scholarly journals N–H⋯O hydrogen bonding to the alkoxy oxygen of a carboxylic ester group: crystal structures of methyl 2,6-diaminobenzoate and its derivatives

CrystEngComm ◽  
2020 ◽  
Vol 22 (21) ◽  
pp. 3701-3712
Author(s):  
Songjie Yang ◽  
A. Christopher Garner ◽  
John D. Wallis
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Oxygen Atom ◽  
Crystal Structures ◽  
Ester Group ◽  
Amino Groups ◽  
Carboxylic Ester

Molecules with hydrogen bonds from amino groups to both oxygens of a carboxylic ester are described, and other examples of hydrogen bonding to an ester's alkoxy oxygen atom are highlighted.

Structure of the adducts methylthiourea: 1,4-dioxane (2:1) and 1,1-dimethylthiourea: morpholine (1:1)

2016 ◽  
Vol 71 (8) ◽  
pp. 905-907 ◽  
Author(s):  
Christina Taouss ◽  
Peter G. Jones
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Oxygen Atom ◽  
Crystal Structures ◽  
Sulfur Atom ◽  
Layer Structure ◽  
Blocking Effect ◽  
Methyl Groups ◽  
Inversion Symmetry

AbstractThe adducts methylthiourea:1,4-dioxane (2:1) (1) and 1,1-dimethylthiourea:morpholine (1:1) (2) were prepared and their crystal structures determined. In 1, hydrogen bonding involving the methylthiourea molecules leads to the formation of ${\rm{R}}_2^2(8)$ rings and thence to molecular ribbons parallel to [110]. The dioxane molecules accept hydrogen bonds from the remaining NH groups, and their inversion symmetry means that they connect adjacent methylthiourea ribbons, forming a layer structure parallel to (11̅1). In the packing of 2, dimethylthiourea dimers cannot link to each other because of the blocking effect of their methyl groups, but instead are linked indirectly via morpholine molecules, the NH groups of which are simultaneously hydrogen bond acceptors from the remaining NH function of dimethylthiourea and donors towards the sulfur atom of a neighbouring dimer. The overall effect is to form broad ribbons parallel to the a axis, with the morpholine molecules occupying the peripheral positions. The morpholine oxygen atom of 2 is not involved in classical hydrogen bonds.

Polymorphs of phenazine hexacyanoferrate(II) hydrate: supramolecular isomerism in a 2D hydrogen-bonded network

2021 ◽  
Vol 77 (2) ◽  
pp. 211-218
Author(s):  
Ivica Cvrtila ◽  
Vladimir Stilinović
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Two Dimensional ◽  
Structural Motifs ◽  
Supramolecular Isomerism ◽  
Other Hand ◽  
Π Stacking ◽  
Hydrogen Bonded

The crystal structures of two polymorphs of a phenazine hexacyanoferrate(II) salt/cocrystal, with the formula (Hphen)3[H2Fe(CN)6][H3Fe(CN)6]·2(phen)·2H2O, are reported. The polymorphs are comprised of (Hphen)2[H2Fe(CN)6] trimers and (Hphen)[(phen)2(H2O)2][H3Fe(CN)6] hexamers connected into two-dimensional (2D) hydrogen-bonded networks through strong hydrogen bonds between the [H2Fe(CN)6]2− and [H3Fe(CN)6]− anions. The layers are further connected by hydrogen bonds, as well as through π–π stacking of phenazine moieties. Aside from the identical 2D hydrogen-bonded networks, the two polymorphs share phenazine stacks comprising both protonated and neutral phenazine molecules. On the other hand, the polymorphs differ in the conformation, placement and orientation of the hydrogen-bonded trimers and hexamers within the hydrogen-bonded networks, which leads to different packing of the hydrogen-bonded layers, as well as to different hydrogen bonding between the layers. Thus, aside from an exceptional number of symmetry-independent units (nine in total), these two polymorphs show how robust structural motifs, such as charge-assisted hydrogen bonding or π-stacking, allow for different arrangements of the supramolecular units, resulting in polymorphism.

scholarly journals Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

2020 ◽  
Vol 48 (15) ◽  
pp. 8302-8319
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Small Molecule ◽  
Base Pair ◽  
Base Pairs ◽  
Standard Pattern ◽  
Planar Structures ◽  
Structural Database ◽  
Derivatives Of

Abstract We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.

