A Combined Experimental and Computational Study of Halogen and Hydrogen Bonding in Molecular Salts of 5-Bromocytosine

Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical and pharmaceutical relevance of these compounds, six different crystals containing proton-transfer derivatives of 5-bromocytosine are prepared and analyzed in the solid-state by single crystal X-ray diffraction. All six compounds are organic salts, with proton transfer occurring to the N_imino atom of the pyridine ring. Experimental results are then complemented with Hirshfeld surface analysis to quantitively evaluate the contribution of different intermolecular interactions in the crystal packing. Furthermore, theoretical calculations, based on different arrangements of molecules extracted from the crystal structure determinations, are carried out to analyze the formation mechanism of halogen bonds (XBs) in these compounds and provide insights into the nature and strength of the observed interactions. The results show that the supramolecular architectures of the six molecular salts involve extensive classical intermolecular hydrogen bonds. However, in all but one proton-transfer adducts, weak to moderate XBs are revealed by C-Br^…O short contacts between the bromine atom in the fifth position, which acts as XB donor (electron acceptor). Moreover, the lone pair electrons of the oxygen atom of adjacent pyrimidine nucleobases and/or counterions or water molecules, which acts as XB acceptor (electron donor).

Short X···N Halogen Bonds With Hexamethylenetetraamine as the Acceptor

Hexamethylenetetramine (HMTA) and N-haloimides form two types of short (imide)X···N and X–X···N (X = Br, I) halogen bonds. Nucleophilic substitution or ligand-exchange reaction on the peripheral X of X–X···N with the chloride of N-chlorosuccinimide lead to Cl–X···N halogen-bonded complexes. The 1:1 complexation of HMTA and ICl manifests the shortest I···N halogen bond [2.272(5) Å] yet reported for an HMTA acceptor. Two halogen-bonded organic frameworks are prepared using 1:4 molar ratio of HMTA and N-bromosuccinimide, each with a distinct channel shape, one possessing oval and the other square grid. The variations in channel shapes are due to tridentate and tetradentate (imide)Br···N coordination modes of HMTA. Density Functional Theory (DFT) studies are performed to gain insights into (imide)X···N interaction strengths (ΔEint). The calculated ΔEint values for (imide)Br···N (−11.2 to −12.5 kcal/mol) are smaller than the values for (imide)I···N (−8.4 to −29.0 kcal/mol). The DFT additivity analysis of (imide)Br···N motifs demonstrates Br···N interaction strength gradually decreasing from 1:1 to 1:3 HMTA:N-bromosuccinimide complexes. Exceptionally similar charge density values ρ(r) for N–I covalent bond and I···N non-covalent bond of a (saccharin)N–I···N motif signify the covalent character for I···N halogen bonding.

Short X···N Halogen Bonds With Hexamethylenetetraamine as the Acceptor

Hexamethylenetetramine (HMTA) and N-haloimides form two types of short (imide)X···N and X-X···N (X = Br, I) halogen bonds. Nucleophilic substitution or ligand-exchange reaction on the peripheral X of X-X···N with the chloride of N-chlorosuccinimide lead to Cl-X···N halogen-bonded complexes. The 1:1 complexation of HMTA and ICl manifests the shortest I···N halogen bond [2.272(5) Å] yet reported for an HMTA acceptor. Two halogen-bonded organic frameworks are prepared using 1:4 molar ratio of HMTA and N-bromosuccinimide, each with a distinct channel shape, one possessing oval and the other square grid. The variations in channel shapes are due to tridentate and tetradentate (imide)Br···N coordination modes of HMTA. Density Functional Theory (DFT) studies are performed to gain insights into (imide)X···N interaction strengths (ΔE_int). The calculated ΔE_int values for (imide)Br···N (-11.2 to -12.5 kcal/mol) are smaller than the values for (imide)I···N (-8.4 to -29.0 kcal/mol). The DFT additivity analysis of (imide)Br···N motifs demonstrates Br···N interaction strength gradually decreasing from 1:1 to 1:3 HMTA:N-bromosuccinimide complexes. Exceptionally similar charge density values ρ(r) for N-I covalent bond and I···N non-covalent bond of a (saccharin)N-I···N motif signify the covalent character for I···N halogen bonding.

Crystal structure and Hirshfeld surface analysis of a third polymorph of 2,6-di-meth-oxy-benzoic acid

A third monoclinic polymorph of 2,6-di­meth­oxy­bnzoic acid is reported. The acidic O—H bond of the carboxyl group adopts a synplanar conformation.

