(S)‐5‐Benzylimidazolidine‐2,4‐dione monohydrate

The crystal structure of the title compound, C₁₀H₁₀N₂O₂·H₂O, also known as l ‐5‐benzylhydantoin monohydrate, is described in terms of two‐dimensional supramolecular arrays built up from infinite chains assembled via N—H...O and O—H...O hydrogen bonds among the organic molecules and solvent water molecules, with graph‐set R³₃(10)C(5)C²₂(6). The hydrogen‐bond network is reinforced by stacking of the layers through C—H...π interactions.     

Phenyl‐ring rotational disorder in the two‐dimensional hydrogen‐bonded structure of the 1:1 proton‐transfer salt of the diazo‐dye precursor 4‐(phenyldiazenyl)aniline (aniline yellow) with l‐tartaric acid

In the structure of the 1:1 proton‐transfer compound from the reaction of l ‐tartaric acid with the azo‐dye precursor aniline yellow [4‐(phenyldiazenyl)aniline], namely 4‐(phenyldiazenyl)anilinium (2R,3R)‐3‐carboxy‐2,3‐dihydroxypropanoate, C₁₂H₁₂N₃⁺·C₄H₅O₆⁻, the asymmetric unit contains two independent 4‐(phenyldiazenyl)anilinium cations and two hydrogen l ‐tartrate anions. The structure is unusual in that all four phenyl rings of the two cations have identical rotational disorder with equal occupancy of the conformations. The two hydrogen l ‐tartrate anions form independent but similar chains through head‐to‐tail carboxyl–carboxylate O—H...O hydrogen bonds [graph set C(7)], which are then extended into a two‐dimensional hydrogen‐bonded sheet structure through hydroxy O—H...O hydrogen‐bonded links. The anilinium groups of the 4‐(phenyldiazenyl)anilinium cations are incorporated into the sheets and also provide internal hydrogen‐bonded extensions, while their aromatic tails are layered in the structure without significant association except for weak π–π interactions [minimum ring centroid separation = 3.844 (3) Å]. The hydrogen l ‐tartrate residues of both anions exhibit the common short intramolecular hydroxy–carboxylate O—H...O hydogen bonds. This work provides a solution to the unusual disorder problem inherent in the structure of this salt, as well as giving another example of the utility of the hydrogen tartrate anion in the generation of sheet substructures in molecular assembly processes.     

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.     

The peptide NCbz‐Val‐Tyr‐OMe and aromatic π–π interactions

The peptide N‐benzyloxycarbonyl‐L‐valyl‐L‐tyrosine methyl ester or NCbz‐Val‐Tyr‐OMe (where NCbz is N‐benzyloxycarbonyl and OMe indicates the methyl ester), C₂₃H₂₈N₂O₆, has an extended backbone conformation. The aromatic rings of the Tyr residue and the NCbz group are involved in various attractive intra‐ and intermolecular aromatic π–π interactions which stabilize the conformation and packing in the crystal structure, in addition to N—H...O and O—H...O hydrogen bonds. The aromatic π–π interactions include parallel‐displaced, perpendicular T‐shaped, perpendicular L‐shaped and inclined orientations.     

The monohydrates of the four polar dipeptides l‐seryl‐l‐asparagine,l‐seryl‐l‐tyrosine,l‐tryptophanyl‐l‐serine and l‐tyrosyl‐l‐tryptophan

The crystal structures of the four dipeptides l ‐seryl‐l ‐asparagine monohydrate, C₇H₁₃N₃O₅·H₂O, l ‐seryl‐l ‐tyrosine monohydrate, C₁₂H₁₆N₂O₅·H₂O, l ‐tryptophanyl‐l ‐serine monohydrate, C₁₄H₁₇N₃O₄·H₂O, and l ‐tyrosyl‐l ‐tryptophan monohydrate, C₂₀H₂₁N₃O₄·H₂O, are dominated by extensive hydrogen‐bonding networks that include cocrystallized solvent water molecules. Side‐chain conformations are discussed on the basis of previous observations in dipeptides. These four dipeptide structures greatly expand our knowledge on dipeptides incorporating polar residues such as serine, asparagine, threonine, tyrosine and tryptophan.     

