scholarly journals When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins

2021 ◽  
Author(s):  
Vyshnavi Vennelakanti ◽  
Helena W. Qi ◽  
Rimsha Mehmood ◽  
Heather J. Kulik
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
High Resolution ◽  
Hydrogen Bonds ◽  
First Principles ◽  
Crystal Structure Analysis ◽  
Hydrogen Bond Donor ◽  
Donor And Acceptor ◽  
Stabilizing Effect ◽  
Better Than

Correlated wavefunction theory predicts and high-resolution crystal structure analysis confirms the important, stabilizing effect of simultaneous hydrogen bond donor and acceptor interactions in proteins.

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.

Benzyldiethylammonium chloride

2006 ◽  
Vol 62 (5) ◽  
pp. o1735-o1737 ◽  
Author(s):  
Daniel Lorono-Gonzalez
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Ionic Species ◽  
Polar Space ◽  
Crystal Structure Analysis ◽  
Two Dimensional ◽  
Compound C ◽  
Dimensional Network

The title compound, C11H18N+·Cl−, crystallizes in a non-centrosymmetric polar space group and possesess normal geometric parameters. The crystal structure analysis reveals a discrete ionic species, for which the packing is consolidated by an N—H...Cl hydrogen bond and C—H...Cl hydrogen bonds, resulting in a two-dimensional network.

C–H⋯S interaction exhibits all the characteristics of conventional hydrogen bonds

2020 ◽  
Vol 22 (31) ◽  
pp. 17482-17493 ◽  
Author(s):  
Sanat Ghosh ◽  
Pragya Chopra ◽  
Sanjay Wategaonkar
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Hydrogen Bond Donor ◽  
Donor And Acceptor

This is a tale of a pair of a hydrogen bond donor and acceptor, namely the CH donor and sulphur acceptor, neither of which is a conventional hydrogen bond participant.

The whole range of hydrogen bonds in one crystal structure: neutron diffraction and charge-density studies of N,N-dimethylbiguanidinium bis(hydrogensquarate)

2011 ◽  
Vol 67 (6) ◽  
pp. 552-559 ◽  
Author(s):  
Mihaela-Diana Şerb ◽  
Ruimin Wang ◽  
Martin Meven ◽  
Ulli Englert
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
High Resolution ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Electron Density ◽  
Organic Salt ◽  
X Ray Diffraction ◽  
Covalent Character ◽  
X Ray

N,N-Dimethylbiguanidinium bis(hydrogensquarate) features an impressive range of hydrogen bonds within the same crystal structure: neighbouring anions aggregate to a dianionic pair through two strong O—H...O interactions; one of these can be classified among the shortest hydrogen bonds ever studied. Cations and anions in this organic salt further interact via conventional N—H...O and nonclassical C—H...O contacts to an extended structure. As all these interactions occur in the same sample, the title compound is particularly suitable to monitor even subtle trends in hydrogen bonds. Neutron and high-resolution X-ray diffraction experiments have enabled us to determine the electron density precisely and to address its properties with an emphasis on the nature of the X—H...O interactions. Sensitive criteria such as the Laplacian of the electron density and energy densities in the bond-critical points reveal the incipient covalent character of the shortest O—H...O bond. These findings are in agreement with the precise geometry from neutron diffraction: the shortest hydrogen bond is also significantly more symmetric than the longer interactions.

scholarly journals Crystallographic study of self-organization in the solid state including quasi-aromatic pseudo-ring stacking interactions in 1-benzoyl-3-(3,4-dimethoxyphenyl)thiourea and 1-benzoyl-3-(2-hydroxypropyl)thiourea

2017 ◽  
Vol 73 (1) ◽  
pp. 52-56 ◽  
Author(s):  
Andrzej Okuniewski ◽  
Damian Rosiak ◽  
Jarosław Chojnacki ◽  
Barbara Becker
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Strong Hydrogen Bond ◽  
Compound I ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Formation ◽  
Oh Groups ◽  
Space Group ◽  
Donor And Acceptor ◽  
Phenyl Rings

