Effect of loop on the stability of intramolecular triplex DNA

Conformation stabilities of intramolecular triple-helical DNAs (intra-tnplex DNAs: 5-d(TC)6-d(T)m-d(CT)6-d(C)n-d(AG)6-3',where m and n are chosen to be 4 and 3) have been examined by molecular mechanics.The four intra-triplexes (H-DNAs) are compared with the mtermolecular triplexes d(TC)6 * d ( AG)6 d(CT)6.The results revealed that loops do not significantly influence the mtratriplex conformations,loop conformations,however,depend partly on its length.Loop also makes strand Ⅱ of every intra-triplex DNA longer than that of the inter-triplex DNA.Most of residue sugar conformations of triple-helical DNAs are S-type,there aiso exist,however,N-type conformation and the conformations between S-type and N-type Possible models of the five triplex DNAs are presented.     

Synthesis of spiro-cyclopropane derivatives containing multiple chiral centers

Tandem asymmetric double Michael addition/internal nucleophilic substitution of the novel chiral source, 5-(l-menthyloxy)-3-bromo-2(5H)-furanone with nucleophilic alcohol compounds has been investigated. The tandem asymmetric reaction can afford four new stereogenic centers with one reaction and give optically pure spiro-cyclopropane derivatives 5a--5d which are difficult to obtain by routine methods. The synthetic method for 5a--5d was studied in detail and the new compounds were identified on the basis of their analytical data and spectroscopic data, such as [α]~(20),IR,~1H NMR,~(13)C NMR, MS and elementary analysis. The absolute configuration of the sprio [5-l-menthyloxy-3-bromo butyrolactocyclopropane-3″, 3′(4′-methyloxy-5′-menthyloxybutyrolactone)] (5a) was established by X-ray crystallography. The work can provide important synthetic strategy in synthesis of some new optically active spiro-cyclopropane analogues and some biologically active molecules with complex structure.     

Thermal Properties of Binary Mixtures of β-Cyclodextrin with Carbamazepine Polymorphs

The thermal behaviour of binary mixtures between β-cyclodextrin (β-CD) and either carbamazepine polymorphic Form I (CBZ I), Form III (CBZ III) or dihydrate was investigated in order to assess possible interactions of CBZ solid phases with β-CD. Physical mixtures and kneaded binaries of β-CD and different CBZ crystal forms were studied by differential scanning calorimetry, thermogravimetric analysis and hot stage microscopy. The pattern of transition of CBZ Form III into Form I is strongly influenced by β-CD. The liquid-solid transition is practically absent when anhydrous CBZ/β-CD mixes are tested, as a consequence of an interaction between β-CD and liquid CBZ that hinders CBZ recrystallisation as Form I occurring after CBZ Form III melting. Water loss on heating of CBZ dihydrate in the presence of β-CD leads in all cases to the formation of CBZ Form I. This revised version was published online in August 2006 with corrections to the Cover Date.     

Cu(I) and Cu(II) helical complexes formed with oligobipyridine ligand

A new asymmetric oligobipyridine ligand, 1- (5’-methyl-2, 2’-bipyridin-5-y1)-2- (6’-methyl-2, 2’-bipyridin-6-yl)ethane (L), in which the bipyridine units are bridged by CH₂CH₂ at 5,6’-position has been synthesized. The ligand L reacts with Cu(I) and Cu(I1) ions giving double-stranded helical complexes [Cu ₂ ¹ L₂](C10₄)₂.Et₂0 (1) and [Cu ₂ ^II L₂,(OH)(H₂0) ] [ClO₄]₃(2), respectively. Complexes 1 and 2 were characterized by X-ray diffraction analyses, ES-MS, ESR and cyclic voltammetry, etc. Differing from the oligobipyridine ligands bridged by CH₂CH₂ at 6,6’-or 5,5’-position, the ligand L not only forms a double-stranded helicate with Cu(1) ion, but also gives a double-stranded helicate with Cu(I1) ion. The results show that the linkage mode of the spacer group to the bipyridine units exerts a great impact on the formation of helix. Project supported by the National Natural Science Foundation of China (Grant NO. 29601003).     