(2S)‐1‐Carbamoylpyrrolidine‐2‐carboxylic acid

In the title compound, also known as N‐carbamoyl‐l ‐proline, C₆H₁₀N₂O₃, the pyrrolidine ring adopts a half‐chair conformation, whereas the carboxyl group and the mean plane of the ureide group form an angle of 80.1 (2)°. Molecules are joined by N—H...O and O—H...O hydrogen bonds into cyclic structures with graph‐set R²₂(8), forming chains in the b‐axis direction that are further connected via N—H...O hydrogen bonds into a three‐dimensional network.     

Redetermination of 6‐amino‐5‐formyl‐1,3‐dimethyluracil monohydrate at 120 K: a polarized molecular structure and two interwoven hydrogen‐bonded frameworks

The title compound [systematic name: 6‐amino‐5‐formyl‐1,3‐dimethylpyrimidine‐2,4(1H,3H)‐dione monohydrate], C₇H₉N₃O₃·H₂O, has been reexamined at 120 K. The improved precision of the intramolecular dimensions provides evidence for a polarized molecular–electronic structure, and the molecular components are linked by one N—H...O and two O—H...O hydrogen bonds into two interwoven three‐dimensional frameworks, which are weakly linked by the longer component of a three‐centre N—H...(O)₂ hydrogen bond.     

An unusual conformation of gabapentin (Gpn) in Pyr‐Gpn‐NH‐NH‐Pyr stabilized by weak interactions

The crystal structure of N‐[(1‐{2‐oxo‐2‐[2‐(pyrazin‐2‐ylcarbonyl)hydrazin‐1‐yl]ethyl}cyclohexyl)methyl]pyrazine‐2‐carboxamide monohydrate (Pyr‐Gpn‐NN‐NH‐Pyr·H₂O), C₁₉H₂₃N₇O₃·H₂O, reveals an unusual trans–gauche (tg⁻) conformation for the gabapentin (Gpn) residue around the C^γ—C^β (θ₁) and C^β—C^α (θ₂) bonds. The molecular conformation is stabilized by intramolecular N—H...N hydrogen bonds and weak C—H...O interactions. The packing of the molecules in the crystal lattice shows a network of strong N—H...O and O—H...O hydrogen bonds together with weak C—H...O and π–π inteactions.     

l‐Cysteinium semioxalate

The title salt, C₃H₈NO₂⁺·C₂HO₄⁻, formed between l ‐cysteine and oxalic acid, was studied as part of a comparison of the structures and properties of pure amino acids and their cocrystals. The structure of the title salt is very different from that formed by oxalic acid and equivalent amounts of d ‐ and l ‐cysteine molecules. The asymmetric unit contains an l ‐cysteinium cation and a semioxalate anion. The oxalate anion is only singly deprotonated, in contrast with the double deprotonation in the crystal structure of bis(dl ‐cysteinium) oxalate. The oxalate anion is not planar. The conformation of the l ‐cysteinium cation differs from that of the neutral cysteine zwitterion in the monoclinic and orthorhombic polymorphs of l ‐cysteine, but is similar to that of the cysteinium cation in bis(dl ‐cysteinium) oxalate. The structure of the title salt can be described as a three‐dimensional framework formed by ions linked by strong O—H...O and N—H...O and weak S—H...O hydrogen bonds, with channels running along the crystallographic a axis containing the bulky –CH₂SH side chains of the cysteinium cations. The cations are only linked through hydrogen bonds via semioxalate anions. There are no direct cation–cation interactions via N—H...O hydrogen bonds between the ammonium and carboxylate groups, or via weaker S—H...S or S—H...O hydrogen bonds.     

Green chemistry synthesis: 2‐amino‐3‐[(E)‐(2‐pyridyl)methylideneamino]but‐2‐enedinitrile monohydrate and 5‐cyano‐2‐(2‐pyridyl)‐1‐(2‐pyridylmethyl)‐1H‐imidazole‐4‐carboxamide

