Persistent hydrogen bonding in polymorphic crystal structures

2009 ◽  
Vol 65 (1) ◽  
pp. 68-85 ◽  
Author(s):  
Peter T. A. Galek ◽  
László Fábián ◽  
Frank H. Allen
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Structural Analysis ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Structural Stability ◽  
Polymorphic Form ◽  
Large Majority ◽  
New Method ◽  
Structural Database

The significance of hydrogen bonding and its variability in polymorphic crystal structures is explored using new automated structural analysis methods. The concept of a chemically equivalent hydrogen bond is defined, which may be identified in pairs of structures, revealing those types of bonds that may persist, or not, in moving from one polymorphic form to another. Their frequency and nature are investigated in 882 polymorphic structures from the Cambridge Structural Database. A new method to compare conformations of equivalent molecules is introduced and applied to derive distinct subsets of conformational and packing polymorphs. The roles of chemical functionality and hydrogen-bond geometry in persistent interactions are systematically explored. Detailed structural comparisons reveal a large majority of persistent hydrogen bonds that are energetically crucial to structural stability.

Extensive analysis of N—H...O hydrogen bonding in four classes of phosphorus compounds: a combined experimental and database study

2017 ◽  
Vol 73 (3) ◽  
pp. 287-297 ◽  
Author(s):  
Farahnaz Hamzehee ◽  
Mehrdad Pourayoubi ◽  
Marek Nečas ◽  
Duane Choquesillo-Lazarte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Neutral Hydrogen ◽  
The Other ◽  
Phosphorus Compounds ◽  
Database Study ◽  
Extensive Analysis ◽  
Structural Database

The N—H...O hydrogen bond is the characteristic interaction in the crystal structures of N-benzyl-P-phenyl-N′-(p-tolyl)phosphonic diamide, C20H21N2OP or (C6H5)P(O)(NHCH2C6H5)(NHC6H4-p-CH3), (I), diphenylphosphinic 1-methylpropylamide, C16H20NOP or (C6H5)2P(O)[NHCH(CH3)(C2H5)], (II), (S)-1-phenylethylammonium N-[(S)-1-phenylethyl]phenylphosphonamidate, C8H12N+·C14H15NO2P− or [S-(C6H5)CH(CH3)NH3][(C6H5)P(O){S-NHCH(CH3)(C6H5)}(O)], (III), and (4-methylbenzyl)ammonium diphenylphosphinate, C8H12N+·C12H10O2P− or [4-CH3-C6H4CH2NH3][(C6H5)2P(O)(O)], (IV). This article focuses on the N—H...O hydrogen bonds by considering the structures of (I), (II), (III) and (IV), and reviewing their analogous compounds, including 43 (C)P(O)(N)2, 102 (C)2P(O)(N), 31 (C)P(O)(N)(O) and 96 (C)2P(O)(O) structures, deposited in the Cambridge Structural Database (CSD). For the structures with a (C)P(O)(N)2 segment, only neutral hydrogen bonds were found in the CSD. The other three classes of compounds included both neutral and `charge-assisted' hydrogen bonds, and the (C)2P(O)(O) structures were particularly noticeable for a high number of cation–anion compounds. The overall tendencies of N...O distances in neutral and cation–anion compounds were compared. The N—H...O hydrogen-bond angles were also analyzed for the four classes of phosphorus compounds.

Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications

2014 ◽  
Vol 70 (1) ◽  
pp. 91-105 ◽  
Author(s):  
Peter T. A. Galek ◽  
James A. Chisholm ◽  
Elna Pidcock ◽  
Peter A. Wood
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Structural Stability ◽  
Statistical Models ◽  
Cambridge Structural Database ◽  
Acceptor Atom ◽  
Coordination Behaviour ◽  
Structural Database

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

Five pseudopolymorphs of 6-amino-2-thiouracil: absence of N—H...S hydrogen bonds

2012 ◽  
Vol 69 (1) ◽  
pp. 93-100 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Hydrogen Bonding Pattern ◽  
Crystallization Experiments ◽  
Structural Database ◽  
Thiouracil Derivatives

In order to study the preferred hydrogen-bonding pattern of 6-amino-2-thiouracil, C4H5N3OS, (I), crystallization experiments yielded five different pseudopolymorphs of (I), namely the dimethylformamide disolvate, C4H5N3OS·2C3H7NO, (Ia), the dimethylacetamide monosolvate, C4H5N3OS·C4H9NO, (Ib), the dimethylacetamide sesquisolvate, C4H5N3OS·1.5C4H9NO, (Ic), and two different 1-methylpyrrolidin-2-one sesquisolvates, C4H5N3OS·1.5C5H9NO, (Id) and (Ie). All structures containR21(6) N—H...O hydrogen-bond motifs. In the latter four structures, additionalR22(8) N—H...O hydrogen-bond motifs are present stabilizing homodimers of (I). No type of hydrogen bond other than N—H...O is observed. According to a search of the Cambridge Structural Database, most 2-thiouracil derivatives form homodimers stabilized by anR22(8) hydrogen-bonding pattern, with (i) only N—H...O, (ii) only N—H...S or (iii) alternating pairs of N—H...O and N—H...S hydrogen bonds.

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.

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.