三链DNA |dA10 2DT10的近红外付立叶拉曼光谱

最近通过核磁共振、振动光谱和分子力学模拟研究表明,在溶液中三螺旋DNA的构象具有一定程度的复杂性和多样性．本文首次采用近红外付立叶拉曼光谱研究了三螺旋DNA dA10•2d10和相应的双螺旋DNA dA10•dT10在溶液中的构象．结果表明该三螺旋DNA同时存在C3’－内褶／反对称（A－型）和C2’－内褶／反对称（B－型）两种构象,而且在823cm－1处的较强谱带暗示还存在一种处于A和B构型之间的中间构型．对出现在1218cm-1和638cm-1处、归属于对糖环构象敏感的胸腺嘧啶残基的两个特征谱带进行分析,获得了除C2’－内褶构象外其它构型存在的证据．另外,双螺旋DNA的FT－Raman光谱表明该双螺旋DNA在溶液中以A－和B－两种构型共存．     

Time-resolved fluorescence analysis of the mobile flavin cofactor in p -hydroxybenzoate hydroxylase

Conformational heterogeneity of the FAD cofactor in p-hydroxybenzoate hydroxylase (PHBH) was investigated with time-resolved polarized flavin fluorescence. For binary enzyme/substrate (analogue) complexes of wild-type PHBH and Tyr222 mutants, crystallographic studies have revealed two distinct flavin conformations; the ‘in’ conformation with the isoalloxazine ring located in the active site, and the ‘out’ conformation with the isoalloxazine ring disposed towards the protein surface. Fluorescence-lifetime analysis of these complexes revealed similar lifetime distributions for the ‘in’ and ‘out’ conformations. The reason for this is twofold. First, the active site of PHBH contains various potential fluorescence-quenching sites close to the flavin. Fluorescence analysis of uncomplexed PHBH Y222V and Y222A showed that Tyr222 is responsible for picosecond fluorescence quenching free enzyme. In addition, other potential quenching sites, including a tryptophan and two tyrosines involved in substrate binding, are located nearby. Since the shortest distance between these quenching sites and the isoalloxazine ring differs only little on average, these aromatic residues are likely to contribute to fluorescence quenching. Second, the effect of flavin conformation on the fluorescence lifetime distribution is blurred by binding of the aromatic substrates: saturation with aromatic substrates induces highly efficient fluorescence quenching. The flavin conformation is therefore only reflected in the small relative contributions of the longer lifetimes.     

Use of broadened13C NMR signals in complexes of nucleosides with Mn(II) to evaluate the conformational equilibrium of the ribose ring

The¹³C NMR spectra of chelate complexes of nucleosides with Mn(II) under fast-exchange conditions have been studied. It has been established that the state of the conformational equilibrium of the ribose ring within the framework of the two-sided exchange 2′-endo (S) ⇆ 3′-endo (N) can easily be evaluated from the broadening of the C-1′ and C-4′ signals. The results obtained by the broadening method agree well with those of methods used previously. All-Union Scientific-Research Institute of Applied Biochemistry, Olaine. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 678–680, September–October, 1980.     

Investigating the thermodynamic properties of lactones at various temperatures

The 11-undecanolide enthalpy of vaporization is obtained from the temperature dependence of the vapor pressure measured by transpiration. A conformational analysis of 8-octanolide (I), 11-undecanolide (II), and 13-tridecanolide (III) is performed. Quantum-chemical calculations are performed to study the moments of inertia, vibrational spectra, and most favorable conformations. The ideal gas thermodynamic properties of these compounds in the temperature range of 0-1500 K are determined. A procedure for the additive determination of polynomial coefficients for temperature-dependent properties is developed to assess the thermochemical data for lactones, lactides, and carboxylic hydroxyacids at 298.15–1000 K.     

(–)‐Dioxosantadienic acid: hydrogen‐bonding patterns in a bicyclic sesquiterpenoid keto acid and its mono­hydrate

The an­hydrous form, (I), of the title compound, (?)‐2‐(1,2,3,4,4a,7‐hexa­hydro‐4a,8‐di­methyl‐1,7‐dioxo‐2‐naphthyl)­propionic acid, C₁₅H₁₈O₄, derived from a naturally occurring sesquiterpenoid, has two mol­ecules in the asymmetric unit, (I) and (I′), differing in the conformations of the saturated ring and the carboxyl group. The compound aggregates as carboxyl‐to‐ketone hydrogen‐bonding catemers [O?O = 2.776 (3) and 2.775 (3) Å]. Two crystallographically independent sets of single‐strand hydrogen‐bonding helices with opposite end‐to‐end orientation pass through the cell in the b direction, one consisting exclusively of mol­ecules of (I) and the other entirely of (I′). Three C—H?O=C close contacts are found in (I). The monohydrate, C₁₅H₁₈O₄·H₂O, (II), with two mol­ecules of (I) plus two water mol­ecules in its asymmetric unit, forms a complex three‐dimensional hydrogen‐bonding network including acid‐to‐water, water‐to‐acid, water‐to‐ketone, water‐to‐water and acid‐to‐acid hydrogen bonds, plus three C—H?O=C close contacts. In both (I) and (II), only the ketone remote from the acid is involved in hydrogen bonding.     