The title compounds, C₁₀H₉N₅O·H₂O (L1·H₂O) and C₁₆H₁₂N₆O (L2), were synthesized by solvent‐free aldol condensation at room temperature. L1, prepared by grinding picolinaldehyde with 2,3‐diamino‐3‐isocyanoacrylonitrile in a 1:1 molar ratio, crystallized as a monohydrate. L2 was prepared by grinding picolinaldehyde with 2,3‐diamino‐3‐isocyanoacrylonitrile in a 2:1 molar ratio. By varying the conditions of crystallization it was possible to obtain two polymorphs, viz. L2‐I and L2‐II; both crystallized in the monoclinic space group P2₁/c. They differ in the orientation of one pyridine ring with respect to the plane of the imidazole ring. In L2‐I, this ring is oriented towards and above the imidazole ring, while in L2‐II it is rotated away from and below the imidazole ring. In all three molecules, there is a short intramolecular N—H...N contact inherent to the planarity of the systems. In L1·H₂O, this involves an amino H atom and the C=N N atom, while in L2 it involves an amino H atom and an imidazole N atom. In the crystal structure of L1·H₂O, there are N—H...O and O—H...O intermolecular hydrogen bonds which link the molecules to form two‐dimensional networks which stack along [001]. These networks are further linked via intermolecular N—H...N(cyano) hydrogen bonds to form an extended three‐dimensional network. In the crystal structure of L2‐I, symmetry‐related molecules are linked via N—H...N hydrogen bonds, leading to the formation of dimers centred about inversion centres. These dimers are further linked via N—H...O hydrogen bonds involving the amide group, also centred about inversion centres, to form a one‐dimensional arrangement propagating in [100]. In the crystal structure of L2‐II, the presence of intermolecular N—H...O hydrogen bonds involving the amide group results in the formation of dimers centred about inversion centres. These are linked via N—H...N hydrogen bonds involving the second amide H atom and the cyano N atom, to form two‐dimensional networks in the bc plane. In L2‐I and L2‐II, C—H...π and π–π interactions are also present.     

4,6‐Diaminopyrimidine‐2(1H)‐thione hemihydrate: a three‐dimensional hydrogen‐bonded framework

In the title compound, C₄H₆N₄S·0.5H₂O, there are two independent pyrimidinethione units, both of which lie across mirror planes in the space group Cmca. Hence, the H atoms bonded to the ring N atoms in each molecule are disordered over two symmetry‐related sites, each having an occupancy of 0.5. The water molecule lies across a twofold rotation axis parallel to [010]. The molecular components of (I) are linked by seven independent hydrogen bonds, of N—H...N, N—H...S, N—H...O and O—H...S types. A combination of disordered N—H...N hydrogen bonds and ordered N—H...S hydrogen bonds links the pyrimidinethione units into a continuous tubular structure. The water molecule acts as both a double donor of hydrogen bonds and a double acceptor, forming hydrogen bonds with components of four distinct pyrimidinethione tubes, thus linking these tubes into a three‐dimensional structure.     

Infinite ladder‐like chains organized into a three‐dimensional zigzag supramolecular architecture in 9‐deazahypoxanthine

The asymmetric unit of the title compound, C₆H₅N₃O, consists of discrete molecules of 9‐deazahypoxanthine [systematic name: 3H‐pyrrolo[3,2‐d]pyrimidin‐4(5H)‐one]. The structure displays N—H...O hydrogen bonding, connecting the molecules into centrosymmetric dimers. These dimers are then connected by N—H...N hydrogen bonds into a ladder‐like chain along the c axis. The secondary structure is stabilized by weak noncovalent contacts of the C—H...O and C—H...C types, as well as by π–π stacking interactions, which organize the structure into a zigzag architecture.     

Structural properties of D‐mannopyranosyl rings containing O‐acetyl side‐chains

The crystal structures of 1,2,3,4,6‐penta‐O‐acetyl‐α‐d ‐mannopyranose, C₁₆H₂₂O₁₁, and 2,3,4,6‐tetra‐O‐acetyl‐α‐d ‐mannopyranosyl‐(1→2)‐3,4,6‐tri‐O‐acetyl‐α‐d ‐mannopyranosyl‐(1→3)‐1,2,4,6‐tetra‐O‐acetyl‐α‐d ‐mannopyranose, C₄₀H₅₄O₂₇, were determined and compared to those of methyl 2,3,4,6‐tetra‐O‐acetyl‐α‐d ‐mannopyranoside, methyl α‐d ‐mannopyranoside and methyl α‐d ‐mannopyranosyl‐(1→2)‐α‐d ‐mannopyranoside to evaluate the effects of O‐acetylation on bond lengths, bond angles and torsion angles. In general, O‐acetylation exerts little effect on the exo‐ and endocyclic C—C and endocyclic C—O bond lengths, but the exocyclic C—O bonds involved in O‐acetylation are lengthened by ～0.02 Å. The conformation of the O‐acetyl side‐chains is highly conserved, with the carbonyl O atom either eclipsing the H atom attached to a 2°‐alcoholic C atom or bisecting the H—C—H bond angle of a 1°‐alcoholic C atom. Of the two C—O bonds that determine O‐acetyl side‐chain conformation, that involving the alcoholic C atom exhibits greater rotational variability than that involving the carbonyl C atom. These findings are in good agreement with recent solution NMR studies of O‐acetyl side‐chain conformations in saccharides. Experimental evidence was also obtained to confirm density functional theory (DFT) predictions of C—O and O—H bond‐length behavior in a C—O—H fragment involved in hydrogen bonding.     