1-Benzoylthioureas contain both carbonyl and thiocarbonyl functional groups and are of interest for their biological activity, metal coordination ability and involvement in hydrogen-bond formation. Two novel 1-benzoylthiourea derivatives, namely 1-benzoyl-3-(3,4-dimethoxyphenyl)thiourea, C16H16N2O3S, (I), and 1-benzoyl-3-(2-hydroxypropyl)thiourea, C11H14N2O2S, (II), have been synthesized and characterized. Compound (I) crystallizes in the space group P\overline{1}, while (II) crystallizes in the space group P21/c. In both structures, intramolecular N—H...O hydrogen bonding is present. The resulting six-membered pseudo-rings are quasi-aromatic and, in each case, interact with phenyl rings via stacking-type interactions. C—H...O, C—H...S and C—H...π interactions are also present. In (I), there is one molecule in the asymmetric unit. Pairs of molecules are connected via two intermolecular N—H...S hydrogen bonds, forming centrosymmetric dimers. In (II), there are two symmetry-independent molecules that differ mainly in the relative orientations of the phenyl rings with respect to the thiourea cores. Additional strong hydrogen-bond donor and acceptor –OH groups participate in the formation of intermolecular N—H...O and O—H...S hydrogen bonds that join molecules into chains extending in the [001] direction.

scholarly journals Hydrogen-bond donor and acceptor cooperative catalysis strategy for cyclic dehydration of diols to access O-heterocycles

2021 ◽  
Vol 7 (22) ◽  
pp. eabg0396
Author(s):  
Huan Wang ◽  
Yanfei Zhao ◽  
Fengtao Zhang ◽  
Zhengang Ke ◽  
Buxing Han ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Free Acid ◽  
Hydrogen Bond Donor ◽  
Metal Free ◽  
Mild Conditions ◽  
Cooperative Catalysis ◽  
Donor And Acceptor ◽  
Green Strategy ◽  
High Yields ◽  
Better Than

Dehydrative cyclization of diols to O-heterocycles is attractive, but acid and/or metal-based catalysts are generally required. Here, we present a hydrogen-bond donor and acceptor cooperative catalysis strategy for the synthesis of O-heterocycles from diols in ionic liquids [ILs; e.g., 1-hydroxyethyl-3-methyl imidazolium trifluoromethanesulfonate ([HO-EtMIm][OTf])] under metal-free, acid-free, and mild conditions. [HO-EtMIm][OTf] is tolerant to a wide diol scope, shows performance even better than H2SO4, and affords a series of O-heterocycles including tetrahydrofurans, tetrahydropyrans, morpholines, dioxanes, and thioxane in high yields. Mechanism investigation indicates that the IL cation and anion serve as hydrogen-bond donor and acceptor, respectively, to activate the C─O and O─H bonds of alcohol via hydrogen bonds, which synergistically catalyze dehydrative cyclization of diols to O-heterocycles. Notably, the products could be spontaneously separated after reaction because of their immiscibility with the IL, and the IL could be recycled. This green strategy has great potential for application in industry.

Predictable close-packing similarities between cis- and trans-2-hydroxy-1-cyclooctanecarboxylic acids and trans-2-hydroxy-1-cyclooctanecarboxamide

2002 ◽  
Vol 58 (5) ◽  
pp. 855-863 ◽  
Author(s):  
Alajos Kálmán ◽  
László Fábián ◽  
Gyula Argay ◽  
Gábor Bernáth ◽  
Zsuzsanna Gyarmati
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Close Packing ◽  
Crystal Structure Analysis ◽  
Crystal Formation ◽  
Acta Cryst ◽  
Oh Groups ◽  
X Ray ◽  
Donor And Acceptor ◽  
Cis And Trans

