Hydrogen Bonds, Tautomers, and Conformation in 2-Hydroxyphenyl 2-hydroxy-2-(β-naphthyl)vinyl Ketone

Single crystal X-ray diffraction and IR spectroscopy have been used to study the conformation of 2-hydroxyphenyl 2-hydroxy-2-(-naphthyl)vinyl ketone in solid state. It was found that one of the two possible enol tautomeric forms is stabilized in the crystal. The 1-hydroxy-3-oxo-1,3-propenylene moiety, O=C—CH=C—OH, shows a strong intramolecular H bond with a definite character of reasonance-assisted hydrogen bond in spite of being in competition with ring intermolecular hydrogen bonds. The comparison of the present results with solution NMR data indicates that the molecular geometry in solid state and in solution are similar.     

Intra- and intermolecular interactions in crystals ofN′-furfurylideneisonicotinic hydrazide and related compounds. IR spectroscopic and X-ray diffraction studies

The reaction of isonicotinic hydrazide with furfural yieldedN′-furfurylideneisonicotinic hydrazide. IR spectroscopic studies demonstrated that crystallization from different solvents afforded products with an intermolecular NH...O=C hydrogen bond. Conditions of crystallization were chosen under which single crystals with the NH...N_Py intermolecular hydrogen bond (1) were grown. X-ray diffraction analysis demonstrated that the molecular and crystal structure of1 is identical to that ofN′-thienylideneisonicotinic hydrazide (2). The crystal structure consists of layers. The molecules in the layers are linked in zigzag chains through NH...N_Py intermolecular hydrogen bonds. The molecules of the adjacent chains (in the layer) are linked through C=O...H?C intermolecular hydrogen bonds between the O atom of the carbonyl group and the α-H atom of the furan ring. (In the structure of2, the chains are linked through specific intermolecular interactions of different nature but with approximately identical energy.) The replacement of the thiophene fragment (2) by the furan ring (1) is accompanied by a change in the intramolecular electronic effects, which is reflected both in the geometric and spectral characteristics of the molecules in the crystal.     

Structural and vibrational study on N-(biphenyl-2-thiocarbamoyl)-4-phenylcarboxamide

A new thiourea derivative, N-(biphenyl-2-thiocarbamoyl)-4-phenylcarboxamide, is synthesized and characterized by elemental analysis, FTIR, NMR and the single crystal X-ray diffraction study. The title compound crystallizes with two molecules in the asymmetric unit. The dihedral angle between the two aromatic rings in the biphenyl unit is 47.9(2) and 56.52(19)°, respectively, for the two molecules in the asymmetric unit. The molecular conformation is stabilized by intramolecular NH?O hydrogen bond. The crystal packing shows that the molecules form centrosymmetric dimers connected by NH?S hydrogen bonds. The vibrational properties have been studied by FTIR and FT-Raman spectroscopy along with quantum chemical calculations at the B3LYP/6-311 + G^* level of approximation. The main normal modes related with the thioamide bands are discussed.     

Conformational analysis of new 14-membered ring diketal dilactam macrocycles: molecular mechanics, liquid and solid state NMR studies

A conformational study of new diversely substituted 14-membered diketal dilactam macrocycles was conducted by NMR spectroscopy in liquid and solid states, molecular mechanics calculations and, for one compound, a previous X-ray analysis. The results obtained by the different techniques show that the conformations depend closely on whether the molecules are chiral or achiral and on the stereochemistry of the ketal OMe groups. In achiral compounds, the most stable conformation of each compound has, in both the liquid and solid states, the two NH-CO links positioned perpendicular to the macrocycle plane, lending to the trans-7,7′-OMe macrocycles 6b and 7b a rectangular [3434]-type structure. In contrast, in chiral compounds, the most stable conformations are not the same in the liquid and solid phases. In the liquid state the conformations are set by the presence of one or two N₄-H?O_1′, N_4′-H?O₁ intramolecular hydrogen bonds that position the amide group parallel to the macrocycle plane, whereas in the solid state the amide moieties again adopt a perpendicular position which can be stabilized, when the 3-R substituent is not too bulky, by intermolecular N-H?OC bonds between parallel sheets, and exceptionally, in the cis-7,7′-OMe-3,3′-Ph compound 1c, by a π-π stacking effect between the phenyl groups.     

