System Of Intermolecular Hydrogen Bonds Research Articles

Synthesis and structure of trans-bis-(4-amino-3-nitro-benzoato-κO)bis-(4-amino-3-nitro-benzoic acid-κO)di-aqua-manganese(II) dihydrate.

The manganese title complex, [Mn(C7H5N2O4)2(C7H6N2O4)2(H2O)2]·2H2O, is one of the first 4-amino 3-nitro-benzoic acid (4 A3NBA) monoligand metal complexes to be synthesized. It crystallizes in the centrosymmetric monoclinic space group P21/n with the complex mol-ecules located on inversion centers. Four 4 A3NBA ligand mol-ecules are monodentately coordinated by the Mn2+ ion through the carb-oxy-lic oxygen atoms while the other two positions of the inner coordination sphere are occupied by water mol-ecules, giving rise to a distorted octa-hedron, and two water mol-ecules are in the outer coordination sphere. There are two intra-molecular hydrogen bonds in the complex mol-ecule. The first is of the common N-H⋯O=N type, while the second is a rarely occurring very strong hydrogen bond in which a common proton is shared by two uncoordinated oxygen atoms of neighboring carboxyl-ate groups. In the crystal, an intricate system of inter-molecular hydrogen bonds links the complex mol-ecules into a three-dimensional-network.

THE STUDY OF INTERMOLECULAR INTERACTIONS IN THE POSS-CONTAINING NANOCOMPOSITES BASED ON POLYURETHANE AND POLYURETHANE/POLY(HYDROXYPROPYL METHACRYLATE) MATRICES

The nanocomposites based on polyurethane matrix and multicomponent polymer matrices consisting of polyurethane and poly(hydroxypropyl methacrylate) with different contents of the last, and 1,2-propanediolisobutyl polyhedral oligomeric silsesquioxane (1,2-propanediolisobutyl-POSS), which was used as a functionalized nanofiller, were synthesized. The influence of the content of 1,2-propanediolisobutyl-POSS on intermolecular interactions and structural features of the nanocomposites was investigated by the method of IR-spectroscopy with Fourier transformation and attenuated total reflection (FTIR-ATR). The study of thermal curing of the model system, which consists of the adduct of trimethylolpropane with toluene diisocyanate and 1,2-propanediolisobutyl-POSS, made it possible to conclude that 1,2-propanediolisobutyl-POSS participates in the reaction of urethane formation using of one of the terminal hydroxyl groups, and it is incorporated into the polymer chain between cross-linking of polyurethane networks. The investigation of multicomponent polymer matrices by FTIR-ATR spectroscopy was done and was shown that photopolymerization of second polymer poly(hydroxypropyl methacrylate) in the matrix of polyurethane was completed by the opening of a double bond and the formation of a linear polymer in the composition of semi-IPN. Studies of nanocomposites based on multicomponent polymer matrices consisting of polyurethane and poly(hydroxypropyl methacrylate) with 15 and 30 % of the last by FTIR-ATR spectroscopy demonstrated the presence of POSS in the nanocomposites and the influence of POSS content on the structure of the studied systems and on the degree of phase separation. The POSS is "embedded" into the polymer chain between cross-linking of the polyurethane networks, with the additional formation of a complex system of intermolecular hydrogen bonds between the carboxyl and amine components of urethane groups in the nanocomposites.

Synthesis and X-ray structural studies of 5-methyl-6-nitro-7-oxo-4,7-dihydro-1,2,4-triazolo[1,5-а]pyrimidine L-arginine and piperidine salts

The previously described L-argininium 5-methyl-6-nitro-7-oxo-4,7-dihydro-1,2,4-triazolo[1,5-a]pyrimidinide monohydrate and piperidinium 5-methyl-6-nitro-7-oxo-4,7-dihydro-1,2,4-triazolo[1,5-a]pyrimidinide, which has not been described previously, were synthesized as promising antiviral drugs. A detailed comparison of the crystal structures of these two compounds was performed. It is shown that the replacement of the L-arginine cation with piperidinium one leads to a serious reorganization of the system of intermolecular hydrogen bonds in the solid state, which, in our opinion, can have a significant impact on the interaction of the new drug with biological targets. Thus, by comparing the X-ray structural analysis data, the probability of the influence of the nature of the counterion on the biological effect of the drug was demonstrated.