Metallodesferals as a new class of DNA cleavers: Specificity, mechanism and targetting of DNA scission reactions

Interaction of metal complexes with nucleic acids is currently attracting wide attention due to their potential utility as drugs, regulators of gene expression and tools for molecular biology. Many metal complexes exhibit nucleolytic activity, the most important examples being Cu(II)-OP, Fe(H)-BLM, Fe(II)-EDTA, metalloporphyrins, Ru and Co complexes of 4,7-diphenyl-l,10-phenanthroline and more recently by Ni(II) complexes. Desferal, a well known siderophore and a highly effective drug in chelation therapy of iron overload diseases, forms a stable octahedral co-ordination Fe(III) complex Eerrioxamine B. We have been interested in the DNA damaging properties of metallodesferals and this paper describes the DNA cleaving ability of metallodesferals, metal-dependent base selectively in DNA scission reactions, mechanistic studies on DNA cleavage by CuDFO and targetting of DNA cutting by covalent MDFO conjugates. This paper reports the synthesis of Cu(II), Co (III) and Ni(II) complexes of a siderophore chelating drug desferal, the studies on cleavage of plasmid DNA, the sequence preference of cleavage reactions, and C1’ as the primary site of hydroxyl radical attack in the reactions. Oligonucleotides covalently linked with this molecular scissor can direct the cleavage of either single or double strand DNA’s, mediated by duplex or triple helix structures respectively. Such targetting of DNA cleavage reactions, mediated by oligonucleotide-Cu(II)/Co(III) desferal conjugates has demonstrated reasonable site specificity and efficiency     

13C-13C spin-spin coupling constants in structural studies: XLI. Stereochemical study on N-(polychloroethylidene)arenesulfonamides and N’-arylsulfonylformimidamides

The second-order polarization propagator approach (SOPPA) was used to calculate ¹³C-¹H, ¹³C-¹³C, and ¹⁵N-¹H coupling constants for a series of N-(polychloroethylidene)arenesulfonamides and N’-arylsulfonylformimidamides, and their configuration with respect to the C=N bond was determined by comparing the calculated data with the experimental values. All the examined compounds were found to exist in solution exclusively as the corresponding E isomers. The most favorable conformations and relative energies of the E and Z isomers in the gas phase were determined in terms of the second-order perturbation theory (MP2/6-311G**). N’-Arylsulfonylformimidamides are characterized by restricted internal rotation of the dialkylamino group about the C-N bond having an increased order. Original Russian Text ? K.A. Chernyshev, L.B. Krivdin, G.N. Rozentsveig, I.V. Ushakova, I.B. Rozentsveig, G.G. Levkovskaya, 2008, published in Zhurnal Organicheskoi Khimii, 2008, Vol. 44, No. 1, pp. 82–91. Dedicated to Full Member of the Russian Academy of Sciences G.A. Tolstikov on his 75th anniversary     

Vibrational spectra and stereochemistry of mono- and polysaccharides. IV. α-methyl-d-glucoside, α-methyl-d-galactopyranoside,and α-methyl-d-mannopyranoside

The IR and Raman spectra of α-methyl-D-glucoside (αMDG), α-methyl-D-galactoside (αMDGal), and α-methyl-D-mannoside (αMDM) are compared. The main distinctions between these spectra have been interpreted using experimental and theoretical data on the frequencies and modes of normal vibrations and on the potential energy distributions over particular bonds and atomic groups of the substances under investigation. Spectral characteristics that are determined by different configurations of C−O (CH) groups attached to C2 and C4 atoms and different conformations of C6H₂O6H fragments have been revealed. It has been established that replacement of hydroxyls at C1 with methoxy groups significantly increases the number of frequencies of normal vibrations that are localized mostly in the C1C2 bonds (particularly in αMDGal). For the αMDGal molecules with axial C4O4 groups, the number of frequencies of normal vibrations that show predominant contributions of these groups of PED is smaller. For the αMDM molecules, in which the conformation of CH₂OH groups (with respect to rotation around the C5C6 bonds) differs from that in αMDG and αMDGal molecules, most vibrations are localized in the C6O6 bonds rather than in the C5O5 bonds. This fact is very important in correlating the vibrational spectra and structural properties of mono- and polysaccharides. B.I. Stepanov Institute of Physics, Belarus Academy of Sciences. V. Tshebyatoski Institute of Low Temperatures and Structural Studies, Polish Academy of Sciences. Translated fromZhurmal Struktumoi Khimii, Vol. 36, No. 3, pp. 456–466, May–June, 1995. Translated by I. Izvekova     

