The electronic structure of the C2H4O···2HF tri-molecular heterocyclic hydrogen-bonded complex: a theoretical study

The geometries of three isomers of the C₂H₄O···2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation of infrared stretching modes, and Bader’s atoms in molecules (AIM) theory calculations was carried out in order to characterize the hydrogen bonds in each isomer of the C₂H₄O···2HF complex. The most stable structure was determined through the identification of hydrogen bonds between C₂H₄O and HF, (O···H), as well as in the hydrofluoric acid dimer, (HF^D–R···HF^D). However, the existence of a tertiary interaction (F^λ···H^α) between the fluoride of the second hydrofluoric acid and the axial hydrogen atoms of C₂H₄O was decisive in the identification of the preferred configuration of the C₂H₄O···2HF system. Figure Geometries of three isomers of the C₂H₄O···2HF tri-molecular heterocyclic hydrogen-bonded complex     

Synthesis of metal paddlanes: X-ray structure determination of bis-(methyl nicotinate)copper(II) acetate dimer

The synthesis of nicotinic acid based N,N′-bidentate ligands capable of spanning the axial sites of copper(II) acetate dimer are reported. Reaction of these ligands with [Cu(C₂H₃0₂)₂]₂·2H₂0 gave the 1:1 adduct: a metal paddlane, which on recrystallization from MeOH/CHCl₃ yielded the trans-esterified complex [Cu(C₂H₃O₂)₂]₂·2C₇H₇N0₂, 3. A single crystal X-ray structure determination of 3 is presented.     

Kinetics of Inhibition of Rabbit Intestine Alkaline Phosphatase by Heteroligand Peroxo Complexes of Vanadium(V) and Tungsten(VI)

The present work was undertaken to examine and compare some biologically important properties of peroxo compounds of V(V) and W(VI) containing biogenic species as ancillary ligand. New anionic peroxovanadate(V) complex of the type Na[VO(O₂)₂(triglycine)]·3H₂O (pV1) and a molecular peroxotungstate(VI) [WO(O₂)₂(triglycine)]·3H₂O (pW1) were synthesized and characterized for the purpose and their stability in solution was ascertained. Studies on kinetics of inhibition of alkaline phosphatase activity by the newly synthesized compounds and series of dipeptide and amino acid containing peroxo complexes of vanadium and tungsten synthesized previously by us viz., Na[VO(O₂)₂(gly-gly)(H₂O)]·H₂O (gly-gly = glycyl-glycine), Na[VO(O₂)₂(asn)]·H₂O (asn = asparagine), Na[VO(O₂)₂(gln)]·H₂O (gln = glutamine), and [WO(O₂)₂(gly-gly)(H₂O)]·3H₂O, revealed that each of these species is a potent mixed-type inhibitor of the enzyme. Significant difference was noted between the peroxovanadium (pV) and peroxotungsten (pW) compounds in terms of their oxidant activity with reduced glutathione.     

Infrared and raman spectra of metal 1,2,4,5-benzenetetracarboxylates: Evidence for very short,strong hydrogen bonds

Salts of 1,2,4,5-benzenetetracarboxylic acid with copper, aluminum, ammonium, cobalt(II), thallium(I), tin(II), uranyl ion, zinc, manganese, iron(II), nickel, potassium and sodium have been prepared and characterized by their IR spectra. The salts of aluminum, ammonium, thallium(I), tin(II), zinc, iron(II), nickel, potassium and sodium had not been reported before with adequate characterization. Raman spectra of selected compounds also aided structural interpretation. The IR spectra of Na₂C₁₀H₄O₈·2H₂O, Fe(C₁₀H₅O₈)₂·12H₂O, Zn(C₁₀H₅O₈)₂·12H₂O, Ni(C₁₀H₅O₈)₂·12H₂O, (NH₄)₃C₁₀H₃O₈·H₂O and CoC₁₀H₄O₈·6H₂O indicate very short, strong hydrogen bonds in these compounds. The IR and Raman spectra can be used to determine the mode of coordination (if any) of the carboxylate groups of 1,2,4,5- benzenetetracarboxylate to metal ions.     