O‐Ethyl and O‐methyl N‐(2,3,4,6‐tetra‐O‐acetyl‐β‐d‐glucopyranosyl)thiocarbamate

In both the title structures, O‐ethyl N‐(2,3,4,6‐tetra‐O‐acetyl‐β‐d ‐gluco­pyran­osyl)­thio­carbam­ate, C₁₇H₂₅NO₁₀S, and O‐methyl N‐(2,3,4,6‐tetra‐O‐acetyl‐β‐d ‐gluco­pyran­osyl)­thiocar­bam­ate, C₁₆H₂₃NO₁₀S, the hexo­pyran­osyl ring adopts the ⁴C₁ conformation. All the ring substituents are in equatorial positions. The acetoxy­methyl group is in a gauche–gauche conformation. The S atom is in a synperi­planar conformation, while the C—N—C—O linkage is antiperiplanar. N—H?O intermolecular hydrogen bonds link the mol­ecules into infinite chains and these are connected by C—H?O interactions.     

Tris(1H‐benzimidazol‐2‐yl­meth­yl)­amine–solvent adducts

The tris­(1H‐benzimidazol‐2‐yl­meth­yl)­amine (ntb) mol­ecule crystallizes in different solvent systems, resulting in two kinds of adduct, namely the monohydrate, C₂₄H₂₁N₇·H₂O or ntb·H₂O, (I), and the acetonitrile–methanol–water (1/0.5/1.5) solvate, C₂₄H₂₁N₇·C₂H₃N·0.5CH₄O·1.5H₂O or ntb·1.5H₂O·0.5MeOH·MeCN, (II). In both cases, ntb adopts a tripodal mode to form hydrogen bonds with a solvent water mol­ecule via two N—H⋯O and one O—H⋯N hydrogen bond. In (I), the ntb·H₂O adduct is further assembled into a two‐dimensional network by N—H⋯N and O—H⋯N hydrogen bonds, while in (II), a double‐stranded one‐dimensional chain structure is assembled via N—H⋯O and O—H⋯O hydrogen bonds, with the acetonitrile mol­ecules located inside the cavities of the chain structure.     

N‐(4‐Nitrobenzoyl)‐N′‐phenylhydrazine: a three‐dimensional hydrogen‐bonded framework

In the title compound (systematic name: N‐anilino‐4‐nitrobenzamide), C₁₃H₁₁N₃O₃, the molecules are linked into a complex three‐dimensional framework structure by a combination of two‐centre N—H...O and C—H...O hydrogen bonds and a three‐centre N—H...(O,N) hydrogen bond.     

Cocrystals of 6‐propyl‐2‐thiouracil: N—H...O versus N—H...S hydrogen bonds

In order to investigate the relative stability of N—H...O and N—H...S hydrogen bonds, we cocrystallized the antithyroid drug 6‐propyl‐2‐thiouracil with two complementary heterocycles. In the cocrystal pyrimidin‐2‐amine–6‐propyl‐2‐thiouracil (1/2), C₄H₅N₃·2C₇H₁₀N₂OS, (I), the `base pair' is connected by one N—H...S and one N—H...N hydrogen bond. Homodimers of 6‐propyl‐2‐thiouracil linked by two N—H...S hydrogen bonds are observed in the cocrystal N‐(6‐acetamidopyridin‐2‐yl)acetamide–6‐propyl‐2‐thiouracil (1/2), C₉H₁₁N₃O₂·2C₇H₁₀N₂OS, (II). The crystal structure of 6‐propyl‐2‐thiouracil itself, C₇H₁₀N₂OS, (III), is stabilized by pairwise N—H...O and N—H...S hydrogen bonds. In all three structures, N—H...S hydrogen bonds occur only within R₂²(8) patterns, whereas N—H...O hydrogen bonds tend to connect the homo‐ and heterodimers into extended networks. In agreement with related structures, the hydrogen‐bonding capability of C=O and C=S groups seems to be comparable.     

