X-ray crystal structures of halogen containing nucleobase derivatives in unsolvated and DMSO solvated forms

A series of halogenated nucleobase derivatives 1–4 is reported to yield solvent-free (2) and DMSO solvated crystals (1, 3, 4) on the crystallization from DMSO with one of them (4) containing an additional molecule of water. The molecular and crystal structures are described and comparatively discussed with reference to previous results on related compounds. The molecule of 1 is planar, molecules of 2 and 3 show syn alignment with reference to the heterocyclic ring and common C2′-endo conformation of the ribose residue, while 4 is also syn aligned but C4′-exo in the sugar conformation. The packing structures reveal typical aggregations created via networks of hydrogen bonds. These involve conventional N–H···N, N–H···O and O–H···O interactions between nucleobase and ribose units as well as solvent molecules, additionally supported by weak C–H···O contacts but excluding the participation of halogen···halogen interactions as well as halogen···heteroatom contacts in the supramolecular structure formation.     

Crystal growth and characterization of N-hydroxyphthalimide (C8H5NO3) crystal

Single crystals of N-hydroxyphthalimide (NHPH) were obtained from saturated aqueous solutions of methanol and acetonitrile by slow cooling method. The grown crystals were bright and transparent. From the crystal structure analysis it can be inferred that the crystal belongs to monoclinic system. The grown crystals were subjected to FTIR analysis for vibrational assignments. The optical transmission spectra showed excellent transmittance from 200 to 1100nm. The thermal stability and thermal decomposition of NHPH crystal have been investigated by means of thermogravimetric analysis and differential thermal analysis.     

Syntheses and crystal structures of two magnesium–tetrazole compounds in salt and polymeric forms

Two alkaline earth–tetrazole compounds, namely catena‐poly[[[triaquamagnesium(II)]‐μ‐5,5′‐(azanediyl)ditetrazolato‐κ³N¹,N^1′:N⁵] hemi{bis[μ‐5,5′‐(azanediyl)ditetrazolato‐κ³N¹,N^1′:N²]bis[triaquamagnesium(II)]} monohydrate], {[Mg(C₂HN₉)(H₂O)₃][Mg₂(C₂HN₉)₂(H₂O)₆]_0.5·H₂O}_n, (I), and bis[5‐(pyrazin‐2‐yl)tetrazolate] hexaaquamagnesium(II), (C₅H₃N₆)[Mg(H₂O)₆], (II), have been prepared under hydrothermal conditions. Compound (I) is a mixed dimer–polymer based on magnesium ion centres and can be regarded as the first example of a magnesium–tetrazolate polymer in the crystalline form. The structure shows a complex three‐dimensional hydrogen‐bonded network that involves magnesium–tetrazolate dimers, solvent water molecules and one‐dimensional magnesium–tetrazolate polymeric chains. The intrinsic cohesion in the polymer chains is ensured by N—H...N hydrogen bonds, which form R₂²(7) rings, thus reinforcing the propagation of the polymer chain along the a axis. The crystal structure of magnesium tetrazole salt (II) reveals a mixed ribbon of hydrogen‐bonded rings, of types R₂²(7), R₂²(9) and R₂⁴(10), running along the c axis, which are linked by R₂⁴(16) rings, generating a 4,8‐c flu net.     

Comparison of the crystal structures and magnetic properties of the low- and high-temperature forms of AgCuPO4: crystal structure determination, magnetic susceptibility measurements, and spin dimer analysis

The crystal structure of the low-temperature form of AgCuPO4 (i.e., alpha-AgCuPO4) was determined by powder X-ray diffraction and was compared with that of the high-temperature form of AgCuPO4 (i.e., beta-AgCuPO4). The magnetic properties of the two forms were examined by measuring their magnetic susceptibilities and evaluating the relative strengths of their spin-exchange interactions on the basis of spin-dimer analysis. Both forms of AgCuPO4 have layers of Cu2P2O8 alternating with silver-atom double layers; beta-AgCuPO4 has two Cu2P2O8 layers per unit cell, while alpha-AgCuPO4 has one. The coordinate environment of each Cu2+ ion is close to being a distorted square pyramid in alpha-AgCuPO4, but it is close to being a distorted trigonal bipyramid in beta-AgCuPO4. The magnetic susceptibilities of alpha- and beta-AgCuPO4 are well simulated by an antiferromagnetic alternating-chain model, which leads to J/k(B) = -146.1 K and alphaJ/k(B) = -75.8 K for alpha-AgCuPO4, and J/k(B) = -82.6 K and alphaJ/k(B) = -31.7 K for beta-AgCuPO4 (with the convention in which the spin-exchange parameter between two adjacent spin sites is written as 2J). The spin gaps, delta/k(B), obtained from these parameters are 93.7 K for alpha-AgCuPO4 and 62.3 K for beta-AgCuPO4. The strongest spin exchange in both forms of AgCuPO4 comes from a super-superexchange path, and this interaction is stronger for alpha-AgCuPO4 than for beta-AgCuPO4 by a factor of approximately 2, in good agreement with the experiment. Our analysis supports the use of this model for beta-AgCuPO4 and indicates that the spin lattice of alpha-AgCuPO4 would be better described by a two-dimensional net made up of weakly interacting alternating chains.     

