Amide hydrogen bonding: control of the molecular and extended structures of two symmetrical pyridine‐2‐carboxamide derivatives

The crystal structures of two symmetrical pyridine‐2‐carboxamides, namely N,N′‐(propane‐1,3‐diyl)bis(pyridine‐2‐carboxamide), C₁₅H₁₆N₄O₂, (I), and N,N′‐(butane‐1,4‐diyl)bis(pyridine‐2‐carboxamide), C₁₆H₁₈N₄O₂, (II), exhibit extended hydrogen‐bonded sequences involving their amide groups. In (I), conventional bifurcated amide–carbonyl (N—H)...O hydrogen bonding favours the formation of one‐dimensional chains, the axes of which run parallel to [001]. Unconventional bifurcated pyridine–carbonyl C—H...O hydrogen bonding links adjacent one‐dimensional chains to form a `porous' three‐dimensional lattice with interconnected, yet unfilled, voids of 60.6 (2) ų which combine into channels that run parallel to, and include, [001]. 4% of the unit‐cell volume of (I) is vacant. Compound (II) adopts a Z‐shaped conformation with inversion symmetry, and exhibits an extended structure comprising one‐dimensional hydrogen‐bonded chains along [100] in which individual molecules are linked by complementary pairs of amide N—H...O hydrogen bonds. These hydrogen‐bonded chains interlock viaπ–π interactions between pyridine rings of neighbouring molecules to form sheets parallel with (010); each sheet is one Z‐shaped molecule thick and separated from the next sheet by the b‐axis dimension [7.2734 (4) Å].     

1,3‐Bis(ethylamino)‐2‐nitrobenzene, 1,3‐bis(n‐octylamino)‐2‐nitrobenzene and 4‐ethylamino‐2‐methyl‐1H‐benzimidazole

1,3‐Bis(ethylamino)‐2‐nitrobenzene, C₁₀H₁₅N₃O₂, (I), and 1,3‐bis(n‐octylamino)‐2‐nitrobenzene, C₂₂H₃₉N₃O₂, (II), are the first structurally characterized 1,3‐bis(n‐alkylamino)‐2‐nitrobenzenes. Both molecules are bisected though the nitro N atom and the 2‐C and 5‐C atoms of the ring by twofold rotation axes. Both display intramolecular N—H...O hydrogen bonds between the amine and nitro groups, but no intermolecular hydrogen bonding. The nearly planar molecules pack into flat layers ca 3.4 Å apart that interact by hydrophobic interactions involving the n‐alkyl groups rather than by π–π interactions between the rings. The intra‐ and intermolecular interactions in these molecules are of interest in understanding the physical properties of polymers made from them. Upon heating in the presence of anhydrous potassium carbonate in dimethylacetamide, (I) and (II) cyclize with formal loss of hydrogen peroxide to form substituted benzimidazoles. Thus, 4‐ethylamino‐2‐methyl‐1H‐benzimidazole, C₁₀H₁₃N₃, (III), was obtained from (I) under these reaction conditions. Compound (III) contains two independent molecules with no imposed internal symmetry. The molecules are linked into chains via N—H...N hydrogen bonds involving the imidazole rings, while the ethylamino groups do not participate in any hydrogen bonding. This is the first reported structure of a benzimidazole derivative with 4‐amino and 2‐alkyl substituents.     

Hydrogen‐bonded sheets in 2‐(2‐aminophenyl)‐1H‐benzimidazol‐3‐ium dihydrogen phosphate

The title salt, C₁₃H₁₂N₃⁺·H₂PO₄⁻, contains a nonplanar 2‐(2‐aminophenyl)‐1H‐benzimidazol‐3‐ium cation and two different dihydrogen phosphate anions, both situated on twofold rotation axes in the space group C2. The anions are linked by O—H...O hydrogen bonds into chains of R₂²(8) rings. The anion chains are linked by the cations, via hydrogen‐bonding complementarities and electrostatic interactions, giving rise to a sheet structure with alternating rows of organic cations and inorganic anions. Comparison of this structure with that of the pure amine reveals that the two compounds generate characteristically different sheet structures. The anion–anion chain serves as a template for the assembly of the cations, suggesting a possible application in the design of solid‐state materials.     