N-substituted ethylcarbamate complexes of thorium(IV) and lanthanum(III) nitrates

N-substituted ethylcarbamates form with thorium nitrate the complexes Th(NO₃)₄·3RHNC(O)OC₂H₅ (where R = CH₃, C₂H₅, C₆H₅(CH₃)CH) and with lanthanum nitrate the complexes La(NO₃)₃· 2RR′NC(O)OC₂H₅·3H₂O (where R = CH₃, C₂H₅, C₆H₅(CH₃)CH; R′ = H and R = CH₃, C₆H₅; R′ = C₂H₅ or R = R′ = CH₃). In addition the anhydrous La(NO₃)₃·3(C₂H₅)₂NC(O)OC₂H₅ has been isolated. From the IR spectra it is deduced that the carbamates coordinate the metal through the carbonyl oxygen atom and that the nitrato groups act as chelated ligands. ¹H nmr spectral data of the complexes are reported and discussed.     

Synthesis,inhibitory activity and molecular docking studies of two Cu(II) complexes against Helicobacter pylori urease

Two mononuclear copper(II) complexes, [Cu(C₁₅H₁₆NO₂)₂] (1) and [Cu(C₆H₉N₂O₄)₂·3H₂O] (2·3H₂O), were synthesised and structurally characterised by single-crystal X-ray analysis. The copper(II) atom adopts a square-planar environment in complex 1, while the geometry in 2·3H₂O could be described as the distorted square pyramidal. Complexes 1 and 2·3H₂O were evaluated for their inhibitory activities against Helicobacter pylori (H. pylori) urease in vitro. They both were found to have strong inhibitory activities against H. pylori urease comparable to that of acetohydroxamic acid (AHA). A docking simulation was performed to position 2 into the H. pylori urease active site to determine the probable binding conformation.     

Vibrational spectra of the diammineplatinum(II) disodium 5′-uridine monophosphate blue complex

The blue complexes produced by reaction of cis-diamminediaquoplatinum(II) nitrate, [cis-Pt(NH₃)₂(H₂O)₂](NO₃)₂, with disodium 5′-uridine monophosphate, 5′-UMP(Na₂), in H₂O and D₂O have been investigated by FT-IR spectroscopy. On the basis of the spectral changes observed in the CO stretching region during the reactions, chelation of the amidate N(3)··O(2) moiety to Pt(II) appears to be more likely than N(4)··O(4) chelation. The antisymmetric PO stretching mode of the PO_3²⁻ group of 5′-UMP splits into a triplet on complex formation indicating that PO_3²⁻ plays an important role in the structure of the platinum blue complexes. In addition, the sugar moiety of 5′-UMP apparently adopts a predominantly C(3′)-endo conformation in the solid blue complex. Finally, Raman microprobe spectroscopy of the solid provides some evidence for PtN(3) bond formation.     

Crystal Structure of 2′-Deoxycytidine Hemidihydrogenphosphate Reveals C+·C Base Pairs and Tight,Hydrogen-Bonded (H2PO4 −)∞ Columns (1)

Abstract

2′-Deoxycytidine hemidihydrogenphosphate has been crystallized in the hexagonal space group P6₂ with α=25.839(3), c = 12.529(1) Å. The structure has been solved using the Patterson search method. The asymmetric unit contains two protonated, base-paired 2′-deoxycytidine dimers and two H₂PO₄ ^? anions. The C⁺·C base pairs are composed of a protonated and a neutral species each and are triple H-bonded, the central N(3)…N(3) bonds being 2.850(7) and 2.884(5) Å. The conformations of the four nucleosides fall in the same category (sugar puckers 2·-endo, glycosidic links anti) but in one of them the glycosidic torsion angle is quite low with consequences in other geometrical parameters. The H₂PO₄ ^? anions are located on twofold axes and form two types of tight columns with P…P separations about 4.18 Å The neighboring units along a column are linked via two very short O…H…O hydrogen bonds (O…O about 2.49 Å) leading to effective equalization of the P-O bonds. The base pairs of the two dC⁺·dC cations are coplanar and form layers perpendicular to the phosphate columns repeating every c/3. Within the layers, the dimers form a network through 0(5′)…O(2) hydrogen bonds but their primary intermolecular interactions have the form of H-bond anchors [N(4)-H…O-P and 0(3′)-H…O-P] to the phosphate groups.     

