X-ray and IR studies of

The propensity of C-F groups to form C-F H-C interactions with C-H groups on other molecules has been analyzed. Crystal structures of molecules containing only carbon, hydrogen, and fluorine, but no oxygen, nitrogen, or other hydrogen-bond-forming elements, were chosen for an initial study in which the intermolecular interactions in crystal-structure determinations of polycyclic aromatic hydrocarbons and their analogous fluoro derivatives were analyzed. It is found that C-F H-C interactions occur, but they are weak, as judged by the intermolecular distances and the angles involved. In a study of crystal structures of molecules containing other elements in addition to carbon, hydrogen, and fluorine, it was found that when an oxygen atom is in a neighboring position on an interacting molecule, a C-O group is more likely than a C-F group to form a linear interaction to the hydrogen atom of a C-H group. Thus, in spite of the high electronegativity of the fluorine atom, a C-F group competes unfavorably with a C-O^–, C-OH, or C=O group to form a hydrogen bond to an O-H, N-H, or C-H group. It is found, however, particularly for polycyclic aromatic hydrocarbons with substituted CF₃ groups that, in the absence of other functional groups that can form stronger interactions, C-F H-C interactions may serve to align molecules and give a different crystal packing from that in the pure hydrocarbon (where fluorine is replaced by hydrogen). Thus, C-F H-X (X = C, N, O) interactions are very weak, much weaker than C=O H-X interactions, but they cannot be ignored in predictions of modes of molecular packing in complexes and in crystals.     

The geometry of intermolecular interactions in some crystalline fluorine-containing organic compounds

The propensity of C-F groups to form C-F H-C interactions with C-H groups on other molecules has been analyzed. Crystal structures of molecules containing only carbon, hydrogen, and fluorine, but no oxygen, nitrogen, or other hydrogen-bond-forming elements, were chosen for an initial study in which the intermolecular interactions in crystal-structure determinations of polycyclic aromatic hydrocarbons and their analogous fluoro derivatives were analyzed. It is found that C-F H-C interactions occur, but they are weak, as judged by the intermolecular distances and the angles involved. In a study of crystal structures of molecules containing other elements in addition to carbon, hydrogen, and fluorine, it was found that when an oxygen atom is in a neighboring position on an interacting molecule, a C-O group is more likely than a C-F group to form a linear interaction to the hydrogen atom of a C-H group. Thus, in spite of the high electronegativity of the fluorine atom, a C-F group competes unfavorably with a C-O^–, C-OH, or C=O group to form a hydrogen bond to an O-H, N-H, or C-H group. It is found, however, particularly for polycyclic aromatic hydrocarbons with substituted CF₃ groups that, in the absence of other functional groups that can form stronger interactions, C-F H-C interactions may serve to align molecules and give a different crystal packing from that in the pure hydrocarbon (where fluorine is replaced by hydrogen). Thus, C-F H-X (X = C, N, O) interactions are very weak, much weaker than C=O H-X interactions, but they cannot be ignored in predictions of modes of molecular packing in complexes and in crystals.     

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.     

The X-ray crystal and molecular structure of 5′-bromo-5′-deoxythymidine

5′-Bromo-5′-deoxythymidine (1) crystallizes with four molecules in a monoclinic unit cell of space group C2. The ribose ring adopts an envelope conformation, transient between T and E₀ (O4′-exo), with the C1′ atom being in the flap position. In the crystal lattice, the molecules are connected by intermolecular one-dimensional chains of hydrogen bondings from the hydroxyl hydrogen H3′(O3′) to the carbonyl oxygen O4. The differences in conformation and a hydrogen-bonding system of 1 with comparison to the structure of thymidine are observed. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9: 591–596, 1998     

A study of DFT and surface enhanced Raman scattering in silver colloids for thymine

The vibrational spectrum of crystal thymine is calculated by density functional theory (DFT) at the B3LYP complex function. Considering the effect of intermolecular H-bonds, we add two water molecules that can form H-bonds with the CO and NH groups of thymine. The experimental spectra of normal Raman of thymine in solid state and surface enhanced Raman (SERS) of thymine adsorbed in silver colloids are presented in this study. The calculated Raman spectrum of thymine by DFT is in agreement with the experimental result of normal Raman spectrum. The appearance of new bands of thymine in SERS shows that molecules of thymine are adsorbed in the surface of silver nanoparticles with a perpendicular orientation through an oxygen atom (O7).     