In order to extend the experimental data already available on the close packing of cyclopentanes substituted with vicinal COX (X = OH, NH2) and OH groups to the analogous cyclohexanes, cycloheptanes and cyclooctanes, (1R*,2S*)-cis-2-hydroxy-1-cyclooctanecarboxylic acid (8C), (1R*,2R*)-trans-2-hydroxy-1-cyclooctanecarboxylic acid (8T) and (1R*,2R*)-trans-2-hydroxy-1-cyclooctanecarboxamide (8T*) were subjected to X-ray crystal structure analysis. In 8T and 8T*, the hydrogen bonds form infinite ribbons of dimers joined by R ^{2}_{2}(12) rings with C i symmetry. Two types of dimer alternate along each ribbon. The dimers differ in the donor and acceptor roles of the functional groups. This pattern was previously deduced topologically among the possible forms of association for heterochiral dimers [Kálmán et al. (2002). Acta Cryst. B58, 494–501]. As they have the same pattern of hydrogen bonds, 8T and 8T* are isostructural. The additional donor (i.e. the second hydrogen of the NH2 group) present in 8T* links the adjacent ribbons so as to form smaller R^{2} _{2}(8) rings between them. The crystals of the cis stereoisomer 8C are built up from antiparallel hydrogen-bonded helices. The topology and symmetry of this structure are the same as for the close packing of (1R*,2R*,4S*)-4-tert-butyl-2-hydroxy-1-cyclopentanecarboxamide [Kálmán et al. (2001). Acta Cryst. B57, 539–550]; only the hydrogen-bond donors and acceptors are interchanged, in the same way as in the two dimer types of 8T and 8T* ribbons. This analogy suggests that helices may originate as homochiral dimers with C 2 symmetry and polymerize into helices during crystal formation. The conformational characteristics of the heterochiral dimers observed in the title compounds and in closely related structures are discussed.

scholarly journals Crystal structure of bis[N,N-bis(2-hydroxyethyl)glycinato-κ3O1,N,O2]cobalt(II) monohydrate

2015 ◽  
Vol 71 (11) ◽  
pp. m199-m200 ◽  
Author(s):  
Yang Liu ◽  
Dan Zhou ◽  
Hai-Hui Liu ◽  
Chen-Cong He
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Water Molecules ◽  
Hydrogen Bond Donor ◽  
Apical Position ◽  
Coordination Environment ◽  
Distorted Octahedral Coordination ◽  
Distorted Octahedral ◽  
Donor And Acceptor ◽  
Distorted Octahedral Coordination Environment

The title compound, [Co(C6H12O4)2]·H2O, was prepared by mild heating of an aqueous solution. The CoIIion has a slightly distorted octahedral coordination environment which is defined by two N atoms occupying the apical position, while the equatorial plane is furnished by two hydroxy O atoms and two carboxylate O atoms. The four hydroxy O atoms from two distinctN,N-bis(2-hydroxyethyl)glycine (bicH2−) ligands act as hydrogen-bond donors with two carboxylate O atoms as acceptors to form O—H...O hydrogen-bonded layers extending parallel to (100). In addition, the guest water molecule acts as both a hydrogen-bond donor and acceptor, so that each Co(bicH2)2molecule is connected simultaneously to six neighbouring Co(bicH2)2and two guest water molecules by hydrogen bonding.

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®).

Crystal structure of osimertinib mesylate Form B (Tagrisso), (C28H34N7O2)(CH3O3S)

2021 ◽  
pp. 1-9
Author(s):  
James A. Kaduk ◽  
Nicholas C. Boaz ◽  
Emma L. Markun ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Amino Nitrogen ◽  
Strong Hydrogen Bond ◽  
Powder Diffraction File ◽  
Dimethylamino Group ◽  
Intramolecular Hydrogen

The crystal structure of osimertinib mesylate Form B has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Osimertinib mesylate Form B crystallizes in space group P-1 (#2) with a = 11.42912(17), b = 11.72274(24), c = 13.32213(22) Å, α = 69.0265(5), β = 74.5914(4), γ = 66.4007(4)°, V = 1511.557(12) Å3, and Z = 2. The crystal structure is characterized by alternating layers of cation–anion and parallel stacking interactions parallel to the ab-planes. The cation is protonated at the nitrogen atom of the dimethylamino group, which forms a strong hydrogen bond between the cation and the anion. That hydrogen atom also participates in a weaker intramolecular hydrogen bond to an amino nitrogen. There are two additional N–H⋅⋅⋅O hydrogen bonds between the cation and the anion. Several C–H⋅⋅⋅O hydrogen bonds also link the cations and anions. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

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