Crystal Engineering Using Bisphenols and Trisphenols. Complexes with Hexamethylenetetramine (HMTA): Strings, Multiple Helices and Chains-of-Rings in the Crystal Structures of the Adducts of HTMA with 4,4'-Thiodiphenol (1/1), 4,4'-Sulfonyldiphenol (1/1), 4,4'-Isopropylidenediphenol (1/1), 1,1,1-Tris(4-hydroxyphenyl)ethane (1/2) and 1,3,5-Trihydroxybenzene (2/3)

1997 ◽  
Vol 53 (3) ◽  
pp. 521-533 ◽  
Author(s):  
P. I. Coupar ◽  
C. Glidewell ◽  
G. Ferguson
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Engineering ◽  
Triple Helix ◽  
Structural Motif ◽  
Rotation Axes ◽  
Double Helices ◽  
Graph Set ◽  
A Chain

The 4,4′-bisphenols (1), X(C6H4OH)2 [a, X = nil; b, X = O; c, X = S; d, X = 502; e, X = CO; f, X = CH2; g, X = CMe2; h, X = C(CF3)2], when co-crystallized from alcoholic solutions with hexamethylenetetramine, (CH2)6N4 (HMTA), form 1:1 adducts (4a)–(h). 4,4′-Thiodiphenol–hexamethylenetetramine (1/1), (4c), C12H10O2S.C6H12N4, and 4,4′- sulfonyldiphenol–hexamethylenetetramine (1/1), (4d), C12H10O4S.C6H12N4, are orthorhombic, Pmn21, (4c) a = 15.029 (2), b = 9.7954 (8), c = 5.9817 (11) Å and (4d) a = 14.779 (2), b = 10.2558 (15), c = 5.9817 (8) Å, with Z = 2, and the structures consist of zigzag chains comprising strings of alternating bisphenol and HMTA units, each lying across mirror planes and linked by O—H...N hydrogen bonds. In addition, both (4c) and (4d) exhibit C—H...\pi(arene) hydrogen bonds with one CH2 group of the HMTA unit acting as a donor to two different arene rings; (4d) also exhibits multiple C—H...O=S hydrogen bonds with three C—H bonds in each HMTA unit acting as donors towards a single sulfone O atom. 4,4′-Isopropylidenediphenol–hexamethylenetetramine (1/1), (4g), C15H16O2.C6H12N4, is monoclinic, C2/c, a = 25.093 (6), b = 7.1742 (13), c = 23.612 (7) Å, \beta = 110.42 (2)°, with Z = 8, and again the structure is built from chains of alternating bisphenol and HMTA units linked by O—H...N hydrogen bonds, but these now form double helices around twofold rotation axes; the double helices are themselves linked into sheets by C—H...O hydrogen bonds. The trisphenol (2), CH3C(C6H4OH)3, forms three adducts (5a)–(c) with HMTA, having trisphenol:HMTA ratios of 1:2 (5a), 2:3 (5b) and 1:1 (5c). 1,1,1-Tris(4-hydroxyphenyl)ethane–hexamethylenetetramine (1/2), (5a), C20H18O3.(C6H12N4)2, is orthorhombic, P212121, a = 6.9928 (10), b = 14.0949 (15), c = 30.999 (4) Å, with Z = 4, and the trisphenol units and half the HMTA units form a triple helix around a 21 axis, in which each strand consists of alternating phenol and HMTA units, linked as usual by O—H...N hydrogen bonds. The remaining HMTA units, which are external to the triple helix, are connected to it by O—H...N hydrogen bonds and are formed into externally buttressing stacks. The triol (3), 1,3,5-C6H3(OH)3, forms a 2:3 adduct (6) with HMTA. 1,3,5-Trihydroxybenzene–hexamethylenetetramine (2/3), (6), C6H6O3.(C6H12N4)1.5, is monoclinic, C2/c, a = 23.598 (2), b = 7.136 (2), c = 19.445 (3) Å, \beta = 96.822 (11)°, with Z = 8, and the dominant structural motif consists of centrosymmetric rings containing two molecules each of (3) and HMTA, connected by O—H...N hydrogen bonds; these rings are themselves linked into a chain-of-rings by further HMTA units lying on twofold rotation axes. The hydrogen-bonding patterns are codified using the graph-set approach.

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.

The hydrogen-bonded complex bis(tert-butylammonium) 2,6-dichlorophenolate 2,4-dichlorophenol–2,4-dichlorophenolate tetrahydrofuran disolvate containing a chiralR53(10) hydrogen-bonded ring as a supramolecular synthon

2016 ◽  
Vol 72 (10) ◽  
pp. 720-723 ◽  
Author(s):  
Xiao-Qing Cai ◽  
Bei Tian ◽  
Jian-Nan Zhang ◽  
Zhi-Min Jin
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Functional Groups ◽  
High Probability ◽  
Internal Symmetry ◽  
Supramolecular Synthon ◽  
Π Interactions ◽  
Graph Set ◽  
Hydrogen Bonded

