Analysis of the less common hydrogen bonds involving ester oxygen sp 3 atoms as acceptors in the crystal structures of small organic molecules

2004 ◽  
Vol 60 (4) ◽  
pp. 424-432 ◽  
Author(s):  
Krešimir Molčanov ◽  
Biserka Kojić-Prodić ◽  
Nenad Raos
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Secondary Amines ◽  
Structural Function ◽  
Hydroxyl Groups ◽  
Donor Group ◽  
Acta Cryst ◽  
Bifurcated Hydrogen Bond

An analysis of hydrogen bonds involving ester Osp 3 atoms as acceptors has been performed based on the data extracted from the Cambridge Structural Database [Allen (2002). Acta Cryst. B58, 380–388; version 5.25, November 2003], using the ConQuest package to evaluate the stereochemical and electronic properties of the acceptors. Evidence for the existence of this particular type of hydrogen bond and its structural function in crystal packing is presented. Using a cut-off limit on residual indices of R < 0.05 (for the structures with hydrogen bonds involving an oxygen as part of the donor group) and R < 0.085 (for nitrogen as part of the donor group), 230 structures out of the total CSD entries of 298 100 were found to contain hydrogen bonds with the ester Osp 3 atoms as acceptors. The hydrogen-bond donors include water molecules, hydroxyl groups, primary and secondary amines and, in a few cases, imino groups. Four modes of the participation of the ester Osp 3 atoms in hydrogen bonding are detected: as a single acceptor, as a double acceptor, as a single acceptor of a H atom involved in an intermolecular bifurcated hydrogen bond, and as a shared acceptor function with the ester Osp 2 atom in a bifurcated hydrogen bond. The role of such directed noncovalent interactions in crystal packing is demonstrated by a small gallery of selected structures.

Crystal structures, packing features, Hirshfeld surface analyses and DFT calculations of hydrogen-bond energy of two homologous 8a-aryl-2,3,4,7,8,8a-hexahydropyrrolo[1,2-a]pyrimidin-6(1H)-ones

2020 ◽  
Vol 76 (5) ◽  
pp. 483-489 ◽  
Author(s):  
Vyacheslav S. Grinev ◽  
Elena I. Linkova ◽  
Mikhail N. Krainov ◽  
Maksim V. Dmitriev ◽  
Alevtina Yu. Yegorova
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Dft Calculations ◽  
Crystal Structures ◽  
Bond Energy ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Hirshfeld Surface ◽  
Hydrogen Bond Energy ◽  
Bicyclic Lactams

The crystal structures and packing features of two homologous Meyer's bicyclic lactams with fused pyrrolidone and medium-sized perhydropyrimidine rings, namely, 8a-phenyl-2,3,4,7,8,8a-hexahydropyrrolo[1,2-a]pyrimidin-6(1H)-one, C13H16N2O (1), and 8a-(4-methylphenyl)-2,3,4,7,8,8a-hexahydropyrrolo[1,2-a]pyrimidin-6(1H)-one, C14H18N2O (2), were elucidated, and Hirshfeld surface plots were calculated and drawn for visualization and a deeper analysis of the intermolecular noncovalent interactions. Molecules of 1 and 2 are weakly linked by intermolecular C=O...H—N hydrogen bonds into chains, which are in turn weakly linked by other C=O...H—Car interactions. The steric volume of the substituent significantly affects the crystal packing pattern.

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.

Pyridine 1:1 adducts of urea (Z′ = 1) and thiourea (Z′ = 8)

2018 ◽  
Vol 74 (4) ◽  
pp. 406-410 ◽  
Author(s):  
Mark Strey ◽  
Peter G. Jones
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Layer Structure ◽  
Urea Adduct ◽  
Standard Type ◽  
Space Group ◽  
Hydrogen Bond System ◽  
Bond System ◽  
Bifurcated Hydrogen Bond ◽  
Urea Adducts