Chemical Structure of Piericidin A

Molecular formula C₂₅H_37–39NO₄ was assigned to Piericidin A. Through the examination of the ultraviolet, infrared and n.m.r. spectra and of chemical evidences, it was shown that Piericidin A contains one secondary alcohol, one acidic hydroxyl group, two methoxyl groups, tri- and tetra-substituted conjugated dienes and one polysubstituted heteroaromatic ring.     

Studies on Mitomycins,Carcinostatic Antibiotics

Mitomycin A (C₁₆H₁₉O₆N₃) and mitomycin C (C₁₅H₁₈O₅N₄) are pigments which have the quinoid structure. When treated with aqueous ammonia, mitomycin A is converted to mitomycin C. Acid hydrolysis of mitomycin C gave three degradation products, namely, C₁₄H₁₅O₅N₄, C₁₄H₁₅O₆N₃ and C₁₃H₁₄O₅N₂. Acetylation with acetic anhydride and pyridine and methylation with methyl iodide gave monoacetyl and monomethyl derivatives of mitomycin C respectively, though diacetate of demethyl derivatives were obtained when boiled with acetic anhydride.     

Conformation and structure of 2-amino-8-(β-d-ribofuranosyl)imidazo [1,2-a]-s-triazin-4-one (5-aza-7-deaza guanosine), a potent antiviral nucleoside

The crystal and molecular structure of one imidazo[1,2-a]-s-triazine nucleoside and its antiviral activity are described. The crystal structure of 2-amino-8-(β-d-ribofuranosyl)imidazo-[1,2-a]-s-triazin-4-one monohydrate (C₁₀H₁₃N₅O₅·H₂O) was solved by X-ray counter data. The compound crystallizes in the monoclinic space group P2₁ with cell dimensions a = 7.353 (1), b = 6.465 (1), c = 13.701 (1) Å, β = 104.64 (1)°. The structure was solved by direct methods and refined by full matrix least-squares technique to a final value of the conventional R-factor of 0.049 using 1998 observed intensities. The orientation of the base relative to the sugar ring defined in terms of rotation about the C(1′)-N(8) glycosyl bond is anti (47.8°). The ribose moiety exhibits C(2′)-endo, ²E conformation. The conformation around C(4′)-C(5′) is gauche^?. Molecular packing is dominated by hydrogen bonds. Base stacking occurs long the b axis. 5-Aza-7-deazaguanosine has shown a marked antiviral activity in vitro against herpes simplex virus despite the fact that N(3) is effective as the hydrogen acceptor only.     

Synthesis,crystal structures and properties of three new lanthanide 2,6-pyridinedicarboxylate complexes with zero-dimensional structure

Three new lanthanide dipicolinate complexes with zero-dimensional structure have been synthesized by mild hydrothermal method. In these complexes the lanthanide is surrounded by three dipicolinate groups in the usual tridentate mode. For two of them, (CN₃H₆)₃[La(C₇H₃NO₄)₃] · 3H₂O I and (C₄N₂H₁₂)_1.5[Ce(C₇H₃NO₄)₃] · 7H₂O II, the dipicolinate groups are wholly unprotonated. The resulting molecular entity is three-times negatively charged and the balance charge is insured by the presence of guanidinium or piperazinium ions for the first and second, respectively. For the third complex, [Eu(C₇H₄NO₄)₃]₂ · 2.5H₂O III, one hydrogen atom remains globally on each dipicolinate and so the molecular entities are neutral. For the latter complex, the resulting molecular entities are connected into chains through strong hydrogen bonding. Thermogravimetric analyses and luminescent behaviour of complex III have been carried out.     