Molecular and crystal structure of quinoline-2-aldehyde thiosemicarbazone

The molecular and crystal structure of quinoline-2-aldehyde thiosemicarbazone is determined. The thiosemicarbazide fragment has cis-arrangement of terminal nitrogen atoms relative to the central N-C bond. The structure is based on a centrosymmetric dimer formed by hydrogen bonds between NH groups and sulfur atoms of thiosemicarbazide fragments of the neighboring molecules. In the crystal, the dimers are joined with each other through a system of hydrogen bonds and intermolecular π-π interactions.     

Calculated structures and heats of formation of some predicted C,N, O,F molecules

Twelve molecules containing only C, N, O, and F, which are of interest in the context of energetic materials, were found to have true local energy minima at the HF/6-31G^* computational level. Both HF/6-31G^* and MP2/6-31G^* geometries are presented. A density functional procedure was used to find gas phase heats of formation. These are strongly positive for most of the molecules. The nitroso group significantly increases H _o ^f.25C compared to the nitro analogue.     

Molecular orbital study of the structure and interactions of ylidene rhodanines

Semiempirical (with the AM1 Hamiltonian) and ab initio (mainly with the 6-31G^* and LANL2DZ+ +(d,p) basis sets) molecular oribital calculations show the predominant tautomer of gas phase methylidene rhodanine is 2-thioxo-4-thiazolidinone in agreement with earlier work on other types of rhodanines. Inclusion of solvation effects in the AM1 calculations corroborates with this tautomer is also preferred in aqueous solution. Energy-optimized bond lengths and angles show good agreement with those for a crystalline benzylidene rhodanine. The geometry of a hydrogen bonded dimer matches closely the crystalline state arrangement. The two N-H O hydrogen bonds that form in the dimer. provide a stabilization energy of about - 10 kcal/mol. The interactions of methylidene rhodanine with a calcium ion are modeled with basis sets as large as LANL2DZ+ +(d,p). The preferred binding site is near the carbonyl oxygen for the neutral rhodanine and near the nitrogen and thione sulfur in a bidentate arrangement for the rhodanine anion. Implications for the interaction of benzylidene rhodanines with various possible protein and metalloprotein receptors are discussed.     

An amyloid-like fibril forming antiparallel supramolecular β-sheet from a synthetic tripeptide: a crystallographic signature

Single crystal X-ray diffraction studies of a terminally blocked tripeptide Boc-Leu(1)-Aib(2)-Leu(3)-OMe 1 demonstrates that it adopts a bend structure without any intramolecular hydrogen bond. Peptide 1 self-assembles to form a supramolecular antiparallel β-sheet structure by various non-covalent interactions including intermolecular hydrogen bonds in the crystal and it exhibits amyloid-like fibrillar morphology in the solid state.     

The structural and theoretical study of 1H-3,5-di-phenyl-1,2,4-diazaphosphole in the solid state

The N-, P-containing five-membered heterocyclic compound 1H-3,5-di-phenyl-1,2,4-diazaphosphole (1) was prepared in good yield and has been structurally characterized. 1H-3,5-Di-phenyl-1,2,4-diazaphosphole (1), crystallizing in two unexpected cyclic dimers with N-H?N hydrogen bonds, presents in the solid state a dynamic proton disorder implying a dynamic equilibrium within both dimers. The conformations of the phenyl rings, the disorder of the NH protons, and the intermolecular hydrogen bond of several 1,2,4-diazaphospholes (1-5) in the solid state have been rationalized by DFT [B3LYP/6-311++G(d,p)] calculations.     

4-hydroxy-2H-1,2-benzothiazine-3-carbohydrazide 1,1-dioxide-oxalohydrazide (1:1): X-ray structure and DFT calculations

The title compound, 4-hydroxy-2H-1,2-benzothiazine-3-carbohydrazide 1,1-dioxide-oxalohydrazide (1:1), is determined using X-ray diffraction techniques and the molecular structure is also optimized at the B3LYP/6-31G(d,p) level using density functional theory (DFT). The asymmetric unit consists of four independent molecules. The oxalohydrazide molecules have the centre of symmetry at the mid-point of the central C-C bond. Each thiazine ring adopts a half-chair conformation. Intermolecular C-H...O, N-H...O and N-H...N hydrogen bonds produce R ₂ ² (10), R ₂ ² (13), R ₃ ³ (12) and R ₃ ³ (15) rings, which lead to one-dimensional polymeric chains. An extensive three-dimensional supramolecular network of N-H...N, N-H...O, C-H...O and O-H...O hydrogen bonds is responsible for crystal structure stabilization.     