Supramolecular hydrogen-bonding patterns in two cocrystals of the N(7)–H tautomeric form ofN6-benzoyladenine:N6-benzoyladenine–3-hydroxypyridinium-2-carboxylate (1/1) andN6-benzoyladenine–DL-tartaric acid (1/1)

2015 ◽  
Vol 71 (11) ◽  
pp. 985-990 ◽  
Author(s):  
Ammasai Karthikeyan ◽  
Robert Swinton Darious ◽  
Packianathan Thomas Muthiah ◽  
Franc Perdih
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Tartaric Acid ◽  
Dihedral Angle ◽  
Tautomeric Form ◽  
Stacking Interactions ◽  
Graph Set ◽  
Purine Ring ◽  
Ring Motif

Two novel cocrystals of the N(7)—H tautomeric form ofN6-benzoyladenine (BA), namelyN6-benzoyladenine–3-hydroxypyridinium-2-carboxylate (3HPA) (1/1), C12H9N5O·C6H5NO3, (I), andN6-benzoyladenine–DL-tartaric acid (TA) (1/1), C12H9N5O·C4H6O6, (II), are reported. In both cocrystals, theN6-benzoyladenine molecule exists as the N(7)—H tautomer, and this tautomeric form is stabilized by intramolecular N—H...O hydrogen bonding between the benzoyl C=O group and the N(7)—H hydrogen on the Hoogsteen site of the purine ring, forming anS(7) motif. The dihedral angle between the adenine and phenyl planes is 0.94 (8)° in (I) and 9.77 (8)° in (II). In (I), the Watson–Crick face of BA (N6—H and N1; purine numbering) interacts with the carboxylate and phenol groups of 3HPA through N—H...O and O—H...N hydrogen bonds, generating a ring-motif heterosynthon [graph setR22(6)]. However, in (II), the Hoogsteen face of BA (benzoyl O atom and N7; purine numbering) interacts with TA (hydroxy and carbonyl O atoms) through N—H...O and O—H...O hydrogen bonds, generating a different heterosynthon [graph setR22(4)]. Both crystal structures are further stabilized by π–π stacking interactions.

N—H...S and N—H...O hydrogen bonds: `pure' and `mixed'R22(8) patterns in the crystal structures of eight 2-thiouracil derivatives

2014 ◽  
Vol 70 (2) ◽  
pp. 241-249 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Ernst Egert
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Dimethyl Sulfoxide ◽  
Crystal Structures ◽  
Thiouracil Derivatives ◽  
Bonding Patterns

The preferred hydrogen-bonding patterns in the crystal structures of 5-propyl-2-thiouracil, C7H10N2OS, (I), 5-methoxy-2-thiouracil, C5H6N2O2S, (II), 5-methoxy-2-thiouracil–N,N-dimethylacetamide (1/1), C5H6N2O2S·C4H9NO, (IIa), 5,6-dimethyl-2-thiouracil, C6H8N2OS, (III), 5,6-dimethyl-2-thiouracil–1-methylpyrrolidin-2-one (1/1), C6H8N2OS·C5H9NO, (IIIa), 5,6-dimethyl-2-thiouracil–N,N-dimethylformamide (2/1), 2C6H8N2OS·C3H7NO, (IIIb), 5,6-dimethyl-2-thiouracil–N,N-dimethylacetamide (2/1), 2C6H8N2OS·C4H9NO, (IIIc), and 5,6-dimethyl-2-thiouracil–dimethyl sulfoxide (2/1), 2C6H8N2OS·C2H6OS, (IIId), were analysed. All eight structures containR22(8) patterns. In (II), (IIa), (III) and (IIIa), they are formed by two N—H...S hydrogen bonds, and in (I) by alternating pairs of N—H...S and N—H...O hydrogen bonds. In contrast, the structures of (IIIb), (IIIc) and (IIId) contain `mixed'R22(8) patterns with one N—H...S and one N—H...O hydrogen bond, as well asR22(8) motifs with two N—H...O hydrogen bonds.

scholarly journals Crystal Structures of Four Novel Thiophene/Phenyl-piperidine Hybrid Chalcones