SYNTHESIS AND X-RAY STRUCTURAL STUDIES OF 5-METHYL-6-NITRO-7-OXO-4,7-DIHYDRO-1,2,4-TRIAZOLO[1,5- а ]PYRIMIDINE L-ARGININE AND PIPERIDINE SALTS

The previously described L-argininium 5-methyl-6-nitro-7-oxo-4,7-dihydro-1,2,4-triazolo[1,5-a]pyrimidinide monohydrate and piperidinium 5-methyl-6-nitro-7-oxo-4,7-dihydro-1,2,4-triazolo[1,5-a]pyrimidinide, which has not been described previously, were synthesized as promising antiviral drugs. A detailed comparison of the crystal structures of these two compounds was performed. It is shown that the replacement of the L-arginine cation with piperidinium one leads to a serious reorganization of the system of intermolecular hydrogen bonds in the solid state, which, in our opinion, can have a significant impact on the interaction of the new drug with biological targets. Thus, by comparing the X-ray structural analysis data, the probability of the influence of the nature of the counterion on the biological effect of the drug was demonstrated.

Crystal structure and phase behavior of the tolyl glycerol ethers. From the conglomerate former to the chirality-driven nanogelator

According to differential scanning calorimetry data ortho-, meta-, and para-tolyl glycerol ethers 1–3 form thermodynamically most stable crystal phases during solution crystallization. For all members of the series the crystal phases formed during melt crystallization have different thermodynamic characteristics from those of the stable ones. Binary melting diagrams were constructed for the stable solid phases; on this basis it was found that 1 is prone to spontaneous resolution, and 2 and 3 form stable solid racemic compounds, the Gibbs energy of formation for which are found to be −2.70 and −2.43 kJ mol−1. Solution grown single crystals of 1–3 were investigated by an X-ray diffraction method. The principal supramolecular crystal formative motifs were revealed: 1D columns for 1 and scal-2, 2D bilayers having developed a 2D system of intermolecular hydrogen bonds (IMHB) for rac-2 and rac-3, and 2D bilayer having 1D spiral IMHB organization for scal-3. The possible reasons preventing the solid racemic compound formation in the case of 1, and the spontaneous resolution manifestation in the cases of 2 and 3 are disclosed. It was demonstrated that, from the whole family of tolyl glycerol ethers, only scal-3 samples are capable of supramolecular gels formation. This property is connected with the peculiarities of the scalemic 3 crystal packing.

Ionic acetamide coordination in its complexes with rare-earth iodides

A series of [Ln(CH3CONH2)4(H2O)4]I3 (Ln = rare-earth metal) complexes was completed with seven new compounds (Ln = Ce, Pr, Sm, Tb, Tm, Yb, Lu); two (Ln = Ce, Tm) were studied by X-ray diffraction. The coordination polyhedron of eight oxygen atoms is a distorted square antiprism. No tetrad effect was found for Ln–O bond lengths. The structure is stabilized by a system of intermolecular hydrogen bonds. The most striking feature of the structures is the recently predicted ionic acetamide coordination. The acetamide molecules are non-planar (the Ln–O–C–N torsion angles are 159–170°) and Ln–O–C bond angles vary in the 146.0–156.8° range.

Semi-organic salts of aniline with inorganic acids: prospective materials for the second harmonic generation

Three novel inorganic salts of aniline with sulfuric and selenic acids were prepared and characterized by X-ray structural analysis. Anilinium(1+) selenate, (C6H5NH3+)2SeO42−, and anilinium sulfate, (C6H5NH3+)2SO42−, crystallize in the monoclinic space groupC2. The crystal structures are based on hydrogen bonded layers of alternating anilinium cations and inorganic anions. Anilinium(1+) selenate dihydrate, (C6H5NH3+)2SeO42−·2H2O, crystallizes in the monoclinic space groupC2/c. The crystal structure is formed by a network of alternating anilinium cations, selenate anions and water molecules connected by a system of intermolecular hydrogen bonds. The FTIR and Raman spectra of all the compounds have been recorded and discussed as well as their crystal structures. According to the DSC curves and temperature dependence of lattice parameters, anilinium sulfate exhibits phase transitions at 217 and 182 K. The appropriate changes of vibrational spectra were also recorded during cooling of the sample especially in the N–H stretching and sulfate antisymmetric stretching (ν3SO42−) spectral regions. The quantitative measurements of the second harmonic generation at 1064 nm were performed using powdered samples of anilinium sulfate, anilinium chloride and anilinium selenate, and the relative efficiencies deff = 0.05dKDP, deff = 2.33dKDP and deff = 0.05dKDP (KDP; i.e.KH2PO4) have been observed, respectively.