Effect of a methyl substituent on the molecular and crystal structure of (2-acetyl-5-nitrofuran)-N-benzoylhydrazone

Conclusions An x-ray diffraction study of (2-acetyl-5-nitrofuran)-N-benzoylhydrazone has shown that the molecules of this compound have a nonplanar structure with syn arrangement of the oxygen and nitrogen atoms of the keto and hydrazone groups and an anti arrangement of the oxygen atom of the furan fragment. With such a conformation, the molecules do not form crystal hydrates; in the crystal, they are connected with one another into chains by intermolecular hydrogen bonds N-H...O 2.26 Å. However, intermolecular N O proton phototransfer does not occur between them.Translated from Izvestiya Akademiii Nauk SSSR, Seriya Khimicheskaya, No. 6, pp. 1319–1322, June, 1988.     

The molecular and crystal structure of tert-butyl Nalpha-tert-butoxycarbonyl-L-(S-trityl)cysteinate and the conformation-stabilizing function of weak intermolecular bonding

The title compound, C31H37NO4S [systematic name: (R)-tert-butyl-2-[(tert-butoxycarbonyl)amino]-3-(tritylsulfanyl)propanoate] is an L-cysteine derivative with three functions: NH2, COOH and SH, blocked by protecting groups tert-butoxycarbonyl, tert-butyl and trityl, respectively. The main chain of the molecule adopts the extended, nearly all-trans C5 conformation with the intramolecular N-H...O=C hydrogen bond. The urethane group is not involved in any intermolecular hydrogen bonding. Only weak intermolecular hydrogen bonds and hydrophobic contacts are observed in the crystal structure. These are C-H...O hydrogen bonds and CH/pi interactions with donor...acceptor distances, C...O ca. 3.5 A and C...C ca. 3.7 A, respectively. The first type of interaction links phenyl H-atoms and carbonyl groups. The second type of interaction is formed between a methyl group of the tert-butyl fragment and a trityl phenyl ring. The resulting molecular conformation in the crystal is very close to an ab initio minimum energy conformer of the isolated molecule. The extended C5 conformation of the main peptide chain is the same and there is slight discrepancy in the disposition of trityl phenyl rings. Their small dislocation creates the possibility of forming the entire network above of extensive, specific, weak intermolecular interactions; these constrain the molecule and permit it to retain the minimum energy C5 conformation of its main chain in the solid state. In contrast, in n-hexane solution, where such specific interactions cannot occur, only a small population of the molecules adopts the extended C5 conformation.     

Crystal and molecular structure analysis of flutamide. Bifurcated helicoidal C-H ⋯ O hydrogen bonds

Crystal structure determination and semiempirical AM1 and PM3 calculations were performed on flutamide {2-methyl-N[4 nitro-3-(trifluoromethyl) phenyl] propamide}, a powerful nonsteroidal androgen antagonist. The molecule is almost planar apart from CF₃, NO₂, and CH₃ groups. The NO₂ plane makes an angle of 36.3(4) with the least-square plane of the phenyl ring. The molecules are intermolecularly linked by one N-H O and one C-H O hydrogen bonds. A bifurcated helicoidal hydrogen bond network is formed by the intermolecular C-H O hydrogen bond together with another intramolecular C-H O hydrogen bond. The calculated structures are in good agreement with the crystallographic conformations. AM1 is more accurate for predicting the intramolecular C-H O hydrogen bond while PM3 gives a better geometry for the crowded nitro group. AM1 and PM3 charges of benzenic hydrogens are used to predict the propensity of these atoms to form hydrogen bonds. The noncentrosymmetric space group of the crystal (Pna2₁), the calculated dipole moment (8.88 D), and the calculated angle between molecular dipoles and the twofold axis (–49) close to the optimal value (54.7) indicate that flutamide might be a possible candidate for nonlinear optical material.     