Semiclathrates of the Ge-P-Te system: synthesis and crystal structures

Novel compounds [Ge_46?xP_x]Te_y (13.9≤x≤15.6, 5.92≤y≤7.75) with clathrate‐like structures have been prepared and structurally characterized. They crystallize in the space group Fm$\bar 3Novel compounds [Ge(46-x) P(x) ]Te(y) (13.9≤x≤15.6, 5.92≤y≤7.75) with clathrate-like structures have been prepared and structurally characterized. They crystallize in the space group Fm ?3 with the unit cell parameter changing from 20.544(2) to 20.698(2) ? (Z=8) on going from x=13.9 to x=15.6. Their crystal structure is composed of a covalently bonded Ge-P framework that hosts tellurium atoms in the guest positions and can be viewed as a peculiar variant of the type?I clathrate superstructure. In contrast to the conventional type I clathrates, [Ge(46-x) P(x) ]Te(y) contain tricoordinated (3b) atoms and no vacancies in the framework positions. As a consequence of the transformation of the framework, the majority of the guest tellurium atoms form a single covalent bond with the host framework and thus the title compounds are the first representative of semiclathrates with covalent bonding. A comparison is made with silicon clathrates and the evolution of the crystal structure upon changing the tellurium content is discussed.     

Fluorinated diphenylpolyenes: crystal structures and emission properties

(E,E,E)-1,6-Diaryl(Ar)-1,3,5-hexatrienes (2, Ar = 4-fluorophenyl; 3, Ar = 2,4-difluorophenyl; 4, Ar = 2,4,6-trifluorophenyl; 5, Ar = perfluorophenyl) and (E,E,E)-1-perfluorophenyl-6-phenyl-1,3,5-hexatriene (6) were prepared. The absorption and fluorescence spectra in methylcyclohexane solution showed only a small dependence on the fluorine ring substituent, and were similar to those of the unsubstituted parent compound (1, Ar = phenyl). The solid-state absorption and fluorescence spectra shifted to red relative to those in solution and strongly depended on the substituent. The emission from crystals 1-5 originated mainly from monomeric species with the maximum wavelength (lambda f(max)) of 440-465 nm, which overlapped the emission from molecular aggregates (1-4) or excimeric species (5) in the red region. Crystal 6 exhibited red-shifted (lambda f(max) = 530 nm) and structureless emission due to excimers. The cocrystal of 1 and 5 (1/5) showed red-shifted (lambda f(max) = 558 nm) and distinctly structured emission, not from exciplexes but from the excited states of molecular aggregates in which molecules 1 and 5 strongly interact already in the ground state. These assignments were confirmed by the results of fluorescence lifetime and quantum yield measurements in the solid state. Single-crystal X-ray structure analyses showed that the molecules were basically planar in each crystal, whereas the crystal packing was strongly substituent-dependent. Weak pi-pi interactions in the herringbone (1 and 2) and in the pi-stacked but largely offset structures (3 and 4) account for their predominantly monomeric origin of emission. The observation of excimer fluorescence from 5 was rather unexpected, since the molecules in this crystal were arranged in an offset stacking fashion due to perfluorophenyl-perfluorophenyl (C6F5...C6F5) interaction. The structures of 6 and 1/5 considerably resembled each other, in which molecules were pi-stacked with more face-to-face geometries than those in 5, as a result of strongly attractive perfluorophenyl-phenyl (C6F5...C6H5) interaction. Nevertheless, the fluorescence origin was clearly different for 6 and 1/5. This can be ascribed to the difference in the strength of orbital-orbital interaction between molecular pi-planes in the ground and excited states in crystals.     