2014 ◽  
Vol 70 (a1) ◽  
pp. C1020-C1020
Author(s):  
Masood Parvez ◽  
Muhammad Bakhtiar ◽  
Muhammad Baqir ◽  
Muhammad Zia-ur-Rehman
Keyword(s):  
Hydrogen Bonding ◽  
Pharmaceutical Industry ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Benzene Ring ◽  
Drug Targets ◽  
Important Class ◽  
Hydrogen Bonding Interactions ◽  
Benzene Rings ◽  
Type C

Chalcones constitute an important class of bioactive drug targets in the pharmaceutical industry that includes anti-ulcerative drug sofalcone. In continuation of our work, the crystal structures of four closely related 1-phenyl-piperidine based chalcones will be presented. I: C19 H21NOS, MW = 311.43, T = 173(2) K, λ = 0.71073 Å, Orthorhombic, P b c a, a = 10.1045(4), b = 10.5358(4), c = 30.6337(12) Å, V = 3261.2(2) Å3, Z = 8, Dc = 1.269 Mg/m3, F (000) = 1328, R [I>2σ(I)] = 0.059. II: C18H19NOS, MW = 297.40, T = 173(2) K, λ = 1.54178 Å, Orthorhombic, P b c a, a = 8.9236(2), b = 11.0227(2), c = 30.8168(6) Å, V = 3031.21(11) Å3 Z = 8, Dc = 1.303 Mg/m3, F (000) = 1264, R [I>2σ(I)] = 0.035. III: C18H19NOS, MW = 297.40, T = 173(2) K, λ = 1.54178 Å, Orthorhombic, P b c a, a = 8.82990(10), b = 11.0061(2), c = 31.2106(5) Å, V = 3033.13(8) Å3, Z = 8, Dc = 1.303 Mg/m3, F (000) = 1264, R [I>2σ(I)] = 0.048. IV: C18H18ClNOS, MW = 331.84, T = 173(2) K, λ = 0.71073 Å, Monoclinic, P 21/c, a = 14.1037(4), b = 11.3153(3), c = 10.1290(2) Å, β = 101.1367(14)0, V = 1586.02(7) Å3, Z = 4, Dc = 1.390 Mg/m3, F (000) = 696, R [I>2σ(I)] = 0.038. The crystals of I, II and III are isomorphous. In all structures, the piperidine rings are in chair conformations, thiophene rings are essentially planar and the C=C bonds in the prop-2-en-1-one fragment adopt E-conformation. All crystal structures are devoid of any classical hydrogen bonds. However, non-classical hydrogen bonding interactions of the type C---H...O in compounds II, III and IV link the molecules into chains extended along the b-axis. Moreover, C---H...Cg interactions involving thiophene rings in I and III and benzene ring in IV and π...π interactions between benzene rings lying about inversion centers are present in II and III.

Knowledge-based model of hydrogen-bonding propensity in organic crystals

2007 ◽  
Vol 63 (5) ◽  
pp. 768-782 ◽  
Author(s):  
Peter T. A. Galek ◽  
László Fábián ◽  
W. D. Samuel Motherwell ◽  
Frank H. Allen ◽  
Neil Feeder
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Chemical Properties ◽  
Organic Crystal ◽  
Training Data ◽  
Survey Method ◽  
Statistical Validation ◽  
Knowledge Based

A new method is presented to predict which donors and acceptors form hydrogen bonds in a crystal structure, based on the statistical analysis of hydrogen bonds in the Cambridge Structural Database (CSD). The method is named the logit hydrogen-bonding propensity (LHP) model. The approach has a potential application in identifying both likely and unusual hydrogen bonding, which can help to rationalize stable and metastable crystalline forms, of relevance to drug development in the pharmaceutical industry. Whilst polymorph prediction techniques are widely used, the LHP model is knowledge-based and is not restricted by the computational issues of polymorph prediction, and as such may form a valuable precursor to polymorph screening. Model construction applies logistic regression, using training data obtained with a new survey method based on the CSD system. The survey categorizes the hydrogen bonds and extracts model parameter values using descriptive structural and chemical properties from three-dimensional organic crystal structures. LHP predictions from a fitted model are made using two-dimensional observables alone. In the initial cases analysed, the model is highly accurate, achieving ∼ 90% correct classification of both observed hydrogen bonds and non-interacting donor–acceptor pairs. Extensive statistical validation shows the LHP model to be robust across a range of small-molecule organic crystal structures.