A third crystalline form of the title compound, C₉H₁₀O₄, crystallizing in the centrosymmetric monoclinic space group P2₁/c, has been identified during screening for co-crystals. The asymmetric unit comprises a non-planar independent mol­ecule with a synplanar conformation of the OH group. The sterically bulky o-meth­oxy substituents force the carb­oxy group to be twisted away from the plane of the benzene ring by 74.10 (6)°. The carb­oxy group exhibits the acidic H atom disordered over two sites between two O atoms. A similar situation has been found for the second tetra­gonal polymorph reported [Portalone (2011 ▸). Acta Cryst. E67, o3394–o3395], in which mol­ecules with the OH group in a synplanar conformation form dimeric units via strong O—H⋯O hydrogen bonds. In contrast, in the first ortho­rhom­bic form reported [Swaminathan et al. (1976 ▸). Acta Cryst. B32, 1897–1900; Bryan & White (1982 ▸). Acta Cryst. B38, 1014–1016; Portalone (2009 ▸). Acta Cryst. E65, o327–o328], the mol­ecular components do not form conventional dimeric units, as an anti­planar conformation adopted by the OH group favors the association of mol­ecules in chains stabilized by linear O—H⋯O hydrogen bonds.

Experimental results and computational insight into sequential reactions of β-(2-aminophenyl)-α,β-ynones with aryl isocyanates/benzoyl isothiocyanate

The selective formation of quinazoline vs. benzoxazine  and benzothiazine derivatives from β-(2-aminophenyl)-α,β-ynones and aryl isocyanates/benzoyl isothiocyanate was explored. DFT calculations provide a plausible rationale.

6-Methyluracil: a redetermination of polymorph (II)

6-Methyluracil, C5H6N2O2, exists in two crystalline phases: form (I), monoclinic, space group P21/c [Reck et al. (1988). Acta Cryst. A44, 417–421] and form (II), monoclinic, space group C2/c [Leonidov et al. (1993). Russ. J. Phys. Chem. 67, 2220–2223]. The structure of polymorph (II) has been redetermined providing a significant increase in the precision of the derived geometric parameters. In the crystal, molecules form ribbons approximately running parallel to the c-axis direction through N—H...O hydrogen bonds. The radical differences observed between the crystal packing of the two polymorphs may be responsible in form (II) for an increase in the contribution of the polar canonical forms C—(O−)=N—H+ relative to the neutral canonical form C(=O)—N—H induced by hydrogen-bonding interactions.

Synthesis and Anti-Rhinovirus Properties of Fluoro-Substituted Flavonoids

Fluoro-substituted flavones and 2-styrykhromones, related to natural and synthetic flavonoids previously described, were prepared, characterized and tested for anti-rhinovirus activity. Structural elucidation of the new compounds was performed by IR, NMR spectra and X-ray crystal structure analysis for 6-fluoro-3-hydroxy-2-styrylchromone. The antiviral potency was evaluated by a plaque reduction assay in HeLa cell cultures infected with rhinoviruses 1B and 14, selected as representative serotypes for viral groups B and A of human rhinoviruses, respectively. In comparison with results previously obtained, the introduction of the fluorine atom seems to exert a positive influence on the activity against serotype 14 while counteracting the effect against serotype 1B.

(Chalcogen)semicarbazones and their cobalt complexes differentiate HL-60 myeloid leukaemia cells and are cytotoxic towards tumor cell lines

Cobalt complexes with semi- and thiosemicarbazones of 8-quinolinecarboxaldehyde have been synthesized and characterized by X-ray diffraction analysis. These novel complexes and a previously synthesized cobalt complex with a selenium-based selenosemicarbazone ligand showed myeloid differentiation activity on all trans retinoic acid resistant HL-60 acute myeloid leukaemia cells. They also showed varying levels of cytotoxicity on five human tumor cell lines: cervix carcinoma cells (HeLa), lung adenocarcinoma cells (A549), colorectal adenocarcinoma cells (LS-174), breast carcinoma cells (MDA-MB-361), and chronic myeloid leukaemia (K562) as well as one normal human cell line: fetal lung fibroblast cells (MRC-5). Leukaemia differentiation was most strongly induced by a metal-free oxygen ligand and the selenium ligand, whilst the latter and the cobalt(ii) complex with an oxygen ligand showed the strongest dose-dependent cytotoxic activity. In four out of five investigated tumor cell lines, it was of the same order of magnitude as cisplatin. These best compounds, however, had lower toxicity on non-transformed MRC-5 cells than cisplatin.

Pro-apoptotic and pro-differentiation induction by 8-quinolinecarboxaldehyde selenosemicarbazone and its Co(iii) complex in human cancer cell lines

The ligand initiated reprogramming of cancer stem cells phenotype in AsPC-1 cells. The complex digested plasmid DNA which might be the cause of its cytotoxic activity.

