A structural and theoretical study of intermolecular interactions in nicotinohydrazide dihydrochloride

In the title compound [systematic name: 3‐(azaniumylcarbamoyl)pyridinium dichloride], C₆H₉N₃O²⁺·2Cl⁻, the ions are connected by N—H...Cl hydrogen bonds to form layers and C—H...Cl interactions expand the layers into a three‐dimensional net. The energies of the N—H...Cl interactions range from typical for very weak interactions (0.17 kcal mol⁻¹) to those observed for relatively strong interactions (29.1 kcal mol⁻¹). C—H...Cl interactions can be classified as weak and mildly strong (energies ranging from 2.2 to 8.2 kcal mol⁻¹). Despite the short contacts existing between the parallel aromatic rings of the cations, π–π interactions do not occur.     

7‐Carboxyl­ato‐8‐hydroxy‐2‐methyl­quinolinium monohydrate and 7‐carboxy‐8‐hydroxy‐2‐methyl­quinolinium chloride monohydrate at 100 K

Both 7‐carboxyl­ato‐8‐hydroxy‐2‐methyl­quinolinium monohydrate, C₁₁H₉NO₃·H₂O, (I), and 7‐carboxy‐8‐hydroxy‐2‐methyl­quinolinium chloride monohydrate, C₁₁H₁₀NO₃⁺·Cl⁻·H₂O, (II), crystallize in the centrosymmetric P space group. Both compounds display an intramolecular O—H⋯O hydrogen bond involving the hydroxy group; this hydrogen bond is stronger in (I) due to its zwitterionic character [O⋯O = 2.4449 (11) Å in (I) and 2.5881 (12) Å in (II)]. In both crystal structures, the HN⁺ group participates in the stabilization of the structure via intermolecular hydrogen bonds with water mol­ecules [N⋯O = 2.7450 (12) Å in (I) and 2.8025 (14) Å in (II)]. In compound (II), a hydrogen‐bond network connects the Cl⁻ anion to the carboxylic acid group [Cl⋯O = 2.9641 (11) Å] and to two water mol­ecules [Cl⋯O = 3.1485 (10) and 3.2744 (10) Å].     

7‐Vinyl‐8‐aza‐7‐de­aza‐2′‐deoxy­adenosine monohydrate

In the title compound, 4‐amino‐1‐(2‐deoxy‐β‐d ‐eythro‐pento­furan­osyl)‐3‐vinyl‐1H‐pyrazolo­[3,4‐d]­pyrimidine monohydrate, C₁₂H₁₅N₅O₃·H₂O, the conformation of the gly­cosyl bond is anti. The furan­ose moiety is in an S conformation with an unsymmetrical twist, and the conformation at the exocyclic C—C(OH) bond is +sc (gauche, gauche). The vinyl side chain is bent out of the heterocyclic ring plane by 147.5 (5)°. The three‐dimensional packing is stabilized by O—H·O, O—H·N and N—H·O hydrogen bonds.     

Polymorphism of methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate: an experimental and theoretical study

Being a close analogue of amflutizole, methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate (C₁₁H₁₀N₂O₂S) was assumed to be capable of forming polymorphic structures. Noncentrosymmetric and centrosymmetric polymorphs have been obtained by crystallization from a series of more volatile solvents and from denser tetrachloromethane, respectively. Identical conformations of the molecule are found in both structures. The two polymorphs differ mainly in the intermolecular interactions formed by the amino group and in the type of stacking interactions between the π‐systems. The most effective method for revealing packing motifs in structures with intermolecular interactions of different types (hydrogen bonding, stacking, dispersion, etc.) is to study the pairwise interaction energies using quantum chemical calculations. Molecules form a column as the primary basic structural motif due to stacking interactions in both polymorphic structures under study. The character of a column (straight or zigzag) is determined by the orientations of the stacked molecules (in a `head‐to‐head' or `head‐to‐tail' manner). Columns bound by intermolecular N—H…O and N—H…N hydrogen bonds form a double column as the main structural motif in the noncentrosymmetric structure. Double columns in the noncentrosymmetric structure and columns in the centrosymmetric structure interact strongly within the ab crystallographic plane, forming a layer as a secondary basic structural motif. The noncentrosymmetric structure has a lower density and a lower (by 0.59 kJ mol^?1) lattice energy, calculated using periodic calculations, compared to the centrosymmetric structure.     

N8‐(2′‐O‐Methyl­ribofuranos­yl)‐8‐aza‐7‐deaza­adenine monohydrate

In the title compound, 4‐amino‐2‐(2‐O‐methyl‐β‐d ‐ribofuranos­yl)‐2H‐pyrazolo[3,4‐d]pyrimidine monohydrate, C₁₁H₁₅N₅O₄·H₂O, the conformation of the N‐glycosylic bond is syn [χ = 20.1 (2)°]. The ribofuran­ose moiety shows a C3′‐endo (³T₂) sugar puckering (N‐type sugar), and the conformation at the exocyclic C4′—C5′ bond is −ap (trans). The nucleobases are stacked head‐to‐head. The three‐dimensional packing of the crystal structure is stabilized by hydrogen bonds between the 2′‐O‐methyl­ribonucleosides and the solvent mol­ecules.     