Yellow Pigments of Aspergillus niger and Asp. awamori

From mycelia of Asp. niger and Asp. awamori aurasperones A, B and C along with related two yellow pigments have been isolated.

Aurasperone A, C₃₂H₂₆O₁₀, is obtained in yellow prisms; m.p. 207°C; [α]_d —136°; gives the diacetate and the dimethyl ether and is assumed to be a dimeric 2-methyl-5- hydroxy-6,8-dimethoxy-4H-naphtho [2,3-b] pyran-4-one (IV). Aurasperone B, [α]_D +46.3°, is the main yellow metabolite, m.p. 186°C, and affords aurasperone A on hydrochloric acid-treatment. It has molecular formula C₃₂H₃₀O₁₂ and is supposed to have the structure (V). The other yellow pigments have been found to be also congeners of aurasperone A.     

Filiation biochimique des acides phénoliques produits parPenicillium brevi-compactum

Résumé LeP. brevi-compactum produit onze substances phénoliques différentes: l'acide mycophénolique, les acides phénoliques C₁₀H₁₀O₅, C₁₀H₁₀O₆, C₁₀H₁₀O₇ et C₈H₆O₆ et les substances phénoliques non identifiées désignées par les chiffres VI, VII, VIII, IX, X et XI. L'acide mycophénolique et les substances X et XI qui en dérivent, sont synthétisés par la moisissure suivant un processus plus complexe que les autres substances phénoliques et sans rapport direct avec lui. Ces dernières dérivent les unes des autres par une série de transformations dont certaines sont réversibles. Il semble que les substances VI et VII soient des intermédiaires entre C₁₀H₁₀O₇ et C₈H₆O₆, tandis que les substances VIII et IX seraient des produits de réduction de C₁₀H₁₀O₅.

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Summary P. brevi-compactum produces eleven phenolic different substances, mycophenolic acid, phenolic acids C₁₀H₁₀O₅, C₁₀H₁₀O₆, C₁₀H₁₀O₇ and C₈H₆O₆, and the non-identified substances designed by the numbers VI, VII, VIII, IX, X and XI. Mycophenolic acid and its derivates X and XI are synthesized by the mould according to a process more complex than the other phenolic substances and have no direct connection with them. The latter derive the one from the other, in a succession of transformations some of which are reversible. It seems that the substances VI and III are intermediaries between C₁₀H₁₀O₇ and C₈H₆O₆, the substances VIII and IX being produced by reduction of C₁₀H₁₀O₅.

     

Luminescence enhancement of terbium(III) perchlorate by 2,2′‐dipyridyl on bis(benzylsulfinyl)methane complex and luminescence mechanism

A novel ternary complex, Tb₂L₄·L′·(ClO₄)₆·8H₂O, has been synthesized using bis(benzylsulfinyl)methane as the first ligand L and 2,2′‐dipyridyl as the second ligand L′. The ternary complex was characterized by element analysis, molar conductivity, coordination titration analysis, infrared, thermogravimetric‐differential scanning calorimetric and ultraviolet spectra. The results indicated that the composition of the complex was Tb₂L₄·L′·(ClO₄)₆·8H₂O (L = C₆H₅CH₂SOCH₂SOCH₂C₆H₅; L′ = Dipy). Fourier transform infrared results revealed that the perchlorate group was bonded with the Tb(III) ion by the oxygen atom, and the coordination was bidentate. The fluorescent spectra illustrated that the complex displayed characteristic fluorescence in the solid state. After the introduction of the second ligand, 2,2‐dipyridyl, the relative emission intensity and fluorescence lifetime of the ternary complex Tb₂L₄·L′·(ClO₄)₆·8H₂O were enhanced compared to the binary complex TbL_2.5(ClO₄)₃·3H₂O. This indicated that the presence of both organic ligand bis(benzylsulfinyl)methane and the second ligand 2,2‐dipyridyl could sensitize the fluorescence intensity of Tb(III) ion, and introduction of the 2,2‐dipyridyl group resulted in an enhancement of the fluorescence of the Tb(III) ternary rare earth complex. The strongest characteristic fluorescence emission intensity of the ternary complex was 9.36 times that of the binary complex. The phosphorescence spectra and fluorescence lifetime of the complex were also measured. Copyright © 2014 John Wiley & Sons, Ltd.     