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.     

Structure and photochemical properties of [N′-(2-thienylidene)]benzhydrazide crystals

The x-ray structural study showed that [N-(2-thienylidene)]benzhydrazide does not form a crystal hydrate. The molecules in the crystal are loosely packed and joined by linear chains of intermolecular hydrogen bonds (IHB),. Like the previously investigated [N-(furfurylidene)] benzhydrazide, [N-(2-thienylidene)]benzhydrazide crystals were sensitive to UV radiation. The similarity in the structure of these compounds confirms the hypothesis that intermolecular N O phototransfer of a proton along the IHB chain can take place efficiently in loose structures in the noncrystal hydrates of the compounds investigated, in contrast to the previously studied crystal hydrates.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 1, pp. 87–90, January, 1991.     

Structural and spectral studies of 3-(2-hydroxyphenylimino)-1-phenylbutan-1-one and its diorganotin(IV) complexes

Two diorganotin(IV) complexes of the general formula R₂Sn[Ph(O)CCH-C(Me)N-C₆H₄(O)] (R = Ph, 1a; R = Me, 1b) have been synthesized from the corresponding diorganotin(IV) dichlorides and the ligand, 3-(2-hydroxyphenylimino)-1-phenylbutan-1-one (1) in methanol at room temperature in presence of triethylamine. Both compounds have been characterized by elemental analyses, IR and ¹H, ¹³C, ¹⁵N, ¹¹⁹Sn NMR spectra. The structures of the free ligand and the complexes have been confirmed by single crystal X-ray diffraction. There are three independent molecules in the crystal structure of the ligand 1 and in all three the O-bound proton is transferred to the imine nitrogen and makes an intramolecular N-H?O hydrogen bond with the carbonyl oxygen. In turn this makes an intermolecular hydrogen bond with the phenolic H atom. The crystal structure of 1 is trigonal and a new polymorph; triclinic and monoclinic forms have already been published. In 1a, the central tin atom adopts distorted trigonal-bipyramidal coordination geometry whereas in dimeric 1b it is distorted octahedral when including the intermolecular Sn-O(phenolic) bond [2.7998(20) Å]. The δ (¹¹⁹Sn) values for the complexes 1a and 1b are −306.6 and −127.9 ppm, respectively, thus indicating penta-coordinated Sn centres in solution.     

Crystal Structure of the Complex of 1,2-Bis[2-(o-hydroxyphenoxy)ethoxy]ethane with Ammonium Thiocyanate

The complex of the podand 1'2-bis[2-(o-hydroxyphenoxy)ethoxy]ethane (L) with ammoniumthiocyanate, [NH₄(SCN)L], was prepared, studied by single crystal X-ray diffraction. This is a host-guestcomplex; in its molecule the podand L is wrapped around the NH ₄ ⁺ cation, which forms hydrogen bondswith all the six oxygen atoms of the podand and one hydrogen bond with the sulfur atom of the SCN^- anion. The geometric parameters (bond lengths, bond angles, torsion angles, etc.) of the molecule of [NH₄(SCN)L] and packing of the molecules in the crystal were determined. The molecules are linked into infinite polymeric chains by intermolecular hydrogen bonds O-H···NCS.     