Structural Studies of Benzene Derivatives, XII [1]. The Molecular Structure of 3,5-Dimethylbenzoic Acid in the Crystal, and a Comparison with the Gas Phase Structure of Related Molecules

The molecular structure of 3,5-dimethylbenzoic acid has been accurately determ ined by X-ray crystallography. The crystals are monoclinic, space group P21/n, with a = 8.165(2), b = 6.992(1), c = 14.422(2) Å , β = 93.21(2)°, Z = 4. The structure has been refined by full-matrix least-squares techniques to R = 0.0415 on 1662 counter intensities. The carbon skeleton of the benzene ring has C2v symmetry within experimental error. The six aromatic C-C bond distances do not differ significantly from each other; some of the internal ring angles, however, deviate from 120° by as much as 2°. After correction for systematic effects, such as the asphericities of the electron density distribution and the libration of the molecule in the crystal, the mean aromatic C-C bond distance is 1.401(1) Å , and the two independent C-CH3 bond distances are 1.509 and 1.511(3) Å. These values are in outstanding agreement with the corresponding rg distances measured by gas electron diffraction in p-xylene (1.400±0.003 Å and 1.512±0.003 Å , respectively) and mesitylene (1.401 ±0.002 A and 1.509±0.002 Å, respectively). The deviations of the ring angles from 120° are interpreted fairly well as arising from the superposition of separate, independent angular distortions from each substituent.

Effects of Through-Conjugation on the Molecular Structure of p-Nitroaniline [1]

A new X-ray diffraction study of p-nitroaniline shows that through-conjugation has highly significant effects on the geometry of the molecule, as compared to aniline and p-nitrobenzoic acid. The effects include a moderate decrease of the internal angles of the ring at substituted carbons, with respect to values derived by superimposing independent angular distortions from each substituent.

Molecular Structures of p-Methylsulphonylbenzoic Acid and Methylphenylsulphone: Comparison of X-Ray and Electron Diffraction Results

The molecular structures of p-methylsulphonylbenzoic acid and methylphenylsulphone have been accurately determined by X-ray crystallography and gas electron diffraction, respectively. After correction for systematic effects, the geometry of the crystal molecule is seen to agree with that of the free molecule within a few thousandths of an Å unit for bond distances and a few tenths of a degree for bond angles. An exception is the S-Me bond distance, which is ca. 0.02 Å shorter in the crystal. The distortion of the benzene ring angles from 120°, an effect of the - SO2Me substituent, is virtually the same from both experiments

Supramolecular association in proton-transfer adducts containing benzamidinium cations. III. Three molecular salts of 3-methoxy-, 4-methoxy- and 3,4,5-trimethoxybenzoates with benzamidine

Three molecular salts, benzamidinium 3-methoxybenzoate, C7H9N2(+)·C8H7O3(-), (I), benzamidinium 4-methoxybenzoate, C7H9N2(+)·C8H7O3(-), (II), and benzamidinium 3,4,5-trimethoxybenzoate monohydrate, C7H9N2(+)·C10H11O5(-)·H2O, (III), were formed from the proton-transfer reactions of 3-methoxy, 4-methoxy- and 3,4,5-trimethoxybenzoic acids with benzamidine (benzenecarboximidamide, benzam). Monoclinic salts (I) and (II) have a 1:1 ratio of cation to anion. In monoclinic salt (III), two cation-anion pairs and two water molecules constitute the asymmetric unit. In all three molecular salts, the amidinium fragments and the carboxylate groups are completely delocalized, and the delocalization favours the aggregation of the molecular components into nonplanar dimers with an R(2)(2)(8) graph-set motif by N(+)-H···O(-) (±) charge-assisted hydrogen bonding (CAHB). Of the three molecular salts, (I) and (II) show similar conformations of the anionic components and exhibit bidimensional isostructurality, which consists of alternating R(2)(2)(8) and R(6)(4)(16) rings resulting in a corrugated sheet propagated parallel to the crystallographic ab plane. In molecular salt (III), the R(2)(2)(8) synthon is retained but the supramolecular structure is different, due to the presence of three bulky methoxy substituents and a water molecule. The structures reported here further demonstrate the robustness of R(2)(2)(8) hydrogen-bonded synthons having the benzamidinium cation as a building block, whereas N(+)-H···O(-) hydrogen bonds external to the salt bridge contribute to the overall structure organization.