During our studies of urea and thiourea adducts, we noticed that no adducts with unsubstituted pyridine had been structurally investigated. The 1:1 adduct of pyridine and urea, C5H5N·CH4N2O, crystallizes in the P21/c space group with Z = 4. The structure is of a standard type for urea adducts, whereby the urea molecules form a ribbon, parallel to the a axis, consisting of linked R 2 2(8) rings, and the pyridine molecules are attached to the periphery of the ribbon by bifurcated (N—H...)2N hydrogen bonds. The 1:1 adduct of pyridine and thiourea, C5H5N·CH4N2S, crystallizes in the P21/n space group, with Z = 32 (Z′ = 8). The structure displays similar ribbons to those of the urea adduct. There are two independent ribbons parallel to the b axis at z ≃ 0 and 1 \over 2, and three at z ≃ 1 \over 4 and 3 \over 4; the latter are crosslinked to form a layer structure by additional long N—H...S interactions, which each formally replace one branch of a bifurcated hydrogen-bond system.

scholarly journals Bis(4,6-di-tert-butyl-2-{N-[4-(diethylamino)phenyl]carboximidoyl}phenolato)cobalt(II)

IUCrData ◽  
2017 ◽  
Vol 2 (6) ◽  
Author(s):  
C.Vidya Rani ◽  
L. Mitu ◽  
G. Chakkaravarthi ◽  
G. Rajagopal
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Title Complex ◽  
Dihedral Angles ◽  
Minor Components ◽  
Tetrahedral Geometry ◽  
Acta Cryst ◽  
Distorted Tetrahedral Geometry ◽  
Benzene Rings

In the title complex, [Co(C25H35N2O)2], the cobalt(II) atom has a distorted tetrahedral geometry provided by pairs of O and N atoms. The dihedral angles between the benzene rings of the same ligand are 52.39 (9) and 34.96 (9)°. The molecular structure is stabilized by weak intramolecular C—H...O hydrogen bonds. The crystal packing is stabilized mainly by van der Waals forces. The structure contains a solvent-accessible void of 276 Å3which was treated using the SQUEEZE routine fromPLATON[Spek (2015).Acta Cryst.C71, 9–18]. The methyl C atoms of thetert-butyl groups are rotationally disordered, with site occupancies of 0.802 (3) and 0.548 (9) for the major components and 0.198 (3) and 0.452 (9) for the minor components.

scholarly journals A new solvate of epalerstat, a drug for diabetic neuropathy

2017 ◽  
Vol 73 (8) ◽  
pp. 1264-1267 ◽  
Author(s):  
Okky Dwichandra Putra ◽  
Daiki Umeda ◽  
Kaori Fukuzawa ◽  
Mihoko Gunji ◽  
Etsuo Yonemochi
Keyword(s):  
Hydrogen Bond ◽  
Acetic Acid ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Diabetic Neuropathy ◽  
Dihedral Angle ◽  
Phenyl Ring ◽  
Acid Moiety ◽  
Acta Cryst ◽  
Carboxylic Acid Groups

Epalerstat {systematic name: (5Z)-5-[(2E)-2-methyl-3-phenylprop-2-en-1-ylidene]-4-oxo-2-sulfanylidene-1,3-thiazolidine-3-acetic acid} crystallized as an acetone monosolvate, C15H13NO3S2·C3H6O. In the epalerstat molecule, the methylpropylenediene moiety is inclined to the phenyl ring and the five-membered rhodamine ring by 21.4 (4) and 4.7 (4)°, respectively. In addition, the acetic acid moiety is found to be almost normal to the rhodamine ring, making a dihedral angle of 85.1 (2)°. In the crystal, a pair of O—H...O hydrogen bonds between the carboxylic acid groups of epalerstat molecules form inversion dimers with an R 2 2(8) loop. The dimers are linked by pairs of C—H...O hydrogen bonds, enclosing R 2 2(20) loops, forming chains propagating along the [101] direction. In addition, the acetone molecules are linked to the chain by a C—H...O hydrogen bond. Epalerstat acetone monosolvate was found to be isotypic with epalerstat tertrahydrofuran solvate [Umeda et al. (2017). Acta Cryst. E73, 941–944].