Is copper(I) really soft? Probing the hardness of Cu(I) with pyridinecarboxaldehyde ligands

Cu(I) complexes of formula Cu(PPh₃)₂LClO₄ [L = 2 or 3 pyridine carboxaldehyde] are synthesised and characterised to explore the coordination of an aldehyde, a hard and neutral oxygen donor to a soft Cu(I) centre. The structural and spectroscopic results illustrate that only in 2-pyridinecarboxaldehyde, the ‘C=O’ group coordinates to soft Cu(I) centres due to a favourable chelate effect, while in 3-pyridinecarboxaldehyde, it remains uncoordinated. Upon chelation via N and O donors, 2-pyridinecarboxaldehyde resembles bipyridine or phenanthroline in terms of its bite angle and spectroscopic features. Such chelation can be easily challenged with coordinating anions like bromide, or more basic pyridines. A drastic change in the MLCT absorption signals the decomplexation of the ‘C=O’ group. The observed results point out that the Cu(I) centre can readily exchange the hard ‘O’ donor for softer ligands.     

Spectrophotometric Microdetermination of Some Pharmaceutically Impor tant Aminoquinoline Antimalarials, as Ion-Pair Complexes

 A simple, rapid, accurate and sensitive spectrophotometric method for the microdetermination of some pharmaceutically important aminoquinoline antimalarials, namely amodiaquine dihydrochloride (I), chloroquine phosphate (II) and primaquine phosphate (III) is described. The method is based on the interaction of these drugs with calmagite indicator to give highly coloured ion-pair complexes which exhibit maximum absorption at 663, 665 and 666 nm, respectively, Beer’s law is obeyed in the concentration ranges 1.0–25.0, 1.0–28.0 and 1.0–33.0 μg/ml for the drugs I, II and III, respectively. For more accurate analysis, the Ringbom optimum concentration ranges are 2.5–22.5, 2.0–26.0 and 3.0–30.0 μg/ml, respectively. The apparent molar absorptivities were calculated. Statistical treatment of the experimental results indicates that the method is sufficiently accurate and precise. The accuracy of the method is indicated by the recovery (99.8±1.4%) and the precision by the relative standard deviation (>1.5%). The proposed method has been applied to the determination of these drugs in certain formulations, with results that compared favourably with those obtained by the official methods. Received November 2, 1998. Revision February 29, 2000.     

Colorimetric Procedure for the Microdetermination of the Antibilharzial Drug Praziquantel and its Applications to Pharmaceutical Formulations

 A procedure for the colorimetric assay of praziquantel has been developed. The method is based on the formation of charge-transfer complexes with p-chloranil (I), dichloronitrophenol (II), 2,3-dichloro-5,6 dicyano-p-benzoquinone (III), 7,7,8,8-tetracyanoquinodimethane (IV) and tetracyanoethylene (V) as π-acceptors to give highly coloured species. The coloured products are measured spectrophotometrically at 550, 425, 460, 844 and 393 nm for I, II, III, IV and V, respectively. Optimization of the different reaction conditions is described. The colour system obeyed Beer’s law in non-aqueous media in the concentration range 2.0–48 μg ml⁻¹. It was stable for at least 4.0 h. The detection limit was found to be 0.6 μg ml⁻¹. Applications of the procedure to the analysis of various pharmaceutical samples gave reproducible and accurate results. Further, the validity of the procedure was confirmed by applying the standard addition technique. The total average recovery was 100.2%. Received June 10, 2000. Revision December 23, 2000.     

Photoelectrochemical behavior of nanostructural composites based on polycrystalline cadmium sulfide

Nanostructural composites can be used as suspension electrodes; they are made by substitution cadmium(II) at the surfaces of CdS microcrystals for Cu(I, II), Fe(III), Bi(III), and Sb(III). Features are considered in the photoelectrochemical action mechanism of the various nanocomposites. L. V. Pisarzhevskii Institute of Physical Chemistry, National Academy of Sciences of Ukraine, 31 Prospekt Nauki, Kiev 252039, Ukraine. Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 35, No. 2, pp. 79–82, March–April, 1999.     