Hydrogen‐bonding patterns in three substituted N‐benzyl‐N‐(3‐tert‐butyl‐1‐phenyl‐1H‐pyrazol‐5‐yl)acetamides

The molecules of N‐(3‐tert‐butyl‐1‐phenyl‐1H‐pyrazol‐5‐yl)‐2‐chloro‐N‐(4‐methoxybenzyl)acetamide, C₂₃H₂₆ClN₃O₂, are linked into a chain of edge‐fused centrosymmetric rings by a combination of one C—H...O hydrogen bond and one C—H...π(arene) hydrogen bond. In N‐(3‐tert‐butyl‐1‐phenyl‐1H‐pyrazol‐5‐yl)‐2‐chloro‐N‐(4‐chlorobenzyl)acetamide, C₂₂H₂₃Cl₂N₃O, a combination of one C—H...O hydrogen bond and two C—H...π(arene) hydrogen bonds, which utilize different aryl rings as the acceptors, link the molecules into sheets. The molecules of S‐[N‐(3‐tert‐butyl‐1‐phenyl‐1H‐pyrazol‐5‐yl)‐N‐(4‐methylbenzyl)carbamoyl]methyl O‐ethyl carbonodithioate, C₂₆H₃₁N₃O₂S₂, are also linked into sheets, now by a combination of two C—H...O hydrogen bonds, both of which utilize the amide O atom as the acceptor, and two C—H...π(arene) hydrogen bonds, which utilize different aryl groups as the acceptors.     

Ethyl N‐[2‐(hydroxy­acetyl)­phenyl]­carbamate,ethyl N‐[2‐(hydroxy­acetyl)‐4‐iodo­phenyl]­carbamate and ethyl N‐[2‐(hydroxy­acetyl)‐4‐methyl­phenyl]­carbamate

In ethyl N‐[2‐(hydroxy­acetyl)phenyl]carbamate, C₁₁H₁₃NO₄, all of the non‐H atoms lie on a mirror plane in the space group Pnma; the mol­ecules are linked into simple chains by a single C—H⋯O hydrogen bond. The mol­ecules of ethyl N‐[2‐(hydroxy­acetyl)‐4‐iodo­phenyl]carbamate, C₁₁H₁₂INO₄, are linked into sheets by a combination of O—H⋯I and C—H⋯O hydrogen bonds and a dipolar I⋯O contact. Ethyl N‐­[2‐(hydroxy­acetyl)‐4‐methyl­phenyl]carbamate, C₁₂H₁₅NO₄, crystallizes with Z′ = 2 in the space group P; pairs of mol­ecules are weakly linked by an O—H⋯O hydrogen bond and these aggregates are linked into chains by two independent aromatic π–π stacking inter­actions.     

Polymorphism in 3‐acetyl‐4‐hydroxy‐2H‐chromen‐2‐one

A new polymorph (denoted polymorph II) of 3‐acetyl‐4‐hydroxy‐2H‐chromen‐2‐one, C₁₁H₈O₄, was obtained unexpectedly during an attempt to recrystallize the compound from salt–melted ice, and the structure is compared with that of the original polymorph (denoted polymorph I) [Lyssenko & Antipin (2001). Russ. Chem. Bull. 50 , 418–431]. Strong intramolecular O—H...O hydrogen bonds are observed equally in the two polymorphs [O...O = 2.4263 (13) Å in polymorph II and 2.442 (1) Å in polymorph I], with a slight delocalization of the hydroxy H atom towards the ketonic O atom in polymorph II [H...O = 1.32 (2) Å in polymorph II and 1.45 (3) Å in polymorph I]. In both crystal structures, the packing of the molecules is dominated and stabilized by weak intermolecular C—H...O hydrogen bonds. Additional π–π stacking interactions between the keto–enol hydrogen‐bonded rings stabilize polymorph I [the centres are separated by 3.28 (1) Å], while polymorph II is stabilized by interactions between α‐pyrone rings, which are parallel to one another and separated by 3.670 (5) Å.