Benzamidinium 2-meth-oxy-benzoate

The title mol­ecular salt, C₇H₉N₂^+.C₈H₇O₃⁻, was synthesized by reaction between benzamidine (benzene­carboximidamide) and 2-meth­oxy­benzoic acid. In the cation, the amidinium group has two similar C—N bonds [1.3070 (17) and 1.3145 (16) Å] and is almost coplanar with the benzene ring, making a dihedral angle of 5.34 (12)°. In the anion, the meth­oxy substituent forces the carboxyl­ate group to be twisted by 69.45 (6)° with respect to the plane of the aromatic fragment. In the crystal, the components are connected by two N⁺—H⋯O⁻ (±)CAHB (charge-assisted hydrogen bonds), forming centrosymmetric ionic dimers with graph-set motif R₂²(8). These ionic dimers are then joined in ribbons running along the b-axis direction by another R₄²(8) motif involving the remaining N⁺—H⋯O⁻ hydrogen bonds. Remarkably, at variance with the well known carb­oxy­lic dimer R₂²(8) motif, the carboxyl­ate–amidinium pair is not planar, the dihedral angle between the planes defined by the CN₂⁺ and CO₂⁻ atoms being 18.57 (12)°.

Cytosinium orotate dihydrate

The title compound, C₄H₆N₃O⁺·C₅H₃N₂O₄⁻·2H₂O or Cyt⁺·Or⁻·2H₂O, was synthesized by a reaction between cytosine (4-amino-2-hy­droxy­pyrimidine, Cyt) and orotic acid (2,4-dihy­droxy-6-carb­oxy­pyrimidine, Or) in aqueous solution. The two ions are joined by two N⁺—H⋯O⁻ (±)-(CAHB) hydrogen bonds, forming a dimer with graph-set motif R₂²(8). In the crystal, the ion pairs of the asymmetric unit are joined by four N—H⋯O inter­actions to adjacent dimers, forming hydrogen-bonded rings with R₂²(8) graph-set motif in a two-dimensional network. The formation of the three-dimensional array is facilitated by water mol­ecules, which act as bridges between structural sub-units linked in R₃²(8) and R₃²(7) hydrogen-bonded rings. The orotate anion is essentially planar, as the dihedral angle between the planes defined by the carboxylate group and the uracil fragment is 4.0 (4)°.

4-Methoxybenzamidinium bromide

The title salt, C₈H₁₁N₂O⁺·Br⁻, was synthesized by the reaction between 4-meth­oxy­benzamidine (4-amidino­anisole) and hydro­bromic acid. In the cation, the amidinium group has two similar C—N bonds [1.304 (2) and 1.316 (2) Å], and its plane forms a dihedral angle of 31.08 (5)° with the benzene ring. The ions are associated in the crystal into a three-dimension hydrogen-bonded supra­molecular network featuring N—H⁺⋯Br⁻ inter­actions.

4-Methoxybenzamidinium nitrate

The title salt, C₈H₁₁N₂O⁺·NO₃⁻, was synthesized by a reaction between 4-meth­oxy­benzamidine (4-amidino­anisole) and nitric acid. The asymmetric unit comprises a non-planar 4-meth­oxy­benzamidinium cation and a nitrate anion. In the cation, the amidinium group has two similar C—N bond lengths [1.302 (3) and 1.313 (3) Å] and its plane forms a dihedral angle of 32.66 (5)° with the mean plane of the benzene ring. The nitrate–amidinium ion pair is not planar, as the dihedral angle between the planes defined by the CN₂⁺ and NO₃⁻ units is 19.28 (6)°. The ionic components are associated in the crystal via N—H⋯O hydrogen bonds, resulting in a three-dimensional network.

4-Meth-oxy-benzamidinium acetate

The title compound, C8H11N2O(+)·CH3CO2(-), was synthesized by a reaction between 4-meth-oxy-benzamidine (4-amidino-anisole) and acetic acid. In the cation, the amidinium group forms a dihedral angle of 11.65 (17)° with the mean plane of the benzene ring. The ionic components are associated in the crystal via N-H(+)⋯O(-) hydrogen bonds, resulting in a one-dimensional structure consisting of dimers and catemers and orientated approximately along the c axis.

4-Meth-oxy-benzamidinium hydrogen oxalate monohydrate

The title hydrated salt, C₈H₁₁N₂O⁺·C₂HO₄⁻·H₂O, was synthesized by a reaction of 4-meth­oxy­benzamidine (4-amidino­anisole) and oxalic acid in water solution. In the cation, the amidinium group forms a dihedral angle of 15.60 (6)° with the mean plane of the benzene ring. In the crystal, each amidinium unit is bound to three acetate anions and one water mol­ecule by six distinct N—H⋯O hydrogen bonds. The ion pairs of the asymmetric unit are joined by two N—H⋯O hydrogen bonds into ionic dimers in which the carbonyl O atom of the semi-oxalate anion acts as a bifurcated acceptor, thus generating an R¹₂(6) motif. These subunits are then joined through the remaining N—H⋯O hydrogen bonds to adjacent semi-oxalate anions into linear tetra­meric chains running approximately along the b axis. The structure is stabilized by N—H⋯O and O—H⋯O inter­molecular hydrogen bonds. The water mol­ecule plays an important role in the cohesion and the stability of the crystal structure being involved in three hydrogen bonds connecting two semi-oxalate anions as donor and a benzamidinium cation as acceptor.

