Initial coordination experiments with Cu(II) were performed and the resulting materials characterised by PXRD. The similarity of the copper coordination between these compounds and copper(II) acetylacetonate complexes was demonstrated by XPS measurements. Based on the evidence of these studies, and on elemental analysis, the formation of the corresponding coordination polymers comprising Cu(II) and the linkers has been proposed

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