A theoretical study on the mechanism of the baeyer–villiger type oxidation of 7‐phosphanorbornene 7‐Oxides

DFT computations have been performed on selected stationary points of the reaction path (reactants, intermediates, and products) of the Baeyer–Villiger type oxidation of 7‐phosphanorbornene 7‐oxide derivatives. Our computations justified the relevance of a Criegee‐type intermediate forming in the first step, analogously to the Baeyer–Villiger oxidation of ketones. The energy profile indicated a high‐energy barrier from the side of the products, supporting the kinetic character of the mechanism. The computations revealed that the mechanism does not include a previously assumed Berry‐pseudorotation step in the Criegee‐type intermediate. On the basis of the present results, we suggest that the regioselectivity of the Baeyer–Villiger type oxidation of the 7‐phosphanorbornene 7‐oxide derivatives may be determined by steric interactions between the leaving meta‐chlorobenzoate group and substituents on the 7‐phosphanorbornene skeleton in the Criegee‐type intermediate. © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:759–766, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20366     

A theoretical study of electronic structures and intermolecular magnetic interactions for spiro-biphenalenyls

In order to inquire into the mechanism of the change in the magnetism of spiro-biphenalnyls, intermolecular magnetic interaction has been investigated in terms of the effective exchange integral of the Heisenberg model for dimeric pairs of diethyl-substituted spiro-biphenalenyl. Variation of the magnetic interaction with respect to temperature has been evaluated for X-ray crystallographic structures at several temperature points by Kohn–Sham hybrid-DFT. The intermolecular magnetic interactions have been calculated for the π-dimers to be antiferromagnetic at each temperature, which has decreased by approximately 30% in the magnitude from 100 to 173 K. In addition, the interactions have been almost none at 100 and 173 K except for one pair and the remaining pair had ferromagnetic interaction. Therefore, it has been found that the change in their magnetism is understood by the formation of a ferromagnetic dimer-pair at 173 K. Moreover, the natural orbital analysis for the electronic structure of diethyl-substituted spiro-biphenelenyl has shown our solutions are essentially identified to Haddon’s proposal in terms of the valence bond picture.     

Supramolecular interactions in carboxylate and sulfonate salts of 2,6‐diamino‐4‐chloropyrimidinium

Two new salts, namely 2,6‐diamino‐4‐chloropyrimidinium 2‐carboxy‐3‐nitrobenzoate, C₄H₆ClN₄⁺·C₈H₄NO₆⁻, (I), and 2,6‐diamino‐4‐chloropyrimidinium p‐toluenesulfonate monohydrate, C₄H₆ClN₄⁺·C₇H₇O₃S⁻·H₂O, (II), have been synthesized and characterized by single‐crystal X‐ray diffraction. In both crystal structures, the N atom in the 1‐position of the pyrimidine ring is protonated. In salt (I), the protonated N atom and the amino group of the pyrimidinium cation interact with the carboxylate group of the anion through N—H…O hydrogen bonds to form a heterosynthon with an R ₂²(8) ring motif. In hydrated salt (II), the presence of the water molecule prevents the formation of the familiar R ₂²(8) ring motif. Instead, an expanded ring [i.e. R ₃²(8)] is formed involving the sulfonate group, the pyrimidinium cation and the water molecule. Both salts form a supramolecular homosynthon [R ₂²(8) ring motif] through N—H…N hydrogen bonds. The molecular structures are further stabilized by π–π stacking, and C=O…π, C—H…O and C—H…Cl interactions.     

Experimental and theoretical structural study of 2‐pyridyl‐ and 4‐hydroxyphenyl‐1,4‐dihydropyridine derivatives

A series of substituted 1,4‐dihydropyridines (1,4‐DHPs) has been synthesised following the well‐known Hantzsch's procedure for symmetrical 1,4‐DHP. The structures of these compounds have been thoroughly studied by X‐ray crystallographic analysis and semiempirical (AMI) calculations. A good agreement is found between the theoretical and experimental results. In all cases, the most stable conformation fulfils all the requirements needed for exhibiting an antagonist calcium effect.     