Cyanocomplexes with one-dimensional structures: preparations,crystal structures and magnetic properties

The review surveys the preparation methods, crystallochemistry and magnetic properties of one-dimensional cyanocomplexes. Their preparation methods are mainly based on reactions in solutions containing suitable building blocks as precursors of the polymeric structure. The analysis of published data on crystal structures is given, as the knowledge of the crystal structure is essential for the study of magneto-structural correlation. Published data on magnetic properties are discussed along with the methods used for the study of magnetic properties.     

Aurophilic interactions in cationic gold complexes with two isocyanide ligands. Polymorphic yellow and colorless forms of [(cyclohexyl isocyanide)2AuI](PF6) with distinct luminescence

Crystallographic studies of yellow and colorless forms of [(C(6)H(11)NC)(2)Au(I)](PF(6)) show that they are polymorphs with differing, but close, contacts between the gold atoms which form extended chains. In the colorless polymorph the gold cations form linear chains with a short Au...Au contact (3.1822(3) A) indicative of an aurophilic attraction. The structure of the yellow polymorph is more complicated with four independent cations forming kinked, slightly helical chains with very short Au...Au contacts of 2.9803(6), 2.9790(6), 2.9651(6), and 2.9643(6) A. However, in the related compound, [(CH(3)NC)(2)Au(I)](PF(6)), each cation is surrounded by six hexafluorophosphate ions and there is no close Au...Au contact despite the fact that the isocyanide ligand has less steric bulk. The crystalline colorless and yellow polymorphs are both luminescent at 298 K, lambda(max): 424 nm (colorless) or 480 nm (yellow). Colorless solutions of the two polymorphs have identical absorption spectra and are nonluminescent at room temperature. Freezing solutions of [(C(6)H(11)NC)(2)Au(I)](PF(6)) produces intense luminescence which varies depending upon the solvent involved. Each polymorph melts to give a colorless but luminescent liquid which reverts to the yellow polymorph upon cooling.     

Quinoxaline-annelated Z-shaped quadruple-bridged orthocyclophanes: synthesis and crystal structures

A three-step synthesis of nineteen Z-shaped quadruple-bridged [6,6] and [6,4]orthocyclophanes comprising two quinoxaline-based sidewalls are described. The synthesis began from the bis-Diels−Alder adducts B1-B3 followed by ruthenium-promoted oxidation of dichloroetheno-bridges in the adducts to generate a bis-α-diketones, which were then condensed with various arene-1,2-diamines (9a-g) to construct sidewalls (phane parts) of Z-shaped quadruple-bridged orthocyclophanes D1-3, D2g, and D3g. Single-crystal structures of six orthocyclophanes (D1a, D2a, D2f, D3f, D2g-α, and D3g-α) were obtained and revealed that the C_Ar−H?π and π?π stacking interactions between N-containing arene rings are the major driving force for molecular assembly and crystal packing, in addition to the interactions involving the polar OCH₃ groups and the solvate molecules.     

Complexes of unsymmetric bis-hydrazide ligands: crystal structures and properties

Two unsymmetric bis-aroyl-hydrazines, N′-(2-hydroxybenzoyl)isonicotinohydrazide (L1) and N′-(2-hydroxybenzoyl)nicotinohydrazide (L2), were synthesized through reactions of salicyl hydrazide with isonicotinoyl chloride and nicotinoyl chloride, respectively. Reactions of metal salts with L1 or L2 gave three new complexes, [Cd(L1)₂(SCN)₂] _n (1), [Zn(L1)₂Cl₂]?·?H₂O (2), and [Zn(L2)₂Cl₂] (3). Complex 1 features a 1-D double-chain structure built by SCN^– bridging six-coordinate Cd^II centers while 2 and 3 are mononuclear Zn^II complexes. In 1–3, isomeric ligands L1 and L2 coordinate with metal ions in a terminal coordination mode. Ligands L1 and L2 through O–H···N and N–H···O hydrogen-bonding interactions in 1–3 are crucial for the structure extension into 3-D supramolecular structures of 1 and 2, or 2-D sheet of 3. Complexes 1–3 emit interesting blue-green luminescence. Thermal behaviors of 1–3 as well as the specific rotation of 2 were also investigated.     