Crystal and Molecular Structure of 5-Acetylamino-3-nitro-1,2,4-triazole

This paper reports on an X-ray diffraction study of 5-acetylamino-3-nitro-1,2,4-triazole. Monoclinic crystals, space group P2_1/c; a=8.2079(7), b=13.096(1), c=13.650(1) , =100.64(1)°. Two independent molecules are identical in conformation and both have an N–H···sO intramolecular hydrogen bond; the difference lies in their interactions with neighbors. In molecule A, the acetyl oxygen atom and all nitrogen atoms (except those of the amino group) are involved in the intermolecular hydrogen bonds; in molecule B, these hydrogen bonds are formed by only two NH groups in addition to the above oxygen. The crystal structure of the title compound is compared with that of 5-amino-3-nitro-1,2,4-triazole.     

Synthesis and Structure of Tetraaqua-bis(2-Formylphenoxyacetato)Zinc(II) Dihydrate

The complex [Zn(Ofpa)₂(H₂O)₄] · 2H₂O (Ofpa is 2-formylphenoxyacetate) is synthesized and characterized by X-ray structural analysis and IR spectroscopy. The crystal is monoclinic: a= 25.254(5), b= 6.952(1), c= 13.951(3) Å, = 116.41(3)°, Z= 4, space group C2/c, R= 0.034. The zinc atom in the centrosymmetric complex is coordinated by two monodentate carboxylate ligands (Zn–O 2.123(1) Å) and by four water molecules (Zn–O 2.085(1) and 2.092(2) Å). The oxygen atom of the aldehyde group is not involved in coordination. Complexes and solvate water molecules in the crystal are united into a three-dimensional framework via hydrogen bonds and – interactions.     

X-Ray structural investigation of the alkaloid speciosine

The molecular and crystalline structures of a tropolone alkaloid of the colchicine series — speciosine — have been determined by x-ray structural analysis. It has been established that the presence of an orthohydroxyphenyl group does not lead to appreciable changes of the colchicine skeleton in the speciosine molecule. In the crystals, the speciosine molecules are linked into zigzag chains through O6–HO1 intermolecular H-bonds.Translated from Khimiya Prirodnykh Soedinenii, No 4, pp. 608–612, July–August, 1997.     

Structural features of light-sensitive crystals of N′-[2-nitrofurfuryl-5-vinyl]benzhydrazide and [N′-furfurylidene)]benzhydrazide

An x-ray structural study found that N-[2-nitrofurfuryl-5-vinyl]benzhydrazide and [N-(furfurylidene)]benzhydrazide do not form crystal hydrates although they have polar syn-conformations. Molecules in the crystal are joined by linear chains of intermolecular H-bonds C=O...H-N. The light-sensitivity of the crystals increases with decreasing packing density.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 7, pp. 1556–1562, July, 1990.     

Synthesis and the molecular and crystal structure of 1, 4-dihydro-1-methyl-4-(2, 3, 3-tricyanoallylidene)quinoline

The reaction of 1, 4-dimethylquinolinium iodide with tetracyanoethylene in presence of triethylamine proceeds highly regioselectively with the formation of l, 4-dihydro-l-methyl-4-(2, 3, 3-tricyanoallylidene)quinoline. It was shown by an x-ray structural investigation that its crystal is built from two, not quite planar, symmetrically independent molecules (IIIa) and (IIIb): The dihedral angles in these between the dihydroquinoline nucleus and the tricyanoallylidene group are 8.6 and 10.8. An examination is made of the influence on the structure of the molecules of steric factors and effects of the conjugation of the donor and acceptor parts of the molecules, leading to considerable intramolecular transfer of charge. In the crystal the molecules form stacks of the type ...aabb... with the participation of both symmetrically independent molecules and with interplanar distances d of 3.341, 3.449, and 3.347 å, which may be conducive to intermolecular transfer of charge.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 3, pp. 690–696, March, 1991.     