Intermolecular hydrogen bonding of the two independent mol­ecules of N‐3,5‐di­nitro­benzoyl‐l‐leucine

The title compound, C₁₃H₁₅N₃O₇, crystallizes as two independent mol­ecules which differ in their conformation. Intermolecular hydrogen bonding between the amide and carboxyl­ic acid groups as N—H?O=C interactions results in the formation of one‐dimensional chains with N?O distances of 2.967 (6) and 3.019 (6) Å. Neighbouring chains are linked by C=O?H—O interactions to form a two‐dimensional network, with O?O distances of 2.675 (6) and 2.778 (6) Å.     

Ethyl 4‐do­decyl‐3,5‐di­methyl‐1H‐pyrrole‐2‐carboxyl­ate: intermolecular interactions in an amphiphilic pyrrole

The title compound, C₂₁H₃₇NO₂, is a new amphiphilic pyrrole with a long hydro­carbon chain, which will be used as a precursor for the synthesis of Langmuir–Blodgett films of porphyrins. Molecules related by an inversion centre are joined head‐to‐head into dimers by strong N—H?O hydrogen bonds. The dimers pack in the structure with their carbon chains parallel to one another, thereby forming alternating layers of carbon chains and pyrrole heads. The structure is further stabilized by two weak C—H?π intermolecular interactions, thereby saturating the hydrogen‐bonding capability of the aromatic π‐electron clouds.     

Crystal packing of two 5‐substituted 2‐methyl‐4‐nitro‐1H‐imidazoles

Infinite chains connected by N—H...N hydrogen bonding form the primary packing motif in two closely related 4‐nitroimidazole derivatives, viz. 5‐bromo‐2‐methyl‐4‐nitro‐1H‐imidazole, C₄H₄BrN₃O₂, (I), and 2‐methyl‐4‐nitro‐1H‐imidazole‐5‐carbonitrile, C₅H₄N₄O₂, (II). These chains are almost identical, even though in (II) there are two symmetry‐independent molecules in the asymmetric unit. The differences appear in the interactions between the chains; in (I), there are strong C—Br...O halogen bonds, which connect the chains into a two‐dimensional grid, while in (II), the cyano group does not participate in specific interactions and the chains are only loosely connected into a three‐dimensional structure.     

4‐Ethynyl‐4‐hydroxycyclohexan‐1‐one and 4‐ethynyl‐4‐hydroxy‐2,3,5,6‐tetramethylcyclohexa‐2,5‐dien‐1‐one

The title compounds, C₈H₁₀O₂, (I), and C₁₂H₁₄O₂, (II), occurred as by‐products in the controlled synthesis of a series of bis­(gem‐alkynols), prepared as part of an extensive study of synthon formation in simple gem‐alkynol derivatives. The two 4‐(gem‐alkynol)‐1‐ones crystallize in space group P2₁/c, (I) with Z′ = 1 and (II) with Z′ = 2. Both structures are dominated by O—H?O=C hydrogen bonds, which form simple chains in the cyclo­hexane derivative, (I), and centrosymmetric dimers, of both symmetry‐independent mol­ecules, in the cyclo­hexa‐2,5‐diene, (II). These strong synthons are further stabilized by C[triple‐bond]C—H?O=C, C_methylene—H?O(H) and C_methyl—H?O(H) interactions. The direct intermolecular interactions between donors and acceptors in the gem‐alkynol group, which characterize the bis­(gem‐alkynol) analogues of (I) and (II), are not present in the ketone derivatives studied here.     