Solvent-extraction complex of uranium(VI) with cis,syn, cis-dicyclohexano-18-crown-6

The extraction of U(VI)with dicyclohexano-18-crown-6 (mixed isomers or isomer A) from HCl medium is effective and selective, and can be used for separating and analysing uranium and thorium. However, little is known of the properties of the extraction complex of uranium with crown-ether in organic phase. In this paper we report the preparation, characteristic and structure of the crystalline extraction complex IaUO₂Cl₂HClH₂O, Iabeing isomer A of dicyclohexano-18-crown-6.After extracting uranium(VI) from aqueous hydrochloric acid solution with Ia in 1,2-dichloroethane, the crystalline product of the extraction complex was prepared from the organic phase by diluting with a non-polar solvent at 25 °C. The content of uranium, crown-ether and HCl was determined. The IR spectrum of the crystals shows that the strong hydronium-crown ether/oxygen hydrogen bond absorption is found in the region 2300–2400 cm⁻¹. The chemical shift in the range 9–12 ppm was observed. The ¹H NMR signal of hydronium protons appears at 9.890 ppm. The results of assay correspond to the formula Ia₂·(H₃O⁺)₂·UO₂Cl₄²⁻.Crystal structure of the extraction complex has been determined by X-ray crystallography. Crystals are monoclinic, space group C_2/c (No. 15) a=32.464, b=10.203, c=21.616 Å, β=119.73° and Z=4. In the complex each of the two H₃O⁺ cations is anchored in the crown-ether cavity by three stronger hydrogen bonds (distances approximately 2.65 Å), whereas uranium forms UO₂Cl₄²⁻ with Cl⁻ as counterion about 8 Å away from the H₃O⁺.     

Molecular Conformation of 2′-Deoxy-2′-methylidene-cytidine: A Potent Antineoplastic Nucleoside

Abstract

2′-Deoxy-2′-methylidenecytidine (DMDC), a potent inhibitor of the growth of tumor cells, was crystallized with two different forms. One is dihydrated (DMDC·2H₂O) and the other is its hydrochloride salt (DMDC·HCLl). Both crystal and molecular structures have been determined by the X-ray diffraction method. In both forms the glycosidic and sugar conformations are anti and C(4′)-exo, respectively, whereas the conformation about the exocyclic bond is trans for DMDC·2H₂O and gauche ⁺ for DMDC·HCl. Proton nuclear magnetic resonance data of DMDC indicate a preference for the anti C(4′)-exo conformation found in the solid state. These molecular conformations were compared with the related pyrimidine nucleosides. When the cytosine bases are brought into coincidence, DMDC displays the exocyclic C(4′)-C(5′) bond located on the very close position to those of pyrimidine nucleosides with typical overall conformations. On the other hand, the hydroxyl O(3′)-H groups are separated by ca. 3 Å in the cases of DMDC and other pyrimidine nucleosides which have the C(2′)-endo sugar conformation. This result may be useful for the implication about the mechanism of the biological activity of DMDC.     

Coordination properties of α-hydroxy carboxylic acids. Part I. Binuclear niobium (V) complex acids and some salts