Supramolecular association in proton-transfer adducts containing benzamidinium cations. II. Concomitant polymorphs of the molecular salt of 2,6-dimethoxybenzoic acid with benzamidine

Two concomitant polymorphs of the molecular salt formed by 2,6-dimethoxybenzoic acid, C(9)H(10)O(4) (Dmb), with benzamidine, C(7)H(8)N(2) (benzenecarboximidamide, Benzam) from water solution have been identified. Benzamidinidium 2,6-dimethoxybenzoate, C(7)H(9)N(2)(+)·C(9)H(9)O(4)(-) (BenzamH(+)·Dmb(-)), was obtained through protonation at the imino N atom of Benzam as a result of proton transfer from the acidic hydroxy group of Dmb. In the monoclinic polymorph, (I) (space group P2(1)/n), the asymmetric unit consists of two Dmb(-) anions and two monoprotonated BenzamH(+) cations. In the orthorhombic polymorph, (II) (space group P2(1)2(1)2(1)), one Dmb(-) anion and one BenzamH(+) cation constitute the asymmetric unit. In both polymorphic salts, the amidinium fragments and carboxylate groups are completely delocalized. This delocalization favours the aggregation of the molecular components of these acid-base complexes into nonplanar dimers with an R(2)(2)(8) graph-set motif via N(+)-H···O(-) charge-assisted hydrogen bonding. Both the monoclinic and orthorhombic forms exhibit one-dimensional isostructurality, as the crystal structures feature identical hydrogen-bonding motifs consisting of dimers and catemers.

4-Meth-oxy-benzamidinium chloride monohydrate

In the cation of the title compound, C(8)H(11)N(2)O(+)·Cl(-)·H(2)O, the C-N bonds of the amidinium group are identical within experiemental error [1.305 (2) and 1.304 (2) Å], and its plane forms a dihedral angle of 25.83 (8)° with the phenyl ring. The ionic components are associated in the crystal into polymeric hydrogen-bonded supra-molecular tapes stabilized by N-H(+)⋯Cl(-) and N-H(+)⋯Ow inter-molecular hydrogen bonds, and by Ow-H⋯Cl(-) inter-actions.

4-Meth-oxy-benzamidinium hydrogen sulfate

The title salt, C₈H₁₁N₂O⁺·HSO₄⁻, has been synthesized by the reaction between 4-meth­oxy­benzamidine and sulfuric acid. The asymmetric unit comprises a nonplanar 4-meth­oxy­benzamidinium cation and one hydrogen sulfate anion. In the cation, the amidinium group has two identical C—N bonds [1.306 (2) and 1.308 (2) Å], and its plane forms a dihedral angle of 6.49 (8)° with the mean plane of the benzene ring. The ionic components are associated in the crystal via N—H⁺⋯O⁻, resulting in chains running approximately along the b-axis direction whicg are interconnected by O—H⋯O⁻ hydrogen bonds.

4-Meth-oxy-benzamidinium 2,6-dimeth-oxy-benzoate

The title compound, C₈H₁₁N₂O⁺·C₉H₉O₄⁻, was synthesized by the reaction of 4-meth­oxy­benzamidine (4-amidino­anisole) and 2,6-dimeth­oxy­benzoic acid. The structure consists of non-planar pairs of hydrogen-bonded 4-meth­oxy­benzamidinium cations and 2,6-dimeth­oxy­benzoate anions. In the cation, the amidinium group is tilted by 27.94 (10)° with respect to the benzene ring. In the anion, the sterically bulky ortho-meth­oxy substituents force the carb­oxy­ate group to be twisted away from the plane of the benzene ring by 73.24 (6)°. The ions are further associated in the crystal into chains along the b-axis direction by inter­molecular N—H⋯O hydrogen bonds.

A new polymorph of 2,6-dimeth-oxy-benzoic acid

A new crystalline form of 2,6-dimeth­oxy­benzoic acid, C₉H₁₀O₄, crystallizing in a tetra­gonal unit cell has been identified during screening for co-crystals. The asymmetric unit comprises a non-planar independent mol­ecule with a synplanar conformation of the carb­oxy group. The sterically bulky o-meth­oxy substituents force the carb­oxy group to be twisted away from the plane of the benzene ring by 65.72 (15)°. The carb­oxy group is disordered over two sites about the C—C bond [as indicated by the almost equal C—O distances of 1.254 (3) and 1.250 (3) Å], the occupancies of the disordered carboxym H atoms being 0.53 (5) and 0.47 (5). In the known ortho­rhom­bic form reported by Swaminathan et al. [Acta Cryst. (1976), B32, 1897–1900], due to the anti­planar conformation adopted by the OH group, the mol­ecular components are associated in the crystal in chains stabilized by linear O—H⋯O hydrogen bonds. However, in the new tetra­gonal polymorph, mol­ecules form dimeric units via pairs of O—H⋯O hydrogen bonds between the carb­oxy groups.