A fixed hydrogen-bonding motif with a high probability of occurring when appropriate functional groups are involved is described as a `supramolecular hydrogen-bonding synthon'. The identification of these synthons may enable the prediction of accurate crystal structures. The rare chiral hydrogen-bonding motifR53(10) was observed previously in a cocrystal of 2,4,6-trichlorophenol, 2,4-dichlorophenol and dicyclohexylamine. In the title solvated salt, 2C4H12N+·C6H3Cl2O−·(C6H3Cl2O−·C6H4Cl2O)·2C4H8O, five components, namely twotert-butylammonium cations, one 2,4-dichlorophenol molecule, one 2,4-dichlorophenolate anion and one 2,6-dichlorophenolate anion, are bound by N—H...O and O—H...O hydrogen bonds to form a hydrogen-bonded ring, with the graph-set motifR53(10), which is further associated with two pendant tetrahydrofuran molecules by N—H...O hydrogen bonds. The hydrogen-bonded ring has internal symmetry, with a twofold axis running through the centre of the 2,6-dichlorophenolate anion, and is isostructural with a previous and related structure formed from 2,4-dichlorophenol, dicyclohexylamine and 2,4,6-trichlorophenol. In the title crystal, helical columns are built by the alignment and twisting of the chiral hydrogen-bonded rings, along and across thecaxis, and successive pairs of rings are associated with each other through C—H...π interactions. Neighbouring helical columns are inversely related and, therefore, no chirality is sustained, in contrast to the previous case.

Comparison of hydrogen bonds and diverse weak interactions of the nitro group in 2-methyl-4-nitroanilinium nitrate, bisulfate and two hexafluoridosilicates: elementary graph-set approach

2016 ◽  
Vol 72 (6) ◽  
pp. 916-926 ◽  
Author(s):  
Marek Daszkiewicz ◽  
Agnieszka Mielcarek
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Nitro Group ◽  
Weak Interactions ◽  
Gradual Expansion ◽  
Graph Set ◽  
Mathematical Relations ◽  
Elementary Graph ◽  
Bonding Patterns

Crystal structures of (H2m4na)NO3(1), (H2m4na)HSO4(2), (H2m4na)2SiF6(3) and (H2m4na)2SiF6·2H2O (4), where 2m4na = 2-methyl-4-nitroaniline, are presented. Two layers of interactions occur in the structures, N—H...O/F hydrogen bonds and interactions with the nitro group. Although diverse, hydrogen-bonding patterns are compared with each other by means of interrelations among elementary graph-set descriptors and descriptors of hydrogen-bonding patterns. Using mathematical relations, the gradual expansion of the ring patterns was shown in the crystal structures. Parallel and perpendicular arranged nitro groups form weak π(N)NO2...π(O)NO2and π(N)NO2...ONO2interactions, respectively. The πNO2...πringinteraction has an impact to the stabilization of parallel oriented nitro groups. Generally, weak interactions constructed by the nitro group occur in the studied crystals as follows: π(N)NO2...π(O)NO2, πring...πring, C—H...O (1); π(N)NO2...π(O)NO2, π(N)NO2...ONO2(2); π(N)NO2...π(O)NO2, π(N)NO2...ONO2(3); C—H...O (4).

Concomitant polymorphs of 1,3-bis(3-fluorophenyl)urea

2016 ◽  
Vol 72 (9) ◽  
pp. 692-696 ◽  
Author(s):  
Christina A. Capacci-Daniel ◽  
Jeffery A. Bertke ◽  
Shoaleh Dehghan ◽  
Rupa Hiremath-Darji ◽  
Jennifer A. Swift
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Engineering ◽  
Structural Motif ◽  
Parallel Orientation ◽  
One Dimensional ◽  
Monoclinic Form ◽  
Engineering Studies ◽  
Hydrogen Bonded

Hydrogen bonding between urea functionalities is a common structural motif employed in crystal-engineering studies. Crystallization of 1,3-bis(3-fluorophenyl)urea, C13H10F2N2O, from many solvents yielded concomitant mixtures of at least two polymorphs. In the monoclinic form, one-dimensional chains of hydrogen-bonded urea molecules align in an antiparallel orientation, as is typical of many diphenylureas. In the orthorhombic form, one-dimensional chains of hydrogen-bonded urea molecules have a parallel orientation rarely observed in symmetrically substituted diphenylureas.

Iodo-nitroarenesulfonamides: interplay of hard and soft hydrogen bonds, I...O interactions and aromatic π...π stacking interactions

2001 ◽  
Vol 58 (1) ◽  
pp. 94-108 ◽  
Author(s):  
Craig J. Kelly ◽  
Janet M. S. Skakle ◽  
James L. Wardell ◽  
Solange M. S. V. Wardell ◽  
John N. Low ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Space Group ◽  
Rotation Axes ◽  
Π Stacking ◽  
Structural Database ◽  
A Chain