The conditions of dissolution of freshly precipitated niobium (V) oxide in α-hydroxy carboxylic acids glycolic, lactic, malic and tartaric were investigated. The dissolution is a function of the molar ratio α-hydroxy carboxylic acid/hydrated niobium(V) oxide, pH of the solution, temperature and time. From solutions of α-hydroxy monocarboxylic acids at 2 < pH < 3 the binuclear complexes H₃O[Nb₂O₄(C₂H₂O₃)(C₂H₃O₃)]·H₂O and H₃O[Nb₂O₄(C₃H₄O₃)(C₃H₅O₃)]·H₂O were isolated. Colourless, poorly-crystalline complexes are 1:1 electrolytes and, according to i.r. spectral evidence, the binuclearity in their structures is achieved through oxygen bridges. With α-hydroxy dicarboxylic acids crystalline M[Nb₂O₃(C₄H₃O₅)(C₄H₄O₅)]·nH₂O and poorly crystalline complexes, M₂[Nb₂O₂(C₄H₂O₆)₂]·nH₂O, M = H₃O⁺, NH₄⁺ were prepared as 1:1 electrolytes for the former and 1:2 electrolytes for the latter. Analytical, spectral, conductometric and potentiometric titration data give evidence for binuclear malatoniobate(V) and tartratoniobate(V) anions with bridging complex-forming agents.     

Metal-penicillamine interactions. Part 1. Preparation and crystal structure of a 1:1 complex of mercuric chloride with d-penicillamine, 2[μ3-Cl){HgSC(CH3)2CH(NH3)COO}3·3(μ2-Cl)· 2(H3O)·(H2O·Cl)3

A 1:1 complex of mercuric chloride with D-peniccillamine has been isolated and characterised as 2[(μ₃-Cl){HgSC(CH₃)₂CH(NH₃)COO}3]·3(μ₂-Cl)·2(H₃O)·(H₂O·Cl)₃. The compound crystallises in cubic space group P4₁32, with a = 18.679(5) Å and Z = 4. The structure, refined to R_F = 0.086 for 443 observed Mo-Kα diffractometer data, features a triply bridging chloride ion linking three equivalent [HgSC(CH₃)₂CH(NH₃)COO]⁺ units [Hg-Cl = 2.37(1) Å, Hg-Cl-Hg′ = 98.5(9)°]. The carboxylate groups of a pair of adjacent penicillamine ligands are strongly linked via a symmetrical O?H?O hydrogen bond of length 2.24(8) Å, and neighboring pyramidal trinuclear [μ₃-Cl){HgSC(CH₃)₂CH(NH₃)-COO}₃]²⁺ moieties are further connected by symmetrical chloride bridges [Hg-Cl = 3.06(2) Å; HgClHg′' = 79.6(7)°] to form a three-dimensional network. The voids in the lattice are filled by hydronium ions and novel planar cyclic hydrogen-bonded (H₂O·Cl^?)₃ rings of edge O-H?Cl = 2.46(4) Å.     

Host-guest Interactions in Intercalates Zr(HPO4)2·2C2H5OH and VOPO4·2C2H5OH

Molecular mechanics simulations using Cerius² modelling environment combined with vibrational spectroscopy (IR and Raman) have been used to study the host-guest interactions in zirconium and vanadyl phosphate intercalated with ethanole. The strategy of investigation is based on the comparison of vibrational spectra for the host compound, intercalate and guest species. This comparison confirmed the rigidity of VOPO₄- and Zr(HPO₄)₂-layers during the intercalation and provided us with the basis for the strategy of modelling. Molecular mechanics simulations revealed the structure of intercalates and enabled to analyse the host-guest interaction energy and bonding geometry. The bilayer arrangement of ethanole molecules in the interlayer space with two differently bonded ethanole molecules has been found in both intercalates. The average interaction energy ethanole-layer for two differently bonded ethanole molecules is : 127.5 and 135.7 kcal·mol^-1 in Zr(HPO₄)₂·2C₂H₅OH, respectively 94.0 and 104.4 kcal·mol^-1 in VOPO₄·2C₂H₅OH. The Coulombic contribution to the ethanole-layer interaction energy is predominant in all cases, but the hydrogen bonding contribution is much higher in Zr(HPO₄)₂·2C₂H₅OH than in VOPO₄·2C₂H₅OH. Present results of modelling enabled the interpretation of vibrational spectra and explanation of small changes in positions and shapes of spectral bands, in infrared and Raman spectra, proceeding from the host structure to intercalates.