Probing the relationships between molecular conformation and intermolecular contacts in N,N‐dibenzyl‐N′‐(furan‐2‐carbonyl)thiourea

In the crystal structure of the title compound, C₂₀H₁₈N₂O₂S, molecules are linked by bifurcated C—H...O hydrogen‐bond interactions, giving rise to chains whose links are composed of alternating centrosymmetrically disposed pairs of molecules and characterized by R₂²(10) and R₂²(20) hydrogen‐bonding motifs. Also, N—H...S hydrogen bonds form infinite zigzag chains along the [010] direction, which exhibit the C(4) motif. Hirshfeld surface and fingerprint plots were used to explore the intermolecular interactions in the crystal structure. This analysis confirms the important role of C—H...O hydrogen bonds in the molecular conformation and in the crystal structure, providing a potentially useful tool for a full understanding of the intermolecular interactions in acylthiourea derivatives.     

4,6‐Dinitro‐N,N′‐di‐n‐octylbenzene‐1,3‐diamine, 4,6‐dinitro‐N,N′‐di‐n‐undecylbenzene‐1,3‐diamine and N,N′‐bis(2,4‐dinitrophenyl)octane‐1,8‐diamine

4,6‐Dinitro‐N,N′‐di‐n‐octylbenzene‐1,3‐diamine, C₂₂H₃₈N₄O₄, (I), 4,6‐dinitro‐N,N′‐di‐n‐undecylbenzene‐1,3‐diamine, C₂₈H₅₀N₄O₄, (II), and N,N′‐bis(2,4‐dinitrophenyl)octane‐1,8‐diamine, C₂₀H₂₄N₆O₈, (III), are the first synthetic meta‐dinitroarenes functionalized with long‐chain aliphatic amine groups to be structurally characterized. The intra‐ and intermolecular interactions in these model compounds provide information that can be used to help understand the physical properties of corresponding polymers with similar functionalities. Compounds (I) and (II) possess near‐mirror symmetry, with the octyl and undecyl chains adopting fully extended anti conformations in the same direction with respect to the ring. Compound (III) rests on a center of inversion that occupies the mid‐point of the central C—C bond of the octyl chain. The middle six C atoms of the chain form an anti arrangement, while the remaining two C atoms take hard turns almost perpendicular to the rest of the chain. All three molecules display intramolecular N—H...O hydrogen bonds between the amine and nitro groups, with the same NH group forming a bifurcated intermolecular hydrogen bond to the nitro O atom of an adjacent molecule. In each case, these interactions link the molecules into one‐dimensional molecular chains. In (I) and (II), these chains pack so that the pendant alkyl groups are interleaved parallel to one another, maximizing nonbonded C—H contacts. In (III), the alkyl groups are more isolated within the molecular chains and the primary nonbonded contacts between the chains appear to involve the nitro groups not involved in the hydrogen bonding.     

Glycosidic linkage,N‐acetyl side‐chain,and other structural properties of methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐β‐d‐mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.     

Hydro­gen‐bonded assemblages in 2,6‐bis­(hydroxy­methyl)‐4‐R‐phenol,with R = methyl,methoxy, phenoxy and 1‐(4‐methoxy­phenyl)‐1‐methyl­ethyl

Four derivatives of 2,6‐bis­(hydroxy­methyl)­phenol, with various para substituents, have been investigated; these are 2,6‐bis­(hydroxy­methyl)‐4‐methyl­phenol, C₉H₁₂O₃, (I), 2,6‐bis­(hydroxy­methyl)‐4‐methoxy­phenol, C₉H₁₂O₄, (II), 2,6‐bis­(hydroxy­methyl)‐4‐phenoxy­phenol, C₁₄H₁₄O₄, (III), and 2,6‐bis­(hydroxy­methyl)‐4‐[1‐(4‐methoxy­phenyl)‐1‐methyl­ethyl]­phenol, C₁₈H₂₂O₄, (IV). All four structures display hydrogen‐bonding networks resulting in sheets, with possible weak inter‐sheet π–π interactions in one case. In all the structures but one, the mol­ecules form centrosymmetric dimeric subunits held together by two hydrogen bonds between the hydroxy­methyl groups and, in two cases, by probable π–π interactions.     