Solid-phase molecular recognition of cytosine based on proton-transfer reaction. Part II. supramolecular architecture in the cocrystals of cytosine and its 5-Fluoroderivative with 5-Nitrouracil

BACKGROUND

Cytosine is a biologically important compound owing to its natural occurrence as a component of nucleic acids. Cytosine plays a crucial role in DNA/RNA base pairing, through several hydrogen-bonding patterns, and controls the essential features of life as it is involved in genetic codon of 17 amino acids. The molecular recognition among cytosines, and the molecular heterosynthons of molecular salts fabricated through proton-transfer reactions, might be used to investigate the theoretical sites of cytosine-specific DNA-binding proteins and the design for molecular imprint.

RESULTS

Reaction of cytosine (Cyt) and 5-fluorocytosine (5Fcyt) with 5-nitrouracil (Nit) in aqueous solution yielded two new products, which have been characterized by single-crystal X-ray diffraction. The products include a dihydrated molecular salt (CytNit) having both ionic and neutral hydrogen-bonded species, and a dihydrated cocrystal of neutral species (5FcytNit). In CytNit a protonated and an unprotonated cytosine form a triply hydrogen-bonded aggregate in a self-recognition ion-pair complex, and this dimer is then hydrogen bonded to one neutral and one anionic 5-nitrouracil molecule. In 5FcytNit the two neutral nucleobase derivatives are hydrogen bonded in pairs. In both structures conventional N-H...O, O-H...O, N-H+...N and N-H...N- intermolecular interactions are most significant in the structural assembly.

CONCLUSION

The supramolecular structure of the molecular adducts formed by cytosine and 5-fluorocytosine with 5-nitrouracil, CytNit and 5FcytNit, respectively, have been investigated in detail. CytNit and 5FcytNit exhibit widely differing hydrogen-bonding patterns, though both possess layered structures. The crystal structures of CytNit (Dpka = -0.7, molecular salt) and 5FcytNit (Dpka = -2.0, cocrystal) confirm that, at the present level of knowledge about the nature of proton-transfer process, there is not a strict correlation between the Dpka values and the proton transfer, in that the acid/base pka strength is not a definite guide to predict the location of H atoms in the solid state. Eventually, the absence in 5FcytNit of hydrogen bonds involving fluorine is in agreement with findings that covalently bound fluorine hardly ever acts as acceptor for available Brønsted acidic sites in the presence of competing heteroatom acceptors.

Testing a Variety of Electronic-Structure-Based Methods for the Relative Energies of 5-Formyluracil Crystals

The lattice energies of the experimental and several hypothetical crystal structures of the RNA base uracil derivative 5-formyluracil are calculated with a range of methods, based either on the electronic structure of the molecule or the lattice. The explicit modeling of the polarization within the crystal in the model intermolecular potential and the inclusion of an empirical dispersion correction to the periodic density functional energy (DFT-D2) were the only methods able to calculate the energy balance between different conformations, hydrogen bonding, and π-π stacking possibilities sufficiently accurately to give the observed structure as the most stable. Even these two methods underestimated the density of the room temperature structure, showing the need for improvement in the modeling of organic crystal structures.

Synthesis and evaluation of new endomorphin-2 analogues containing (Z)-alpha,beta-didehydrophenylalanine (Delta(Z)Phe) residues

New endomorphin-2 (EM-2) analogues incorporating (Z)-alpha,beta-didehydrophenylalanine (Delta(Z)Phe) in place of the native phenylalanine in EM-2 are reported. Tyr-Pro-Delta(Z)Phe-Phe-NH(2) {[Delta(Z)Phe(3)]EM-2} (1), Tyr-Pro-Phe-Delta(Z)Phe-NH(2) {[Delta(Z)Phe(4)]EM-2} (2), and Tyr-Pro-Delta(Z)Phe-Delta(Z)Phe-NH(2) {[Delta(Z)Phe(3,4)]EM-2}(3) have been synthesized, their opioid receptor binding affinities and tissue bioassay activities were determined, and their conformational properties were examined. Compound 2 shows high mu opioid receptor selectivity and mu agonist activity comparable to those of the native peptide. The conformation adopted in solution and in the crystal by N-Boc-Tyr-Pro-Delta(Z)Phe-Phe-NH(2) (8) is reported.