Secondary bonding in functionalized organotellurium compounds: preparation and structural characterization of bis(acetamido)tellurium(IV) diiodide and bis(4-methylbenzoylmethyl)tellurium(II)

Elemental tellurium inserts, under mild conditions, between C-I bond of iodoacetamide to afford bis(acetamido)tellurium(IV) diiodide (NH₂COCH₂)₂TeI₂, 1. Heating of N-bromomethylphthalimide with activated tellurium powder however, resulted in the formation of bis(phthalimido)methane, 2, instead of the expected product bis(phthalimidomethyl)tellurium(IV) dibromide. The IR spectrum of 1 is indicative of intramolecular Te?OC interaction which is also substantiated by its single-crystal structure. The compound with planar small-bite chelating organic ligands acquires butterfly shape that imparts almost perfect C_2v molecular symmetry but unlike other organotellurium(IV) iodides, the solid state structure of 1 is devoid of any intermolecular Te?I or I?I secondary interactions owing to the presence of intramolecular Te?O secondary bonds as well as intermolecular N-H?O, N-H?I and C-H?I hydrogen bonds. Bis(4-methylbenzoylmethyl)telluride (4-MeC₆H₄COCH₂)₂Te, 3b, prepared by the reduction of the corresponding dibromide, is the first structurally characterized acyclic dialkyltelluride and interestingly, does not involve intramolecular Te?OC interaction invariably present in the parent dihalides (4-YC₆H₄COCH₂)₂TeX₂ (Y = H, X = I 4a; Y = H, X = Br 5a; Y = MeO, X = Br 5c). Weak intermolecular Te?Te and C-H?O hydrogen bonds appear to be the non covalent intermolecular associative forces that dominate its crystal packing in the solid state of this Te(II) derivative. The dialkyltellurides (4-YC₆H₄COCH₂)₂Te, (Y = H, 3a, Me, 3b) undergo oxidation in presence of (SCN)₂ to give the corresponding bis(isothiocyanato)tellurium(IV) derivatives and form 2:1 adducts with Pt(II) and Pd(II) chlorides.     

Three-dimensional supramolecular architecture based on 4,4′-methylene-bis(benzenamine) and aromatic carboxylic acid guests: Synthons cooperation, robust motifs and structural diversity

The two-component solid forms involving 4,4??-methylene-bis(benzenamine) included both salts and co-crystals, while 4,4??-methylene-bis(benzenamine) crystallized exclusively as a salt, in agreement with the differences in the pK _a values. Many of the crystal structures displayed either the neutral or the ionic form of the carboxylic acid-amino heterosynthon, and the similarity in crystal structures between the neutral and the ionized molecules makes the visual distinction between a salt and co-crystal dependent on the experimental location of the acidic proton. A variety of supramolecular hydrogen bonded motifs involving interactions between the aza molecules and carboxylic acid groups are observed rather than just the O-H??N/O-H??O motif. The motifs are identical in all the two compounds analyzed showing the robustness of these supramolecular synthons. In all adducts, recognition between the constituents is established through either N-H??O and/or O-H??O/O-H??N pairwise hydrogen bonds. In all adducts, COOH functional groups available on 1 and 2 interact with the N-donor compounds. The COOH moieties in 1 forms only single N-H??O hydrogen bonds, whereas in 2, it forms pairwise O-H??N/N-H??O hydrogen bonds. The supramolecular architectures are elegant and simple, with stacking of networks in 2, but a rather complex network with a threefold interpenetration pattern was found in 1. Thermal stability of these compounds has been investigated by thermogravimetric analysis (TGA) of mass loss.     

Synthesis, characterization, and X-ray crystal structures of copper(II) and nickel(II) complexes with Schiff base

New copper(II) complexes, [Cu₂L¹L²] · ClO₄ (I) and [Ni(L³)₂] (II), where L¹ is the monoanionic form of 2-[1-(2-emthylaminoethylimino)ethyl]phenol, L² is the dianionic form of N,N′-ethylene-bis(2-hydroxyacetophenonylideneimine), L³ is the mono-anionic form of 2-(1-iminoethyl)phenol, were prepared and characterized using elemental analysis, FT-IR spectroscopy, and X-ray single-crystal diffraction. In complex I, the Cu(1) atom is coordinated by the NNO tridentate ligand L¹ and the two phenolate O atoms of L², forming a square pyramidal geometry. The Cu(2) atom in complex I is coordinated by the NNOO tetradenate ligand L², forming a square planar geometry. The Ni atom in complex II is coordinated by two phenolate O and two imine N atoms from two ligands L³, forming a square planar geometry. In the crystal structure of I, the perchlorate anions are linked to the dinuclear copper(II) complex cations through intermolecular N-H...O hydrogen bonds. In the crystal structure of II, the mononuclear nickel complex molecules are linked through intermolecular N-H...O hydrogen bonds, forming a trimer.     