Hydrogen bonding due to regioisomerism and its effect on the supramolecular architecture of diethyl 2‐[(2/4‐hydroxyanilino)methylidene]malonates

Diethyl 2‐[(2‐hydroxyanilino)methylidene]malonate, (I), and diethyl 2‐[(4‐hydroxyanilino)methylidene]malonate, (II), both C₁₄H₁₇NO₅, crystallize in centrosymmetric orthorhombic and monoclinic crystal systems, respectively. Compound (I) resides on a crystallographic mirror plane and displays bifurcated intramolecular hydrogen bonding, as well as intermolecular hydrogen bonding due to the position of the hydroxy group. Compound (II) has a single intramolecular N—H...O hydrogen bond. Infinite one‐dimensional head‐to‐tail chains formed by O—H...O hydrogen bonding are present in both structures. The molecular packing is mainly influenced by the intermolecular O—H...O interactions. Additionally, C—H...O interactions crosslinking the chains are found in (II).     

Syntheses,Structures, and Electrochemical Properties of Two Bis‐triazole‐bis‐amide‐based Copper(II) Pyridine‐2,3‐dicarboxylate Coordination Polymers

Abstract. Two bis‐triazole‐bis‐amide‐based copper(II) pyridine‐2,3‐dicarboxylate coordination polymers (CPs), [Cu(2,3‐pydc)(dtb)_0.5(DMF)] · 2H₂O ( 1 ) and [Cu(2,3‐pydc)(dth)_0.5(DMF)] · 2H₂O ( 2 ) (2,3‐H₂pydc = pyridine‐2,3‐dicarboxylic acid, dtb = N,N′‐bis(4H‐1,2,4‐triazole)butanamide, and dth = N,N′‐bis(4H‐1,2,4‐triazole)hexanamide), were synthesized under solvothermal conditions. CPs 1 and 2 show similar two‐dimensional (2D) structures. In 1 , the 2,3‐pydc anions bridge the Cu^II ions into a one‐dimensional (1D) chain. Such 1D chains are linked by the dtb ligands to form a 2D layer. The adjacent 2D layers are extended into a three‐dimensional (3D) supramolecular architecture by hydrogen‐bonding interactions. The electrochemical properties of 1 and 2 were investigated.     

A new two‐dimensional ZnII coordination polymer based on 1,3‐bis(2‐methyl‐1H‐imidazol‐1‐yl)benzene and 5‐nitrobenzene‐1,3‐dicarboxylic acid: synthesis,crystal structure and physical properties

A novel two‐dimensional (2D) Zn^II coordination framework, poly[[μ‐1,3‐bis(2‐methyl‐1H‐imidazol‐1‐yl)benzene](μ‐5‐nitrobenzene‐1,3‐dicarboxylato)zinc(II)], [Zn(C₈H₃NO₆)(C₁₄H₁₄N₄)]_n or [Zn(NO₂‐BDC)(1,3‐BMIB)]_n [1,3‐BMIB is 1,3‐bis(2‐methyl‐1H‐imidazol‐1‐yl)benzene and NO₂‐H₂BDC is 5‐nitrobenzene‐1,3‐dicarboxylic acid], has been prepared and characterized by IR, elemental analysis, thermal analysis and single‐crystal X‐ray diffraction. Single‐crystal X‐ray diffraction analysis revealed that the compound is a new 2D polymer with a 6³ topology parallel to the (10) crystal planes based on left‐handed helices, right‐handed helical NO₂‐BDC–Zn chains and [Zn₂(1,3‐BMIB)₂]_n clusters. In the crystal, adjacent layers are further connected by C—H…O hydrogen bonds, C—H…π interactions, C—O…π interactions and N—O…π interactions to form a three‐dimensional structure in the solid state. In addition, the compound exhibits strong fluorescence emissions in the solid state at room temperature.     