Synthesis and fluorescence properties of substituted 7‐aminocoumarin‐3‐carboxylate derivatives

4‐Trifluoromethyl‐ or 6‐bromo‐substituted 7‐diethylaminocoumarin‐3‐carboxamide derivatives 2 and 3, each containing a maleimide have been synthesized as potential fluorescent labeling reagents for thiol groups in proteins and their fluorescence properties have been determined. The 4‐trifluoromethyl substituted compound 2 has a significantly greater Stokes shift than the comparable compound lacking this group, but both the new coumarins have low fluorescence quantum yields (?_f). When a 4‐trifluoromethyl substituent is present, the 3‐carboxamide is unusually labile to hydrolysis. Bromination of ethyl 7‐diethylaminocoumarin‐3‐carboxylate 17 gave the 6‐ and 8‐bromo derivatives 18 and 19 respectively, and also the 8‐bromo‐7‐monoethylamino compound 20. ?_f for the latter compound is 100‐fold greater than for its diethylamino analogue 19. Fluorescence lifetime measurements support an interpretation based on the twisted intramolecular charge transfer (TICT) model to explain these large differences in ?_f.     

Hydrogen‐bonding interactions in the 4‐aminobenzoic acid salt of atenolol monohydrate

Atenolol {or 4‐[2‐hydroxy‐3‐(isopropylamino)propoxy]phenylacetamide} crystallizes with 4‐aminobenzoic acid to give the salt {3‐[4‐(aminocarbonylmethyl)phenoxy]‐2‐hydroxypropyl}isopropylammonium 4‐aminobenzoate monohydrate, C₁₄H₂₃N₂O₃⁺·C₇H₆NO₂⁻·H₂O. In the crystal structure, the water molecule, the carboxylate group of 4‐aminobenzoate, and the hydroxy and ether O atoms of atenolol form a supramolecular R₃³(11) heterosynthon. Three other types of supramolecular synthons link the asymmetric unit into a two‐dimensional structure.     

A locked derivative of 8‐aza‐7‐deazaadenosine

The title compound [systematic name: (1S,3S,4R,7S)‐3‐(4‐amino‐1H‐pyrazolo[3,4‐d]pyrimidin‐1‐yl)‐1‐hydroxymethyl‐2,5‐dioxabicyclo[2.2.1]heptan‐7‐ol], C₁₁H₁₃N₅O₄, belongs to a family of nucleosides with modifications in both the sugar and nucleobase moieties: these modifications are known to increase the thermodynamic stability of DNA and RNA duplexes. There are two symmetry‐independent molecules in the asymmetric unit that differ significantly in conformation, and both exhibit a high‐anti conformation about the N‐glycosidic bond, with χ torsion angles of −85.4 (3) and −87.4 (3)°. The sugar C atom attached to the nucleobase N atom is −0.201 (4) and 0.209 (4) Å from the 8‐aza‐7‐deazaadenine skeleton plane in the two molecules. The molecules are assembled into layers via hydrogen bonds and π–π stacking interactions between the modified nucleobases.     

A combined experimental and theoretical study of carboxylate coordination modes: a structural probe

The variations of the frequency differences of symmetric and asymmetric stretching vibrations in a series of carboxylato Fe(II) complexes have been theoretically studied. It is shown that structural information can be obtained from a direct comparison between the difference (Delta = nu(as) - nu(s)) in the asymmetric (nu(as)) and symmetric (nu(s)) carboxylate vibrations of the free anion and that of the coordinated species. The coordination mode approaches C(2v) symmetry as Delta decreases with respect to its value for the noncoordinated carboxylate. The use of IR spectroscopy in the resolution of speculated crystallographic structures is suggested.     

A TD‐DFT study on the cyanide‐chemosensing mechanism of 8‐formyl‐7‐hydroxycoumarin

Proton transfer (PT) and excited‐state PT process are proposed to account for the fluorescent sensing mechanism of a cyanide chemosensor, 8‐formyl‐7‐hydroxycoumarin. The time‐dependent density functional theory method has been applied to investigate the ground and the first singlet excited electronic states of this chemosensor as well as its nucleophilic addition product with cyanide, with a view to monitoring their geometries and spectrophotometrical properties. The present theoretical study indicates that phenol proton of the chemosensor transfers to the formyl group along the intramolecular hydrogen bond in the first singlet excited state. Correspondingly, the nucleophilic addition product undergoes a PT process in the ground state, and shows a similar structure in the first singlet excited state. This could explain the observed strong fluorescence upon the addition of the cyanide anion in the relevant fluorescent sensing mechanism. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Hydrogen‐bonding and C—H⋯π interactions in ethyl 4‐acetyl‐5‐methyl‐3‐phenyl‐1H‐pyrrole‐2‐carboxylate monohydrate

In the title compound, C₁₆H₁₇NO₃·H₂O, the pyrrole ring is distorted slightly from ideal C_2v symmetry. Three strong hydrogen bonds link the substituted pyrrole and water mol­ecules to form infinite chains, in which the hydrogen bonds form rings and chain patterns. Two intermolecular C—H?π interactions maintain the internal cohesion between these chains. The molecular structure differs slightly from that of the isolated mol­ecule calculated by ab initio quantum‐mechanical calculations. In the latter model, the non‐H substituent atoms share the plane of the pyrrole ring, except for the phenyl group, which lies almost perpendicular to this plane.     