Supramolecular association in proton-transfer adducts containing benzamidinium cations. I. Four molecular salts with uracil derivatives

Four organic salts, namely benzamidinidium orotate (2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylate) hemihydrate, C(7)H(9)N(2)(+).C(5)H(3)N(2)O(4)(-).0.5H(2)O (BenzamH(+).Or(-)), (I), benzamidinium isoorotate (2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate) trihydrate, C(7)H(9)N(2)(+).C(5)H(3)N(2)O(4)(-).3H(2)O (BenzamH(+).Isor(-)), (II), benzamidinium diliturate (5-nitro-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate) dihydrate, C(7)H(9)N(2)(+).C(4)H(2)N(3)O(5)(-).2H(2)O (BenzamH(+).Dil(-)), (III), and benzamidinium 5-nitrouracilate (5-nitro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-ide), C(7)H(9)N(2)(+).C(4)H(2)N(3)O(4)(-) (BenzamH(+).Nit(-)), (IV), have been synthesized by a reaction between benzamidine (benzenecarboximidamide or Benzam) and the appropriate carboxylic acid. Proton transfer occurs to the benzamidine imino N atom. In all four acid-base adducts, the asymmetric unit consists of one tautomeric aminooxo anion (Or(-), Isor(-), Dil(-) and Nit(-)) and one monoprotonated benzamidinium cation (BenzamH(+)), plus one-half (which lies across a twofold axis), three and two solvent water molecules in (I), (II) and (III), respectively. Due to the presence of protonated benzamidine, these acid-base complexes form supramolecular synthons characterized by N(+)-H...O(-) and N(+)-H...N(-) (+/-)-charge-assisted hydrogen bonds (CAHB).

A redetermination of 2-nitro-benzoic acid

The crystal structure of the title compound, C₇H₅NO₄, was first reported by Kurahashi, Fukuyo & Shimada [(1967). Bull. Chem. Soc. Jpn, 40, 1296]. It has been re-examined, improving the precision of the derived geometric parameters. The asymmetric unit comprises a non-planar independent mol­ecule, as the nitro and the carb­oxy substituents force each other to be twisted away from the plane of the aromatic ring by 54.9 (2) and 24.0 (2)°, respectively. The mol­ecules form a conventional dimeric unit via centrosymmetric inter­molecular hydrogen bonds.

Redetermination of 2,6-dimethoxy-benzoic acid

The crystal structure of the title compound, C₉H₁₀O₄, was first reported by Swaminathan, Vimala & Lotter [Acta Cryst. (1976), B32, 1897–1900]. It has been re-examined, improving the precision of the derived geometric parameters. The asymmetric unit comprises a non-planar independent mol­ecule, as the meth­oxy substituents force the carb­oxy group to be twisted away from the plane of the aromatic ring by 56.12 (9)°. Due to the anti­planar conformation adopted by the OH group, the mol­ecular components do not form the conventional dimeric units, but are associated in the crystal in chains stabilized by linear O—H⋯O hydrogen bonds, involving the OH groups and the carbonyl O atoms, which form C(3) motifs.

Acetoguanamine N,N-dimethyl-formamide solvate

The structure of acetoguanamine (or 2,4-diamino-6-methyl-1,3,5-triazine) has been determined as the N,N-dimethyl-formamide solvate, C(4)H(7)N(5)·C(3)H(7)NO. The mol-ecular components are associated in the crystal structure to form ribbons stabilized by three N-H⋯N and one N-H⋯O hydrogen bonds which involve NH groups as donors and the N atoms of the heterocyclic ring and the carbonyl O atom of the solvent as acceptors.

Benzamidinium tetra-hydro-penta-borate sesquihydrate

The asymmetric unit of the title compound [systematic name: benzamidinium 3,3′,5,5′-tetra­hydr­oxy-1,1′-spirobi[2,4,6-trioxa-1,3,5-triboracyclo­hexa­ne](1−) sesquihydrate], C₇H₉N₂⁺·B₅H₄O₁₀⁻·1.5H₂O, is composed of two protonated benzamidinium cations, two tetra­hydro­penta­borate anions and three water mol­ecules of crystallization. The ions and water molecules are associated in the crystal structure by an extensive three-dimensional hydrogen-bonding network, which consists mainly of cation-to-anion N—H⋯O and anion-to-anion O—H⋯O hydrogen bonds.

Redetermination of 3-deaza-uracil

The crystal structure of the title compound, 4-hydr­oxy-2-pyridone, C₅H₅NO₂, which has been the subject of several determinations using X-rays and neutron diffraction, was first reported by Low & Wilson [Acta Cryst. (1983). C39, 1688–1690]. It has been redetermined, providing a significant increase in the precision of the derived geometric parameters. The asymmetric unit comprises a planar 4-enol tautomer having some degree of delocalization of π-electron density through the mol­ecule. In the crystal structure, the mol­ecules are connected into chains by two strong O—H⋯O and N—H⋯O hydrogen bonds between the OH and NH groups and the carbonyl O atom.