Inorganic salts of biguanide – Searching for new materials for second harmonic generation

Five inorganic salts of biguanide with carbonic, nitric, phosphoric and phosphorous acids were prepared and X-ray structural analysis has been performed for three novel compounds. Biguanidium(1+) phosphite trihydrate crystallizes in the triclinic space group P 1 ¯ , a = 7.1470(1) Å, b = 9.6530(2) Å, c = 11.3140(2) Å, α = 70.094(1)°, β = 75.688(1)°, γ = 86.099(1)°, V = 713.71(2) Å 3, Z = 2, R = 0.0350 for 3031 observed reflections. The crystal structure is based on a network of phosphite anions and water molecules. Biguanidium(1+) cations form pairs through two intermolecular hydrogen bonds of the N–H…N type and fill the network with anions and water molecules. Biguanidium(2+) phosphite monohydrate crystallizes in the triclinic space group P 1 ¯ , a = 6.9690(2) Å, b = 7.3500(3) Å, c = 8.1730(3) Å, α = 82.518(2)°, β = 83.015(2)°, γ = 82.811(2)°, V = 409.44(3) Å 3, Z = 2, R = 0.0308 for 1779 observed reflections. The structure is formed of a network of alternating biguanidium(2+) cations, phosphite anions and pairs of water molecules interconnected by a system of intermolecular hydrogen bonds. Biguanidium(2+) hydrogen phosphate monohydrate crystallizes in the triclinic space group P 1 ¯ , a = 7.0630(2) Å, b = 7.8740(3) Å, c = 8.1120(3) Å, α = 102.706(2)°, β = 104.976(2)°, γ = 92.632(3)°, V = 422.61(3) Å 3, Z = 2, R = 0.0337 for 1827 observed reflections. The crystal structure is formed by pairs of anions that are mutually connected in chains through two water molecules. These chains are interconnected by biguanidium(2+) cations to form a three-dimensional network. The FTIR and FT Raman spectra of all five compounds were recorded, calculated (HF, B3LYP and MP2 methods) and discussed. Quantitative measurements of second harmonic generation of powdered biguanidium(2+) nitrate and novel biguanidium(2+) carbonate monohydrate at 800 nm were performed and a relative efficiency (compared to KDP) of 87% and 20% was observed, respectively.

Supramolecular Organization in Crystals Containing Quinoline‐2‐ Carboxylates and 9,10‐Dihydro‐9‐oxo‐10‐acridineacetates

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Supramolecular organization in crystals containing quinoline-2-carboxylates and 9,10-dihydro-9-oxo-10-acridineacetates

Coordination compounds containing quinoline-2-carboxylate (quin-2-c) or 9,10-dihydro-9-oxo-10-acridineacetate ion (CMA) and ancillary ligands capable of hydrogen bond formation self assemble into 1D, 2D or 3D networks. The system of intermolecular hydrogen bonds that emerges depends mainly on the nature of the ancillary ligand. Aromatic–aromatic and C–H … π interactions are important forces for stabilizing crystal structures. Very strong stacking of aromatic heteropolycycles is found. An overview of complexes with quin-2-c and CMA is given and the organization of their crystal structures discussed.

Synthesis and structure of the mixed-ligand cobalt(III) complex [Co(DH)(Hthsc)2][SiF6] · 2.3H2O

The compound [Co(DH)(Hthsc)2][SiF6] · 2.3H2O, where DH− is a dimethylglyoxime residue and Hthsc is a thiosemicarbazide molecule, was synthesized and studied by X-ray diffraction. The coordination polyhedron of the central metal ion (distorted octahedron) is formed by two sulfur atoms, two nitrogen atoms of two Hthsc molecules coordinated in the bidentate mode, and two nitrogen atoms of the DH− ligand. The positions of three metal rings are fixed by two intramolecular hydrogen bonds (N-H…O). A bifurcated system of intermolecular hydrogen bonds forms a framework structure in the crystal.