scholarly journals The crystal structures of two novel polymorphs of bis(oxonium) ethane-1,2-disulfonate

2019 ◽  
Vol 75 (11) ◽  
pp. 1586-1589
Author(s):  
Jaroslaw Mazurek ◽  
Ana Fernandez-Casares
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Acta Cryst ◽  
Crystal Forms ◽  
Crystal Density ◽  
Hydrogen Bonding Network

Two novel crystal forms of bis(oxonium) ethane-1,2-disulfonate, 2H3O−·C2H4O6S2 2−, are reported. Polymorph II has monoclinic (P21/n) symmetry, while the symmetry of form III is triclinic (P\overline{1}). Both structures display extensive networks of O—H...O hydrogen bonds. While this network in Form II is similar to that observed for the previously reported Form I [Mootz & Wunderlich (1970). Acta Cryst. B26, 1820–1825; Sartori et al. (1994). Z. Naturforsch. 49, 1467–1472] and extends in all directions, in Form III it differs significantly, forming layers parallel to the ab plane. The sulfonate molecule in all three forms adopts a nearly identical geometry. The other observed differences between the forms, apart from the hydrogen-bonding network, are observed in the crystal density and packing index.

scholarly journals Polymorphism of 2-(5-benzyl-6-oxo-3-phenyl-1,6-dihydropyridazin-1-yl)acetic acid with two monoclinic modifications: crystal structures and Hirshfeld surface analyses

2020 ◽  
Vol 76 (3) ◽  
pp. 432-437
Author(s):  
Said Daoui ◽  
Cemile Baydere ◽  
Tarik Chelfi ◽  
Fouad El Kalai ◽  
Necmi Dege ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Acetic Acid ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Hirshfeld Surface ◽  
Two Dimensional ◽  
Asymmetric Unit ◽  
Monoclinic System ◽  
Compound C ◽  
Ring Motif

Two polymorphs of the title compound, C19H16N2O3, were obtained from ethanolic (polymorph I) and methanolic solutions (polymorph II), respectively. Both polymorphs crystallize in the monoclinic system with four formula units per cell and a complete molecule in the asymmetric unit. The main difference between the molecules of (I) and (II) is the reversed position of the hydroxy group of the carboxylic function. All other conformational features are found to be similar in the two molecules. The different orientation of the OH group results in different hydrogen-bonding schemes in the crystal structures of (I) and (II). Whereas in (I) intermolecular O—H...O hydrogen bonds with the pyridazinone carbonyl O atom as acceptor generate chains with a C(7) motif extending parallel to the b-axis direction, in the crystal of (II) pairs of inversion-related O—H...O hydrogen bonds with an R 2 2(8) ring motif between two carboxylic functions are found. The intermolecular interactions in both crystal structures were analysed using Hirshfeld surface analysis and two-dimensional fingerprint plots.

scholarly journals Crystal structures and hydrogen-bonding analysis of a series of benzamide complexes of zinc(II) chloride

2021 ◽  
Vol 77 (9) ◽  
Author(s):  
Elizabeth Tinapple ◽  
Sam Farrar ◽  
Dean H. Johnston
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Physical Properties ◽  
Crystal Structures ◽  
Organic Molecules ◽  
Inorganic Salt ◽  
Carbonyl Oxygen ◽  
Bonding Analysis ◽  
Amide Carbonyl ◽  
Improve Stability

Ionic co-crystals are co-crystals between organic molecules and inorganic salt coformers. Co-crystals of pharmaceuticals are of interest to help control polymorph formation and potentially improve stability and other physical properties. We describe the preparation, crystal structures, and hydrogen bonding of five different 2:1 benzamide or toluamide/zinc(II) chloride co-crystal salts, namely, bis(benzamide-κO)dichloridozinc(II), [ZnCl2(C7H7NO)2], dichloridobis(2-methylbenzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], dichloridobis(3-methylbenzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], dichloridobis(4-methylbenzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], and dichloridobis(4-hydroxybenzamide-κO)zinc(II), [ZnCl2(C7H7NO2)2]. All of the complexes contain hydrogen bonds between the amide N—H group and the amide carbonyl oxygen atoms or the chlorine atoms, forming extended networks.

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