Crystal structure of rivastigmine hydrogen tartrate Form I (Exelon®), C14H23N2O2(C4H5O6)

2016 ◽  
Vol 31 (2) ◽  
pp. 97-103 ◽  
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Carbonyl Oxygen ◽  
Strong Hydrogen Bond ◽  
Hydroxyl Groups ◽  
A Chain ◽  
Tartrate Anion

The crystal structure of rivastigmine hydrogen tartrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Rivastigmine hydrogen tartrate crystallizes in space group P21 (#4) with a = 17.538 34(5), b = 8.326 89(2), c = 7.261 11(2) Å, β = 98.7999(2)°, V = 1047.929(4) Å3, and Z = 2. The un-ionized end of the hydrogen tartrate anions forms a very strong hydrogen bond with the ionized end of another anion to form a chain. The ammonium group of the rivastigmine cation forms a strong discrete hydrogen bond with the carbonyl oxygen atom of the un-ionized end of the tartrate anion. These hydrogen bonds form a corrugated network in the bc-plane. Both hydroxyl groups of the tartrate anion form intramolecular O–H⋯O hydrogen bonds. Several C–H⋯O hydrogen bonds appear to contribute to the crystal energy. The powder pattern is included in the Powder Diffraction File™ as entry 00-064-1501.

scholarly journals Molecular interactions in nanocellulose assembly

2017 ◽  
Vol 376 (2112) ◽  
pp. 20170047 ◽  
Author(s):  
Yoshiharu Nishiyama
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Molecular Modelling ◽  
Hydroxyl Group ◽  
Enthalpy Of Sublimation ◽  
Dispersion Force ◽  
Hydroxyl Groups ◽  
Range Interaction ◽  
Simple Arithmetic ◽  
London Dispersion

The contribution of hydrogen bonds and the London dispersion force in the cohesion of cellulose is discussed in the light of the structure, spectroscopic data, empirical molecular-modelling parameters and thermodynamics data of analogue molecules. The hydrogen bond of cellulose is mainly electrostatic, and the stabilization energy in cellulose for each hydrogen bond is estimated to be between 17 and 30 kJ mol −1 . On average, hydroxyl groups of cellulose form hydrogen bonds comparable to those of other simple alcohols. The London dispersion interaction may be estimated from empirical attraction terms in molecular modelling by simple integration over all components. Although this interaction extends to relatively large distances in colloidal systems, the short-range interaction is dominant for the cohesion of cellulose and is equivalent to a compression of 3 GPa. Trends of heat of vaporization of alkyl alcohols and alkanes suggests a stabilization by such hydroxyl group hydrogen bonding to be of the order of 24 kJ mol −1 , whereas the London dispersion force contributes about 0.41 kJ mol −1  Da −1 . The simple arithmetic sum of the energy is consistent with the experimental enthalpy of sublimation of small sugars, where the main part of the cohesive energy comes from hydrogen bonds. For cellulose, because of the reduced number of hydroxyl groups, the London dispersion force provides the main contribution to intermolecular cohesion. This article is part of a discussion meeting issue ‘New horizons for cellulose nanotechnology’.

scholarly journals (E)-2-(4-Benzyloxy-2-hydroxybenzylidene)-N-methylhydrazinecarbothioamide

2014 ◽  
Vol 70 (2) ◽  
pp. o112-o113
Author(s):  
N. R. Sajitha ◽  
M. Sithambaresan ◽  
M. R. Prathapachandra Kurup
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Least Squares ◽  
Benzene Ring ◽  
Dihedral Angle ◽  
Title Compound ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Compound C ◽  
Benzene Rings