A Comparison of the Enamino Carbonyl Conjugation Efficiency for Hydrogen Bonding Formation in Pyridone and Dihydropyridone Systems

2000 ◽  
Vol 55 (1) ◽  
pp. 5-11 ◽  
Author(s):  
Teresa Borowiak ◽  
Irena Wolska ◽  
Artur Korzański ◽  
Wolfgang Milius ◽  
Wolfgang Schnick ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Steric Hindrance ◽  
Crystal Packing ◽  
Intermolecular Hydrogen Bond ◽  
Asymmetric Unit ◽  
Intermolecular Hydrogen Bonds

The crystal structures of two compounds containing enaminone heterodiene systems and forming intermolecular hydrogen bonds N-H·O are reported: 1) 3-ethoxycarbonyl-2-methyl-4-pyridone (hereafter ETPY) and 2) 3-ethoxycarbonyl-2-phenyl-6-methoxycarbonyl-5,6-di-hydro-4-pyridone (hereafter EPPY). The crystal packing is controlled by intermolecular hydro­ gen bonds N-H·O = C connecting the heteroconjugated enaminone groups in infinite chains. In ETPY crystals the intermolecular hydrogen bond involves the heterodienic pathway with the highest π-delocalization that is effective for a very short N·O distance of 2.701(9) Å (average from two molecules in the asymmetric unit). Probably due to the steric hindrance, the hydrogen bond in EPPY is formed following the heterodienic pathway that involves the ester C = O group, although π-delocalization along this pathway is less than that along the pyridone-part pathway resulting in a longer N·O distance of 2.886(3) Å

Hydrogen bonding at C=Se acceptors in selenoureas, selenoamides and selones

2016 ◽  
Vol 72 (3) ◽  
pp. 317-325 ◽  
Author(s):  
Dikima Bibelayi ◽  
Albert S. Lundemba ◽  
Frank H. Allen ◽  
Peter T. A. Galek ◽  
Juliette Pradon ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Crystal Engineering ◽  
Cambridge Structural Database ◽  
Bond Lengths ◽  
Partial Charges ◽  
Structural Database

In recent years there has been considerable interest in chalcogen and hydrogen bonding involving Se atoms, but a general understanding of their nature and behaviour has yet to emerge. In the present work, the hydrogen-bonding ability and nature of Se atoms in selenourea derivatives, selenoamides and selones has been explored using analysis of the Cambridge Structural Database andab initiocalculations. In the CSD there are 70 C=Se structures forming hydrogen bonds, all of them selenourea derivatives or selenoamides. Analysis of intramolecular geometries andab initiopartial charges show that this bonding stems from resonance-induced Cδ+=Seδ−dipoles, much like hydrogen bonding to C=S acceptors. C=Se acceptors are in many respects similar to C=S acceptors, with similar vdW-normalized hydrogen-bond lengths and calculated interaction strengths. The similarity between the C=S and C=Se acceptors for hydrogen bonding should inform and guide the use of C=Se in crystal engineering.

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.

scholarly journals Hydrogen Bonding Guests Direct the Packing of a Small Organic Cage Molecule

2019 ◽  
Author(s):  
Thomas Anglim Lagones ◽  
Stephanie Boer ◽  
Nicholas White
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Hydrogen Bond Donor ◽  
Crystalline Phases ◽  
Cage Molecule

<div> <p>A small organic cage molecule (<b>1</b>) containing six nitrile groups was crystallized in the presence of a number of guests with hydrogen bond donor groups, and from different solvents. In total, eight crystal structures of <b>1</b> were obtained, six of which are guest-free and two of which are co-crystals. When the guest was resorcinol or pyrogallol co-crystals did not form, but the presence of the guests directed formation of new crystalline phases that were not observed when the cage was crystallized alone. When the guest was hydroquinone or diaminobenzene, it was possible to isolate co-crystals where the guest hydrogen bonds to some of the nitrile groups of the cage. </p> </div> <br>

Interplay between steric and electronic factors in determining the strength of intramolecular N—H...O resonance-assisted hydrogen bonds in β-enaminones

2006 ◽  
Vol 62 (6) ◽  
pp. 1112-1120 ◽  
Author(s):  
Valerio Bertolasi ◽  
Loretta Pretto ◽  
Valeria Ferretti ◽  
Paola Gilli ◽  
Gastone Gilli
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Structural Features ◽  
Membered Ring ◽  
Resonance Assisted Hydrogen Bond ◽  
Electronic Resonance ◽  
Hydrogen Bonded

The crystal structures of five β-enaminones are reported: (2Z)-3-(benzylamino)-1,3-diphenyl-prop-2-en-1-one, (2Z)-3-(benzylamino)-3-(2-hydroxyphenyl)-1-phenyl-prop-2-en-1-one, (2Z)-3-(benzylamino)-3-(4-methoxyphenyl)-1-(3-nitrophenyl)-prop-2-en-1-one, 2-{1-[(4-methoxyphenyl)amino]ethylidene}cyclohexene-1,3-dione and 2-{1-[(3-methoxyphenyl)amino]ethylidene}cyclohexene-1,3-dione. The structures were analysed and compared with those of similar compounds in order to establish which factors determine the range (2.53–2.72 Å) of N...O hydrogen-bond distances in intramolecularly hydrogen-bonded β-enaminones. It has been shown that, beyond electronic resonance-assisted hydrogen-bond effects modulated by substituents, the necessary requirements to produce very short N—H...O hydrogen bonding are steric intramolecular repulsions, including the embedding of an enaminonic C—C or C—N bond in an aliphatic six-membered ring. By considering the structural features it is possible to expect the strength of N—H...O hydrogen bonds adopted by specific β-enaminones.

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