Synthesis, structure, and configuration of new spirooxyndol compound

Structure of a new spirooxyndol compound, [indoline-3,2′(3′H)-[3′-acetyl-2′-acetamide-[1,3,4]-thiodiazoline]-1-benzyl]-2, has been determined by X-ray diffraction analysis. Crystal is monoclinic, unit cell parameters are: a = 12.097(1) A, b = 10.172(1) A, c = 32.987(1) A; β = 97.731(3)°, space group P21/n, Z = 4, compound C42H44N8O7S2. Independent part of the unit cell is formed by two crystallographically independent molecules, practically equal in composition and configuration. Two independent molecules are united by the exosphere molecule of ethanol. Phenyl and pyrol rings are located virtually in one plane, dihedral angle formed by mean-square planes of these rings vary within 1.5(2)–3.3(2)°. In both molecules thiodiazoline and pyrol rings are spiro-joint over carbon atom, the dihedral angle formed by the latter is 89.1(1)° and 88.5(1)°, sulfur and nitrogen atoms in the molecules A and B being on different sides of pyrol ring keeping identical configuration of carbon node. Crystal structure is composed due to branched system of intermolecular hydrogen bonds.

Acyclic tautomers in crystalline carbohydrates: the keto forms of 1-deoxy-1-carboxymethylamino-D-2-pentuloses (pentulose-glycines).

NMR and X-ray diffraction studies on acyclic carbohydrate keto tautomers of N-(1-deoxy-d-erythro-2-pentulos-1-yl)- and N-(1-deoxy-d-threo-2-pentulos-1-yl)glycines (ribulose-glycine, 1 and xylulose-glycine, 2), are reported. In aqueous solutions, both 1 and 2 exist as a tautomeric mixture, with the beta-furanose as a major form, followed by the alpha-furanose and the acyclic keto tautomer. Both 1 and 2 crystallize as zwitterions in the acyclic keto form. Solid-state 13C NMR spectra reveal the existence of two crystallographically independent molecules in 2 but only one in crystalline 1. The structure of 2 was solved by X-ray diffraction; in the crystal, two conformational isomers, 2a and 2b in a 1:1 ratio, were identified. The conformers are packed in stacks of similar molecules, with a system of intermolecular hydrogen bonds involving all hydroxyl, ammonium, and carboxyl groups. The structural data indicate that the sugar portion of acyclic 2 adopts conformations similar to those proposed for the parent d-xylulose.

Molecular and Crystal Structure of 4,6-Dimethyl-2-(phenylhydrazino)pyrimidine and Its Alkylation and Protonation Products

It was established by X-ray crystallographic analysis that 4,6-dimethyl-2-(phenylhydrazino)pyrimidine forms 2-(2-n-butyl-2-phenylhydrazino)-4,6-dimethylpyrimidine during alkylation with n-butyl bromide and 4,6-dimethyl-2-(phenylhydrazino)-1(H)-pyrimidinium nitrate during protonation with nitric acid. The structure of the molecules and the system of intermolecular hydrogen bonds in the crystals of the compounds are discussed.

Infrared spectra and structure of hydrogen bonds in N′-substituted isonicotinic hydrazides formed by crystallization from solution and via solid phase transformations

Crystal chemical and IR spectroscopic data for N′-substituted isonicotinic hydrazides (INH) of the general formula Py:C(:O):N(H):N′:C(H):R [R : thineyl, furyl, 5-nitrofuryl, and o-nitrophenyl] have been analysed. Crystalline compounds (hydrates, solvates, solvate hydrates, salts) of a specified composition and structure, i.e. a desired system of intermolecular hydrogen bonds, can be obtained by deliberately varying the solvent composition during synthesis or recrystallization. The systematic effects of substituent R on composition and structure of INH solvates and on their thermodynamic stability have been revealed.

X-ray structural study of 2-amino-5,5-dimethoxy-3-cyano-4-dicyanomethylene-4,5-dihydropyrrole and its sodium salt

According to the XSA data, a conjugation system in which both endo- and exocyclic bonds are included is realized in the molecule of 2-amino-5,5-dimethoxy-3-cyano-4-dicyanomethylene-4,5-dihydropyrrole and the anion of its sodium salt due to the planar structure, and this is reflected in their unusual length. Due to the developed system of intermolecular hydrogen bonds, the molecules in the crystals are joined in infinite three-dimensional motifs.