Molecules of N-(4′-iodophenylsulfonyl)-4-nitroaniline, 4-O2NC6H4NHSO2C6H4I-4′ (1), are linked by three-centre I...O2N interactions into chains and these chains are linked into a three-dimensional framework by C—H...O hydrogen bonds. In the isomeric N-(4′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4NHSO2C6H4NO2-4′ (2), the chains generated by the I...O2N interactions are again linked into a three-dimensional framework by C—H...O hydrogen bonds. Molecules of N,N-bis(3′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4N(SO2C6H4NO2-3′)2 (3), lie across twofold rotation axes in space group C2/c and they are linked into chains by paired I...O=S interactions: these chains are linked into sheets by a C—H...O hydrogen bond, and the sheets are linked into a three-dimensional framework by aromatic π...π stacking interactions. In N-(4′-iodophenylsulfonyl)-3-nitroaniline, 3-O2NC6H4NHSO2C6H4I-4′ (4), there are R^2_2(8) rings formed by hard N—H...O=S hydrogen bonds and R^2_2(24) rings formed by two-centre I...nitro interactions, which together generate a chain of fused rings: the combination of a C—H...O hydrogen bond and aromatic π...π stacking interactions links the chains into sheets. Molecules of N-(4′-iodophenylsulfonyl)-4-methyl-2-nitroaniline, 4-CH3-2-O2NC6H3NHSO2C6H4I-4′ (5), are linked by N—H...O=S and C—H...O(nitro) hydrogen bonds into a chain containing alternating R^2_2(8) and R^2_2(10) rings, but there are no I...O interactions of either type. There are two molecules in the asymmetric unit of N-(4′-iodophenylsulfonyl)-2-nitroaniline, 2-O2NC6H4NHSO2C6H4I-4′ (6), and the combination of an I...O=S interaction and a hard N—H...O(nitro) hydrogen bond links the two types of molecule to form a cyclic, centrosymmetric four-component aggregate. C—H...O hydrogen bonds link these four-molecule aggregates to form a molecular ladder. Comparisons are made with structures retrieved from the Cambridge Structural Database.

scholarly journals Crystal structures of three 3,4,5-trimethoxybenzamide-based derivatives

2016 ◽  
Vol 72 (5) ◽  
pp. 675-682 ◽  
Author(s):  
Ligia R. Gomes ◽  
John Nicolson Low ◽  
Catarina Oliveira ◽  
Fernando Cagide ◽  
Fernanda Borges
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Methoxy Group ◽  
Combined Effect ◽  
Donor Group ◽  
Methoxy Substituent ◽  
A Chain ◽  
Benzamide Derivatives

The crystal structures of three benzamide derivatives,viz. N-(6-hydroxyhexyl)-3,4,5-trimethoxybenzamide, C16H25NO5, (1),N-(6-anilinohexyl)-3,4,5-trimethoxybenzamide, C22H30N2O4, (2), andN-(6,6-diethoxyhexyl)-3,4,5-trimethoxybenzamide, C20H33NO6, (3), are described. These compounds differ only in the substituent at the end of the hexyl chain and the nature of these substituents determines the differences in hydrogen bonding between the molecules. In each molecule, them-methoxy substituents are virtually coplanar with the benzyl ring, while thep-methoxy substituent is almost perpendicular. The carbonyl O atom of the amide rotamer istransrelated with the amidic H atom. In each structure, the benzamide N—H donor group and O acceptor atoms link the molecules intoC(4) chains. In1, a terminal –OH group links the molecules into aC(3) chain and the combined effect of theC(4) andC(3) chains is a ribbon made up of screw relatedR22(17) rings in which the ...O—H... chain lies in the centre of the ribbon and the trimethoxybenzyl groups forms the edges. In2, the combination of the benzamideC(4) chain and the hydrogen bond formed by the terminal N—H group to an O atom of the 4-methoxy group link the molecules into a chain ofR22(17) rings. In3, the molecules are linked only byC(4) chains.

Hydrogen-bonding patterns in the cocrystal 2,4-diamino-6-phenyl-1,3,5-triazine–sorbic acid (1/1)

2007 ◽  
Vol 63 (11) ◽  
pp. o4450-o4451 ◽  
Author(s):  
Kaliyaperumal Thanigaimani ◽  
Packianathan Thomas Muthiah ◽  
Daniel E. Lynch
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Sorbic Acid ◽  
Carboxyl Group ◽  
Amino Group ◽  
Acid Molecule ◽  
Asymmetric Unit ◽  
Graph Set ◽  
Bonding Patterns

In the title cocrystal, C9H9N5·C6H8O2, the asymmetric unit contains one 2,4-diamino-6-phenyl-1,3,5-triazine molecule and a sorbic acid molecule. The triazine molecules are base-paired [with a graph set of R 2 2(8)] on either side via N—H...N hydrogen bonds, forming a supramolecular ribbon along the c axis. Each triazine molecule interacts with the carboxyl group of a sorbic acid molecule via N—H...O and O—H...N hydrogen bonds, generating R 2 2(8) motifs. The supramolecular ribbons are interlinked by N—H...O hydrogen bonds involving the 2-amino group of the triazine molecules and the carboxyl O atom of the sorbic acid molecule.

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.

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.

Sign in / Sign up

Export Citation Format

Share Document