Hydrogen bonding in cyclic imides and amide carboxylic acid derivatives from the facile reaction of cis‐cyclohexane‐1,2‐carboxylic anhydride with o‐ and p‐anisidine and m‐ and p‐aminobenzoic acids

The structures of the open‐chain amide carboxylic acid rac‐cis‐2‐[(2‐methoxyphenyl)carbamoyl]cyclohexane‐1‐carboxylic acid, C₁₅H₁₉NO₄, (I), and the cyclic imides rac‐cis‐2‐(4‐methoxyphenyl)‐3a,4,5,6,7,7a‐hexahydroisoindole‐1,3‐dione, C₁₅H₁₇NO₃, (II), chiral cis‐3‐(1,3‐dioxo‐3a,4,5,6,7,7a‐hexahydroisoindol‐2‐yl)benzoic acid, C₁₅H₁₅NO₄, (III), and rac‐cis‐4‐(1,3‐dioxo‐3a,4,5,6,7,7a‐hexahydroisoindol‐2‐yl)benzoic acid monohydrate, C₁₅H₁₅NO₄·H₂O, (IV), are reported. In the amide acid (I), the phenylcarbamoyl group is essentially planar [maximum deviation from the least‐squares plane = 0.060 (1) Å for the amide O atom] and the molecules form discrete centrosymmetric dimers through intermolecular cyclic carboxy–carboxy O—H...O hydrogen‐bonding interactions [graph‐set notation R₂²(8)]. The cyclic imides (II)–(IV) are conformationally similar, with comparable benzene ring rotations about the imide N—C_ar bond [dihedral angles between the benzene and isoindole rings = 51.55 (7)° in (II), 59.22 (12)° in (III) and 51.99 (14)° in (IV)]. Unlike (II), in which only weak intermolecular C—H...O_imide hydrogen bonding is present, the crystal packing of imides (III) and (IV) shows strong intermolecular carboxylic acid O—H...O hydrogen‐bonding associations. With (III), these involve imide O‐atom acceptors, giving one‐dimensional zigzag chains [graph‐set C(9)], while with the monohydrate (IV), the hydrogen bond involves the partially disordered water molecule which also bridges molecules through both imide and carboxy O‐atom acceptors in a cyclic R₄⁴(12) association, giving a two‐dimensional sheet structure. The structures reported here expand the structural database for compounds of this series formed from the facile reaction of cis‐cyclohexane‐1,2‐dicarboxylic anhydride with substituted anilines, in which there is a much larger incidence of cyclic imides compared to amide carboxylic acids.     

cis‐Tetra­carbonyl­[(4‐fluoro­phenyl)di­phenyl­phosphine‐P](piperidine‐N)molybdenum(0)

The title mol­ecule, [Mo{P(C₆H₅)₂(C₆H₄F)}(HNC₅H₁₀)(CO)₄] or [Mo(C₁₈H₁₄FP)(C₅H₁₁N)(CO)₄], has irregular octahedral geometry about the Mo atom. The mol­ecules form a complicated hydrogen‐bonded network comprising C—H?O, C—H?F and C—H?π hydrogen bonds and π–π interactions. The C—H?π and π–π interactions form chains containing C—H?π/π–π dimers linked via C—H?π interactions and the chains are linked into a three‐dimensional network via C—H?O and C—H?F hydrogen bonds.     