Rearrangement of the crystal structure during solid-phase elimination of solvate acetic acid fromN?-(5-nitrofurfurylidene)isonicotinic hydrazide monohydrate

A new crystal modification ofN′-(5-nitrofurfurylidene)isonicotinic hydrazide (1) was studied by IR spectroscopy and X-ray structural analysis. The compound studied is the product of solid-phase desolvation of solvate hydrate1 of the composition [MeCOOH · 1 · H2O]. Spontaneous elimination of solvate acetic acid results in complex overall rearrangement of the crystal structure and formation of a new system of intermolecular hydrogen bonds. The crystal hydrate of 1 : 1 composition (1c) was formed from compound1. In the crystal structure of1c molecules1 are linked in infinite chains through intermolecular C=O...W...H-N hydrogen bonds. The second hydrogen atom of the molecule of the crystallization water is involved in formation of an intermolecular O-H...N(Py) hydrogen bond with the nitrogen atom of the pyridine ring of the molecule of the adjacent chain.

X-ray diffraction and theoretical studies of the methyl ester of ( R,R)-tartaric acid monoamide: semiempirical and ab initio calculations of some model compounds

In its crystal structure, determined by X-ray diffraction, the methyl ester of ( R,R)-tartaric acid monoamide crystallizes with two molecules per assymetric unit. Each molecule displays subtle conformational differences effected by 180° rotation by the methyl ester group about the C-C* bond, whereas the staggered conformation around the central C*-C* bond, with a trans arrangement of the ester and amide substituents, and the eclipsed orientation of the amide nitrogen atom with respect to the nearest hydroxyl group, remains the same in both molecules. MNDO and ab initio single-point energies for the two molecules indicate that the lower energy molecule is that with the α-hydroxyl group eclipsed by the carbonyl group rather than the methoxy oxygen atom. Conformers observed in the crystal structure differ from those obtained by full MNDO optimization in the planarity of α-hydroxyester and α-hydroxyamide residues. Ab initio calculations at the 6-31G* level on smaller systems, i.e. (2 R,3 R)-2,3-butanediol and (2 R,3 R)-2,3-dihydroxy-butanedinitrile, suggest different conformational preferences for the two model compounds (gauche vs. trans with respect to the carbon chain), and point to the importance of the intramolecular hydrogen bond in stabilizing the gauche orientation of the vicinal OH groups. A similar hydrogen bond may be present in one of two crystallographically independent molecules of the methyl ester of ( R,R)-tartaric acid monoamide, but only as a minor component in a complex system of intermolecular hydrogen bonds.

X-ray diffraction and theoretical studies of the methyl ester of ( R, R)-tartaric acid monoamide: semiempirical and ab initio calculations of some model compounds

In its crystal structure, determined by X-ray diffraction, the methyl ester of ( R, R)-tartaric acid monoamide crystallizes with two molecules per assymetric unit. Each molecule displays subtle conformational differences effected by 180° rotation by the methyl ester group about the CC∗ bond, whereas the staggered conformation around the central C∗C∗ bond, with a trans arrangement of the ester and amide substituents, and the eclipsed orientation of the amide nitrogen atom with respect to the nearest hydroxyl group, remains the same in both molecules. MNDO and ab initio single-point energies for the two molecules indicate that the lower energy molecule is that with the α-hydroxyl group eclipsed by the carbonyl group rather than the methoxy oxygen atom. Conformers observed in the crystal structure differ from those obtained by full MNDO optimization in the planarity of α-hydroxyester and α-hydroxyamide residues. Ab initio calculations at the 6–31G∗ level on smaller systems, i.e. (2 R,3 R)-2,3-butanediol and (2 R,3 R)-2,3-dihydroxybutanedinitrile, suggest different conformational preferences for the two model compounds (gauche vs. trans with respect to the carbon chain), and point to the importance of the intramolecular hydrogen bond in stabilizing the gauche orientation of the vicinal OH groups. A similar hydrogen bond may be present in one of two crystallographically independent molecules of the methyl ester of ( R, R)-tartaric acid monoamide, but only as a minor component in a complex system of intermolecular hydrogen bonds.

Crystal structure of bis[3-amino-4-(4-aminophenoxy)] diphenylsulfone

1. X-ray structural analysis has established that the molecular structure of bis[3-amino-4-(4-aminophenoxy)]diphenylsulfone exhibits a nonplanar twisted structure, in which the four cyclic fragments are nearly perpendicular to one another. 2. The crystal structure features an extended system of intermolecular hydrogen bonds of the type N-H...O, which unite the molecules in an infinite three-dimensional framework.