Disordering in the crystal structures of thienylgermatranes

The crystal structure of a series of thienylgermatranes has been studied using X-ray diffraction. Disorder of the thiophene ring in a 2-thienylgermatrane has been established. In the same positions of the unit cell of the crystal there are found both molecules with an O(2)-Ge-C-S torsional angle of −166.8(4)° and molecules in which this angle is 14.0(4)°. The lengths of the transannular N→Ge bonds (2.183–2.283 Å) agrees in value with the values of crystalline germatrane structures with a Ge-C bond. The length of the transannular N→Ge bond (2.248 Å) in 4-(2-thienyl)phenylgermatrane (molecule A) is the largest amongst germatranes with a Ge-C_ar bond. Introduction of a second thiophene ring into the 2-thienylgermatrane molecule lowers the acute toxicity of the compound by about 27 times (LD₅₀ for the 2,2′-bithienylgermatrane = 447 mg/kg). __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 299–306, February, 2007.     

The further crystallographic refinement of trichosanthin at 2.7A resolution and the comparison among the three molecular structures in two crystal forms

The three-dimensional structure of trichosanthin at 2.7A resolution has been improved further, by refitting one of the C-terminal tails, adjusting 16 residues in the molecular surface regions, discarding some water molecules with high B values, and adjusting weights during the further refinement. The R-factor has been reduced to 18.5% and the r.m.s deviations from ideal geometry are also improved. The structures of the two molecules in the monoclinic asymmetric unit and the only molecule in the orthorhombic asymmetric unit are compared with one another. The main-chain structures for most of the residues in the three molecules are substantially the same. However, the courses of the three C-terminal tails are completely different, and the intermolecular interactions resulting from the particular packing of the molecules in the crystals account for the differences. The strand Be-2 and the preceding B-turn in small domain show large r.m.s. deviations among the three molecules and they are also involved in i     

Mechanism of the catalytic oxidation of hydrocarbons by N-hydroxyphthalimide: a theoretical study

The mechanism of the recently proposed catalytic oxidation of hydrocarbons by oxygen in the presence of N-hydroxyphthalimide (NHPI) was established by quantum chemical calculations, consistent with experiments.     

Stereoisomers of 1,3,5,7-tetrahydroxy-1,3,5,7-tetraisopropylcyclotetrasiloxane: synthesis and structures in the crystal

The first synthesis of all four stereoisomers of 1,3,5,7-tetrahydroxy-1,3,5,7-tetraisopropylcyclotetrasiloxane, [i-PrSiO(OH)]4 (all-trans-, cis-cis-trans-, cis-trans-cis-, and all-cis-1), is presented. The starting compounds, all-trans-, cis-cis-trans-, cis-trans-cis-, and all-cis-1,3,5,7-tetraaryl-1,3,5,7-tetraisopropylcyclotetrasiloxanes, were prepared by the hydrolysis of the corresponding arylisopropyldichlorosilanes, i-PrArSiCl2 (Ar = Ph, p-tolyl), and subsequent separation of isomers. A combination of dephenylchlorination of tetraarylcyclotetrasiloxanes and the following hydrolysis proved to be an efficient method for the stereospecific transformation of aryl-substituted cyclotetrasiloxanes into (i-PrSiO(OH))4. For example, treatment of cis-trans-cis-1,3,5,7-tetraphenyl-1,3,5,7-tetraisopropylcyclotetrasilane with HCl and AlCl3, followed by hydrolysis in the presence of pyridine, resulted in the exclusive formation of cis-trans-cis-1 in 92% yield. The structures of cis-cis-trans-1, cis-trans-cis-1, and all-cis-1 were determined by X-ray crystallography. All isomers were found to construct unique packing structures by intermolecular hydrogen bonding; cis-trans-cis-1 composed an infinite antiladder structure, and cis-cis-trans-1 formed a sheetlike structure.     

Preparation and crystal structures of technetium phosphides

The system technetium-phosphorus was investigated for the first time. Samples prepared at 1220 K using the tin-flux technique or iodine as a mineralizer showed the existence of six technetium phosphides. Only those with the lowest and highest phosphorus content are isotypic with known manganese or rhenium phosphides. Tc₃P crystallizes in the tetragonal Mn₃P (Fe₃P type) structure: a = 9.568 ± 0.005, c = 4.736 ± 0.003 Å; TcP₄ has the orthorhombic ReP₄-type structure: a = 6.238 ± 0.001, b = 9.215 ± 0.003, c = 10.837 ± 0.003 Å. The crystal structures of these two compounds were refined from single-crystal X-ray diffractomer data to conventional residual values of R = 0.039 for Tc₃P (19 variables, 1698 F values) and R = 0.031 for TcP₄ (23 variables, 1848 F values). The crystal chemistry of these two compounds is discussed.