Mechanistic study of 7-endo selective radical cyclization of the aryl radical

Mechanistic studies on the novel 7-endo selective radical cyclization were carried out. The reaction afforded three products, 7-endo product, 6-exo product, and reduced product. The distribution of these products was estimated by GC analyses. The 7-endo/6-exo selectivity was almost constant against variation in the concentration of Bu₃SnH, while the reduction/cyclization ratio was sensitive to the concentration of Bu₃SnH. The reduction/cyclization ratio was mainly affected by the rotational isomeric ratio of the cyclization precursor. Kinetic analyses indicated that the cyclization process should be irreversible, and the rate constant of 7-endo/6-exo radical cyclization was estimated to be about 3.3 × 10⁸ s⁻¹ at 80 °C.     

Molecular mechanics study on conformation of perylene-quinonoid photosensitizers

Using molecular mechanics method,values of the heat of formation (HF) of different conformations,of perylenequinonoid photosensitizes hypocrellin A (HA) and hypocrellin B (HB) were calculated and the variance of HF after phenolic protons' dissociation were calculated as well The following was found:(i) The HF values of lour conformational isomers of HA and HB are similar to each other,so the four isomcrs can transform to each other room temperature,(ii) There exists the difference between the ability of dissociation of phenolic protons of HA and that of HB,the former is higher than the latter (iii) There exist two intramolecular hydrogen bonds in HA and HB The bond energy is approximately 8 kJ/mol and the energy of conformation Ⅰ is lower than that of conformationⅡ The bond energy of HA is lower than that of HB.(iv) There exists a low energy snot when phenolic hydroxyl bond twists 180° from the position where hydrogen bond is formed,which suggests that this kind of conformation probably exists,(v) Th     

Underpotential surface reduction of mesoporous CeO<Subscript>2</Subscript> nanoparticle films

The formation of variable-thickness CeO₂ nanoparticle mesoporous films from a colloidal nanoparticle solution (approximately 1–3-nm-diameter CeO₂) is demonstrated using a layer-by-layer deposition process with small organic binder molecules such as cyclohexanehexacarboxylate and phytate. Film growth is characterised by scanning and transmission electron microscopies, X-ray scattering and quartz crystal microbalance techniques. The surface electrochemistry of CeO₂ films before and after calcination at 500 °C in air is investigated. A well-defined Ce(IV/III) redox process confined to the oxide surface is observed. Beyond a threshold potential, a new phosphate phase, presumably CePO₄, is formed during electrochemical reduction of CeO₂ in aqueous phosphate buffer solution. The voltammetric signal is sensitive to (1) thermal pre-treatment, (2) film thickness, (3) phosphate concentration and (4) pH. The reversible ‘underpotential reduction’ of CeO₂ is demonstrated at potentials positive of the threshold. A transition occurs from the reversible ‘underpotential region’ in which no phosphate phase is formed to the irreversible ‘overpotential region’ in which the formation of the cerium(III) phosphate phase is observed. The experimental results are rationalised based on surface reactivity and nucleation effects.     

Spectral Interferences in Light Element Analysis

 Interferences (overlaps) occurring when lines of other elements affect either peak or background measurements can cause errors in quantitative WD analysis, but may be minimised by suitable choices of analysis conditions such as spectrometer crystal, background offsets, and pulse-height analyser settings. Computer spectrum-simulation is much more effective than reference to wavelength tables for investigating interferences. The ‘Virtual WDS’ simulation program developed by the present authors, hitherto applied only to ‘ordinary’ elements (Z ≥ 11), has been extended to light elements for which evaporated multilayers are used in place of true crystals. ‘Virtual WDS’ utilises experimentally recorded light-element K spectra and L and M spectra of heavier elements in the same wavelength range. It is impractical to record all high-order peaks, so computed line profiles are used, with widths and intensities interpolated from a limited set of observations. The relative positions of first and higher order peaks are affected significantly by the refractive index of the multilayer, requiring modification of the Bragg equation. Suppression of high orders by pulse-height analysis is less effective than for ‘normal’ wavelengths, owing to the breadth of the pulse-height distribution for low X-ray energies. Simulation using a Gaussian expression aids optimisation of threshold and window-width settings.