(3R,5S)-5(3)-Carboxy-3,4,5,6-tetrahydro-2H-1,4-thiazin-4-ium-3(5)-carboxylate

The molecule of the zwitterionic title compound, C₆H₉NO₄S, which lies on a mirror plane, shows a puckered chair conformation of the six-membered ring with the S and N atoms out of the mean plane of the other four C atoms by 0.929 (2) and 0.647 (2) Å, respectively. The ionized carboxyl group is equatorially oriented. The hydrogen-bonding network includes very short O—H⋯O [2.470 (2) Å] and N—H⋯S [3.471 (2) and 3.416 (2) Å] inter­molecular contacts.

Biguanidinium dichloride

The asymmetric unit of the title compound, C(2)H(9)N(5) (2+)·2Cl(-), is composed of one diprotonated biguanidinium cation and two chloride anions. The diprotonated cation consists of two planar halves twisted by 36.42 (6)°. The ions are associated in the crystal structure by extensive hydrogen bonding into a three-dimensional network; the diprotonated biguanidinium cation is hydrogen bonded to the chloride anions.

Redetermination of orotic acid monohydrate

The crystal structure of the title compound, which is also known as vitamin B(13) (systematic name: 2,6-dioxo-1,2,3,6-tetra-hydro-pyrimidine-4-carboxylic acid monohydrate), C(5)H(4)N(2)O(4)·H(2)O, was reported for the first time by Takusagawa & Shimada [Bull. Chem. Soc. Jpn (1973 ▶), 46, 2011-2019]. The present redetermination provides more precise values of the mol-ecular geometry. The asymmetric unit comprises a planar diketo tautomer and a solvent water mol-ecule. In the crystal structure, mol-ecules are connected by O-H⋯O, N-H⋯O and C-H⋯O hydrogen bonds involving NH groups, two carbonyl O atoms and the solvent water mol-ecule.

Redetermination of 5-iodo-uracil

The title compound (systematic name: 2,4-dihydr­oxy-5-iodo­pyrimidine), C₄H₃IN₂O₂, which was first reported by Sternglanz, Freeman & Bugg [Acta Cryst. (1975 ▶), B31, 1393–1395], has been redetermined, providing a significant increase in the precision of the derived geometric parameters. The asymmetric unit comprises a non-planar mol­ecule in a slightly distorted B₂₅ boat conformation. The mol­ecules are associated in the crystal structure to form ribbons stabilized by N—H⋯O hydrogen bonds which involve NH groups and two carbonyl O atoms.

Nicotinohydrazide

In the title compound (alternative name: pyridine-3-carbo­hydrazide, C₆H₇N₃O), the asymmetric unit contains a single mol­ecule. In contrast with nicotinic acid and nicotinamide, the C=O bond is found to be oriented cis with respect to the C_ipso C N fragment in the pyridine ring. The pyridine ring and the hydrazide group make a dihedral angle of 34.0 (2)°. In the crystal structure, mol­ecules are associated into a three-dimensional framework by a combination of N—H⋯N and three-centre N—H⋯O hydrogen bonds.

Hydrogen-bonded supramolecular motifs in the 1:1 monohydrated molecular adduct of acetoguanaminium chloride with acetoguanamine and in 2,4,6-triaminopyrimidinediium dichloride dihydrate

In the 1:1 monohydrated molecular adduct 2,4-diamino-6-methyl-1,3,5-triazin-1-ium chloride 2,4-diamino-6-methyl-1,3,5-triazine monohydrate, C(4)H(8)N(5)(+).Cl(-).C(4)H(7)N(5).H(2)O, formed between 2,4-diamino-6-methyl-1,3,5-triazin-1-ium chloride (acetoguanaminium chloride) and 2,4-diamino-6-methyl-1,3,5-triazine (acetoguanamine), and in triaminopyrimidinediium dichloride dihydrate, C(4)H(9)N(5)(2+).2Cl(-).2H(2)O, whose cationic component lies across a twofold rotation axis, the protonation occurs at the ring N atoms and the bond distances in the protonated molecules indicate significant bond alterations, consistent with charge-separated polar forms. The supramolecular structures of both compounds are stabilized by systems of hydrogen bonds forming complex sheets, interlinked by sets of hydrogen bonds involving the solvent water molecules and the chloride anions.

Evidence of the Facile Hydride and Enolate Addition to the Imine Bond of an Aluminum−Salophen Complex

The isolation of complexes 2 and 3, unambiguously characterized by single-crystal X-ray diffraction, demonstrates that nucleophilic additions to the aluminum-coordinated imino bond of salophen complex 1 can be achieved under very mild conditions.