X-ray and IR spectroscopic studies of specific intermolecular interactions inN′-substituted isonicotinohydrazides

_N-Thenylidene- andN-(o-nitrobenzylidene)hydrazides of isonicotinic acid have been studied by X-ray structural analysis and IR spectroscopy. In the crystalline state, these molecules are linked through intermolecular N—H ... Np_y hydrogen bonds. Carbonyl groups are not involved in intermolecular hydrogen bonds. However, it was found that the C=O group participates in an attractive interaction with the sulfur atom of the thiophene group. The energy of this interaction is comparable with the energies of intermolecular C=O ... H—N hydrogen bonds in amides.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 896–900, April, 1996.     

Crystal packing effects within [Mn3O] single-molecule magnets: Controlling intermolecular antiferromagnetic interactions

The reactions of 2-hydroxyphenylethanone oxime (Me-H₂salox) and (2-hydroxy-phenyl)-phenyl-methanone oxime (Ph-H₂salox) with Mn(ClO₄)₂·6H₂O in MeOH afford trinuclear manganese complexes of [Mn₃O(Me-salox)₃(MeOH)₃(ClO₄)]·MeOH (1·MeOH) and [Mn₃O(Ph-salox)₃(MeOH)₃(ClO₄)]·2MeOH (2·2MeOH), respectively. X-ray analysis shows that both complexes contain a manganese triangle core, [Mn^III₃O]⁷⁺. The structural distortion from the twisting of the oxime ligands dominates the ferromagnetic interactions within the three Mn ions in both compounds and results in an S = 6 ground state. The frequency dependence of out-of-phase signals in the alternating current (AC) magnetic susceptibility measurements and the temperature-dependent and sweep-rate-dependent hysteresis loops are indicative of single-molecule magnet behavior. Moreover, both complexes show step-wise magnetization, indicating the occurrence of quantum tunneling of magnetization (QTM). Interestingly, a tail to tail arrangement in the crystal packing of complex 1·MeOH results in strong intermolecular H-bonding interactions and leads to the exchange-bias effect from the antiferromagnetic interaction between the adjacent Mn₃ molecules. In contract, QTM steps of complex 2·2MeOH show an absence of the exchange-bias effect due to a weak intermolecular interaction from a head to tail arrangement.     

(4R)-4-Hydroxy-1-nitroso-l-proline: synthesis, X-ray structure, ab initio and conformational calculations

4-Hydroxy-l-proline, an amino acid, an important component of collagen, was transformed into its N-nitroso-derivative, (4R)-4-hydroxy-1-nitroso-l-proline, 1 by butylnitrite in the acidic medium. The structure is a cyclic hydroxy-N-nitrosoacid with the carboxyl and hydroxyl groups trans to each other. The carboxyl group is in the syn-conformation. In the structure, the neutral molecules are connected via classical intermolecular O-H?O hydrogen bonds involving the hydroxyl and carboxyl groups [O?O=2.6251(14) Å], and form chains along the a-axis direction. The chains are linked into sheets via O-H?O hydrogen bond, [O?O=2.6813(15) Å] with participation of oxygen atom of nitroso group. Ab initio calculations based on density functional theory at the B3LYP/6-311++G(d, p) level of theory were performed to analyze the influence of 4-hydroxy-l-proline (Hyp) nitrosation on the conformation of the synthesized N-nitroso-compound. The geometry optimization of 1 and initial 4-hydroxy-l-proline was carried out in the gas phase and in solution using the polarizable continuum model. The single-point calculation was performed for the crystal structure of 1. The most stable conformer of 1 is observed in an aqueous solution. In this state, the pyrrolidine ring adopts an envelope conformation, which is also maintained in the gas phase. The twisted conformation of the pyrrolidine ring is present in all states of Hyp and in the crystal structure of 1. In 1 the interchange of five-membered ring conformation in solution and in the gas phase in comparison with the crystal is accompanied by an increase of the dipole moment of the molecule, which is maximal in solution.     

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.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 2501–2505, October, 1996.