The role of hydroxyl groups in interchain interactions in cellulose Iα and Iβ

Complex networks of hydrogen bonds within the cellulose I_α and I_β contribute greatly to cellulose's anisotropic physical properties such as material stiffness. The interchain hydrogen bonding interactions through hydroxyl groups are isolated in each of the three lattice planes of the adjacent chains within the unit cell of two allomorphs of natural cellulose. In our density function theory study with dispersion corrected Perdew–Burke–Ernzerhof (PBE‐D2) functional, these hydroxyl groups participate in strong hydrogen bonding interactions (?24.8 and ?24.8 kcal/mol for cellulose I_α and I_β, respectively) in the side‐to‐side lattice plane. Unexpectedly, the hydroxyl groups also participate significantly in hydrogen bonding interactions (?11.0 and ?12.4 kcal/mol for cellulose I_α and I_β, respectively) in one of the diagonal lattice planes in both cellulose I_α and I_β. Both PM7 and PBE‐D2 method predict that the overall interaction is asymmetric and stronger in the right diagonal lattice plane. While hydrogen bonding interactions are strongest in side‐to‐side lattice plane as expected, the role of hydrogen bonding interactions for keeping the sheet together is more significant than previously thought.     

基于2,4′-二羧基二苯甲酮构筑的具有一维梯状链和一维隧道的三维超分子体系

采用水热法设计合成了两个新型三维超分子化合物H₂L·H₂O (1)和[Ag(bpy)₂]·HL·H₂O (2) (其中bpy=2,2'-联吡啶, H₂L=2,4′-二羧基二苯甲酮),晶体结构分析表明,它们均是通过氢键采用不同的连接方式拓展而成。其中,化合物1 是2,4′-二羧基二苯甲酮和水分子通过O–H···O氢键形成的一维梯状链扩展构筑的三维超分子体系;化合物2 则是2,4′-二羧基二苯甲酮和水分子通过两种氢键形成含有一维隧道的三维超分子体系。有趣的是,[Ag(bpy)₂]⁺ 阳离子通过π–π 堆积和弱的Ag···Ag相互作用连在一起,进而以客体形式填充其中。荧光性质研究表明,由于存在bpy的螯合与堆积效应,化合物2相比配体和化合物1,其荧光发射峰发生红移。     

Benzyl N,N‐bis[2‐(pentafluoroanilino)ethyl]carbamate

The title compound, C₂₄H₁₇F₁₀N₃O₂, exhibits intramolecular N—H...O hydrogen bonding, as well as intramolecular Ar...Ar^F face‐to‐face interactions. The molecules are linked together by N—H...F—C hydrogen bonds, forming chains parallel to the a axis. Adjacent symmetry‐related chains are combined in double zipper‐like ribbons by parallel Ar^F...Ar^F offset π‐stacking interactions.     

Intermolecular interactions in the chiral and racemic forms of 3‐­hydroxy‐2‐(1‐oxoisoindolin‐2‐yl)­butanoic acid derived from threonine

The title compounds, C₁₂H₁₃NO₄, are derived from l ‐threonine and dl ‐threonine, respectively. Hydro­gen bonding in the chiral derivative, (2S/3R)‐3‐hydroxy‐2‐(1‐oxoisoindolin‐2‐yl)­butanoic acid, consists of O—H_acid?O_alkyl—H?O=C_indole chains [O?O 2.659 (3) and 2.718 (3) Å], Csp³—H?O and three C—H?π_arene interactions. In the (2R,3S/2S,3R) racemate, conventional carboxylic acid hydrogen bonding as cyclical (O—H?O=C)₂ [graph set R₂²(8)] is present, with O_alkyl—H?O=C_indole, Csp³—H?O and C—H?π_arene interactions. The COOH group geometry differs between the two forms, with C—O, C=O, C—C—O and C—C=O bond lengths and angles of 1.322 (3) and 1.193 (3) Å, and 109.7 (2) and 125.4 (3)°, respectively, in the chiral structure, and 1.2961 (17) and 1.2210 (18) Å, and 113.29 (12) and 122.63 (13)°, respectively, in the racemate structure. The O—C=O angles of 124.9 (3) and 124.05 (14)° are similar. The differences arise from the contrasting COOH hydrogen‐bonding environments in the two structures.