7‐Iodo‐8‐aza‐7‐deaza‐2′‐deoxy­adenosine and 7‐bromo‐8‐aza‐7‐deaza‐2′‐deoxyadenosine

The isomorphous structures of the title molecules, 4‐amino‐1‐(2‐deoxy‐β‐d ‐erythro‐pento­furan­osyl)‐3‐iodo‐1H‐pyrazolo‐[3,4‐d]pyrimidine, (I), C₁₀H₁₂IN₅O₃, and 4‐amino‐3‐bromo‐1‐(2‐deoxy‐β‐d ‐erythro‐pento­furan­osyl)‐1H‐pyrazolo[3,4‐d]­pyrimidine, (II), C₁₀H₁₂BrN₅O₃, have been determined. The sugar puckering of both compounds is C1′‐endo (^1′E). The N‐­glycosidic bond torsion angle χ¹ is in the high‐anti range [?73.2 (4)° for (I) and ?74.1 (4)° for (II)] and the crystal structure is stabilized by hydrogen bonds.     

7‐Methoxy‐2,3‐dioxo‐1,4‐dihydroquinoxalin‐6‐aminium chloride monohydrate

Single crystals of the title compound, C₉H₁₀N₃O₃⁺·Cl⁻·H₂O, were obtained by recrystallization from hydrochloric acid. The cations stack along the crystallographic a direction. The 2,3‐dioxo‐1,4‐dihydroquinoxaline group shows a significant deviation from planarity [r.m.s. deviation from the best plane = 0.063 (2) Å]. Hydrogen bonding links the cations, chloride anions and water molecules to form an extended three‐dimensional architecture.     

8‐Aza‐7‐deaza‐7‐propynyladenosine methanol solvate

In the title compound, 4‐amino‐3‐propynyl‐1‐(β‐d ‐ribofur­anosyl)‐1H‐pyrazolo[3,4‐d]pyrimidine methanol solvate, C₁₃H₁₅N₅O₄·CH₃OH, the torsion angle of the N‐glycosylic bond is between anti and high‐anti [χ = −101.8 (5)°]. The ribofuranose moiety adopts the C3′‐endo (³T₂) sugar conformation (N‐type) and the conformation at the exocyclic C—C bond is +sc (gauche, gauche). The propynyl group is out of the plane of the nucleobase and is bent. The compound forms a three‐dimensional network which is stabilized by several hydrogen bonds (O—H·O and O—H·N). The nucleobases are stacked head‐to‐tail. The methanol solvent mol­ecule forms hydrogen bonds with both the nucleobase and the sugar moiety.     

2,3‐Dihydro‐1,3‐benzothiazol‐2‐iminium hydrogen oxydiacetate: a combined structural and theoretical study

In the title compound, C₇H₇N₂S⁺·C₄H₅O₅⁻, the ions are connected by N—H...O hydrogen bonds. The hydrogen oxydiacetate residues are linked together by O—H...O hydrogen bonds disordered about centres of inversion into hydrogen‐bonded ribbon layers crosslinked by weak C—H...O and stacking interactions. The cation exists mainly in the 2,3‐dihydro‐1,3‐benzothiazol‐2‐iminium form, with a small participation of the 2‐aminobenzothiazolium form, based on the structural data and quantum mechanical calculations. This study provides structural insights relevant to the biochemical activity of benzothiazole molecules.     

Hydrogen‐bonding interactions in (3,4‐dimethoxyphenyl)acetic acid monohydrate

The crystal structure of the title compound, C₁₀H₁₂O₄·H₂O, consists of (3,4‐dimethoxyphenyl)acetic acid and water molecules linked by O—H...O hydrogen bonds to form cyclic structures with graph‐set motifs R₁²(5) and R₄⁴(12). These hydrogen‐bond patterns result in a three‐dimensional network with graph‐set motifs R₄⁴(20) and R₄⁴(22), and the formation of larger macrocycles, respectively. The C—C bond lengths and the endocyclic angles of the benzene ring show a noticeable asymmetry, which is connected with the charge‐transfer interaction of the carboxyl or methoxy groups and the benzene ring. The title compound is one of the simple carboxylic acid systems that form hydrates. Thus, the significance of this study lies in the analysis of the interactions in this structure and the aggregations occurring via hydrogen bonds in two crystalline forms of (3,4‐dimethoxyphenyl)acetic acid, namely the present hydrate and the anhydrous form [Chopra, Choudhury & Guru Row (2003). Acta Cryst. E 59 , o433–o434]. The correlation between the IR spectrum of this compound and its structural data are also discussed.