The molecule of the title compound, C16H17N3O2S, adopts anEconformation with respect to the azomethine C=N bond. The hydrazinecarbothioamide fragment is close to planar, with a largest deviation from the least-squares plane of 0.079 (2) Å for the hydrazide N atom. This fragment forms a dihedral angle of 9.43 (9)° with the central benzene ring. The benzene rings are inclined to one another by 67.55 (12)°. The molecular conformation is stabilized by an intramolecular O—H...N hydrogen bond involving the azomethine N atom. In the crystal, molecules are linked through weak N—H...S and N—H...O hydrogen bonds into double ribbons along [010]. The crystal packing also features C—H...π interactions.

scholarly journals (2Z)-2-{[N-(2-Formylphenyl)-4-methylbenzenesulfonamido]methyl}-3-(4-methylphenyl)prop-2-enenitrile

2012 ◽  
Vol 68 (4) ◽  
pp. o1084-o1084
Author(s):  
D. Kannan ◽  
M. Bakthadoss ◽  
R. Madhanraj ◽  
S. Murugavel
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Benzene Ring ◽  
Title Compound ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Dihedral Angles ◽  
Compound C ◽  
Centroid Distance ◽  
Ring Motif

In the title compound, C25H22N2O3S, the sulfonyl-bound benzene ring forms dihedral angles of 36.8 (2) and 81.4 (2)°, respectively, with the formylbenzene and methylbenzene rings. The molecular conformation is stabilized by an intramolecular C—H...O hydrogen bond, which generates anS(5) ring motif. The crystal packing is stabilized by C—H...O hydrogen bonds, which generateC(11) chains along thebaxis. The crystal packing is further stabilized by π–π interactions [centroid–centroid distance = 3.927 (2) Å].

scholarly journals Crystal structures of 2-aminopyridine citric acid salts: C5H7N2 +·C6H7O7 − and 3C5H7N2 +·C6H5O7 3−

2018 ◽  
Vol 74 (8) ◽  
pp. 1111-1116 ◽  
Author(s):  
Shet M. Prakash ◽  
S. Naveen ◽  
N. K. Lokanath ◽  
P. A. Suchetan ◽  
Ismail Warad
Keyword(s):  
Hydrogen Bond ◽  
Citric Acid ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Engineering ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Almost All

2-Aminopyridine and citric acid mixed in 1:1 and 3:1 ratios in ethanol yielded crystals of two 2-aminopyridinium citrate salts, viz. C5H7N2 +·C6H7O7 − (I) (systematic name: 2-aminopyridin-1-ium 3-carboxy-2-carboxymethyl-2-hydroxypropanoate), and 3C5H7N2 +·C6H5O7 3− (II) [systematic name: tris(2-aminopyridin-1-ium) 2-hydroxypropane-1,2,3-tricarboxylate]. The supramolecular synthons present are analysed and their effect upon the crystal packing is presented in the context of crystal engineering. Salt I is formed by the protonation of the pyridine N atom and deprotonation of the central carboxylic group of citric acid, while in II all three carboxylic groups of the acid are deprotonated and the charges are compensated for by three 2-aminopyridinium cations. In both structures, a complex supramolecular three-dimensional architecture is formed. In I, the supramolecular aggregation results from Namino—H...Oacid, Oacid...H—Oacid, Oalcohol—H...Oacid, Namino—H...Oalcohol, Npy—H...Oalcohol and Car—H...Oacid interactions. The molecular conformation of the citrate ion (CA3−) in II is stabilized by an intramolecular Oalcohol—H...Oacid hydrogen bond that encloses an S(6) ring motif. The complex three-dimensional structure of II features Namino—H...Oacid, Npy—H...Oacid and several Car—H...Oacid hydrogen bonds. In the crystal of I, the common charge-assisted 2-aminopyridinium–carboxylate heterosynthon exhibited in many 2-aminopyridinium carboxylates is not observed, instead chains of N—H...O hydrogen bonds and hetero O—H...O dimers are formed. In the crystal of II, the 2-aminopyridinium–carboxylate heterosynthon is sustained, while hetero O—H...O dimers are not observed. The crystal structures of both salts display a variety of hydrogen bonds as almost all of the hydrogen-bond donors and acceptors present are involved in hydrogen bonding.

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