A theoretical study of 1-amino-3-butene and 3-butene-1-thiol

Conformational analysis of 1-amino-3-butene and 3-butene-1-thiol was carried out using the 4-21G basis set. The conformers obtained were subjected to 6-31G^* single-point analysis for the calculation of energies, charge distributions, and dipole moments. The geometries and stabilities obtained are in good agreement with available experimental data. The results are interpreted in terms of intramolecular hydrogen bonding and anomeric interactions: Some of the most stable conformers of both molecules have intramolecular hydrogen bonds between the hydrogens of the amino or thiol groups and the electrons of the double bond. The 4-21G geometries were refined to obtain rotational constants closer to the experimental values.     

Effect of the orientation of the water molecules in the system of hydrogen bonds in the crystal hydrate of m-bromo-N′-(5-nitrofurylidene)benzohydrazide on its sensitivity to light

On the basis of a crystal-chemical analysis of the structure of the investigated benzohydrazides, the structural characteristics typical of light-sensitive crystal hydrates of this type were formulated: the formation of intermolecular polar chains of hydrogen bonds of the C=O...H₂O...H-N type with the water molecules; head-to-tail stacking of the molecules. It was shown that the investigated m-bromo-N-(5-nitrofurylidene)benzohydrazide forms 12 crystal hydrates. The dimeric associates of the water molecules link the benzohydrazide molecules in the stacks by hydrogen bonds. Polar chains of hydrogen bonds, along which intermolecular N O-phototransfer of a proton occur, are formed between the stacks with the participation of one of the water molecules. An assignment was made of the bands for the OH stretching vibrations of the water molecules in the investigated crystal hydrate.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 3, pp. 567–572, March, 1990.     

X-ray diffraction investigation of siloxanes. I. Effects of organic substituents at the silicon atoms on the structure of acyclic trisiloxane-1,5-diols and on formation of different hydrogen bond systems

The molecular and crystal structure of four acyclic trisiloxane compounds, which differ in substituents at the silicon atoms (Ph-phenyl, mPh-methoxyphenyl, 2mPh-dimethoxyphenyl), was investigated by X-ray diffraction analysis. Due to intermolecular hydrogen bonding between the oxygen atoms of the diol fragments, the crystal structure of 1,1,5,5-tetramethyl-3,3-diphenyl-1,3,5-trisiloxane-1,5-diol (C₁₆H₂₄O₄Si₃) (I) is a double chain architecture with hydrogen-bonded dimeric motifs of C(8)R ₄ ⁴ (12) type in graph set representation. In 1,1,5,5-tetramethyl-3,3-(2-methoxybenzo)-1,3,5-trisiloxane-1,5-diol (C₁₈H₂₈O₆Si₃) (II) and 1,1,5,5-tetramethyl-3,3-(2,6-dimethoxybenzo)-1,3,5-trisiloxane-1,5-diol (C₂₀H₃₂O₈Si₃) (III), a double chain structure with a graph set R ₃ ³ (8)D ₃ ³ (10) is formed. In contrast to I–III, 1,1,3,3,5,5-hexaphenyl-1,3,5-trisiloxane-1,5-diol (C₃₆H₃₂O₄Si₃) (IV) has an intramolecular hydrogen bond S(8). The independent molecules are joined by O-H...O intermolecular hydrogen bonds into centrosymmetrical dimers; the system of hydrogen bonds in general may be described as S(8)R ₄ ⁴ (8).     

Four different types of hydrogen bonds observed in 1,2-bis(N-benzenesulfonylamino)benzenes due to conformational properties of the sulfonamide moiety

The crystal structures of 1,2-bis(N-benzenesulfonylamino)benzenes with secondary and/or tertiary sulfonamide groups were determined by X-ray crystallographic analysis. Every Ar-sulfonamide group existed in synclinal conformation in the crystals even though it was secondary or tertiary. Each compound showed different types of hydrogen bonds in the crystal structure. 1,2-Bis(N-benzenesulfonylamino)benzene (1) formed two double hydrogen bonds connected to the next molecules, 1-(N-benzenesulfonylamino)-2-(N-benzenesulfonyl-N-methylamino)benzene (2) contained double hydrogen bond involved by both the sulfonamide moieties, 1,2-bis(N-4-toluenesulfonylamino)benzene (3) had both intra- and intermolecular hydrogen bonds, and 1-(N-methyl-N-4-toluenesulfonylamino)-2-(N-4-toluenesulfonylamino)benzene (4) had one double hydrogen bond involved by only one sulfonamide moiety. Sulfonamides 1 and 3 formed infinite arrays of the molecules, and sulfonamides 2 and 4 formed racemic dimer of their conformational enantiomers via the hydrogen bonds.