An ab initio theoretical study of electronic structure and properties of 2'-deoxyguanosine in gas phase and aqueous media

Molecular geometries of two structural forms of 2'-deoxyguanosine (keto-N9R and keto-N7R, R = the sugar moiety) considering both the C2'-endo and C3'-endo conformations of the sugar ring and those of the complexes of these species with two water molecules each were optimized employing the ab initio RHF procedure. A mixed basis set consisting of the 6-311+G* basis set for the nitrogen atom of the amino group and the 4-31G basis set for all the other atoms was used. The RHF calculations were followed by correlation correction of the total energy at the MP2 level. Both the structural forms of 2'-deoxyguanosine were solvated using the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory and the corresponding RHF optimized geometries at the RHF and MP2 levels. Geometry optimization was also performed in aqueous media using the Onsager model at the RHF level using the above-mentioned mixed basis set, and subsequently, using the reoptimized geometries, single-point MP2 calculations were performed. It is found that both the keto-N9R and keto-N7R forms of 2'-deoxyguanosine as well as their complexes with two water molecules each would occur, particularly at the water-air interface. Though the normal Watson-Crick-type base pairing would not be possible with the keto-N7R form of 2'-deoxyguanosine(G*), two other (G*-C and G*-T) base pairing schemes may occur with this form of the nucleoside, which may cause mutation. The present calculated geometry of the keto-N9R form of the anti-conformation of 2'-deoxyguanosine including the dihedral angle chi(CN) agree satisfactorily with the available crystallographic results. The present results also agree satisfactorily with those obtained by other authors earlier for the keto-N9R form of 2'-deoxyguanosine using B3LYP and MP2 methods employing the 6-31G* basis set. Using transition state calculations, it is shown that tautomerism of guanine and other similar molecules where the tautomers would coexist would be facilitated by the occurrence of the H(+) and OH(-) fragments of water molecules. Further, this coexistence of the two tautomers appears to make the C8 carbon atom located between the N7 and N9 nitrogen atoms susceptible to attack by the OH(-) group. Thus, an explanation is obtained for the efficient formation of the reaction product 8-hydroxy-2'-deoxyguanosine, which serves as a biomarker for oxidative damage to DNA in biological systems.     

Heterocyclic Quinones in ihe Nenitzescu Reaction. Synthesis of Furo- And Pyrroloquinolines from 2-Methoxycarbonyl-4-oxo-5,8-quinolinequinone

Derivatives of furo[2,3-f]quinoline were synthesized by the reaction of the enamines of acetylacetone and benzoylacetone with 2-methoxycarbonyl-4-oxo-5,8-quinolinequinone. A derivative of pyrrolo[2,3-h]quinoline was obtained from N-benzyl--aminocrotonic ester.     

Synthesis and some heterocyclization reactions of new diethyl (1,1-difluoro-3,3-dicyano-2-trifluoromethylallyl)phosphonate and ethyl 3,3-dicyano-2-[(diethoxyphosphoryl)difluoromethyl]acrylate

A new CF₂X-analogue of 1,1-bis(trifluoromethyl)-2,2-dicyanoethylene (X = P(O)(OEt)₂), diethyl (1,1-difluoro-3,3-dicyano-2-trifluoromethylallyl)phosphonate, has been synthesized from diethoxyphosphoryl pentafluoroacetone 1. A similar phosphoryl analogue of ethyl 3,3-dicyano-2-trifluoromethylacrylate, ethyl 3,3-dicyano-2-[(diethoxyphosphoryl)difluoromethyl]acrylate, has been obtained from ethyl 3-(diethoxyphosphoryl)-3,3-difluoro-2-oxopropionate 2. By heterocyclization of these new ethylenes with 3-methyl-2-pyrazoline-5-ones, 3(5)-aminopyrazoles, dimedone, 2-aminopyridines, 1-aryl-3-methyl-5-aminopyrazoles, 1,3,3-trimethylisoquinolines, as well as by condensation with anilines and ketones, the difluoromethylphosphonate-substituted derivatives of 1,4-dihydropyrano[2,3-c]pyrazole, 4,5-dihydropyrazolo[1,5-a]pyrimidine, 5,6,7,8-tetrahydro-4H-chromene, 2H-pyrido[1,2-a]pyrimidine, 4,7-dihydro-1H-pyrazolo[3,4-b]pyridine, 1,4-dihydropyridine, 4,5,6,7-tetrahydro-1H-[1]pyrindine, 1,4,5,6,7,8-hexahydroquinoline, and 6,7-dihydro-2H-pyrido[2,1-a]isoquinoline have been obtained in one stage.     

Facile design of poly(3,4-ethylenedioxythiophene)-tris(2,2′-bipyridine)ruthenium (II) composite film suitable for a three-dimensional light-harvesting system

It has been confirmed that octasulfonatocalix[8]arene (Calx-S8) and tris(2,2′-bipyridine)ruthenium (II) (Ru(bpy)₃²⁺) can form a stable host-guest complex in aqueous solution. The binding constant for 1:1 [Calx-S8⁸⁻·Ru(bpy)₃²⁺]⁶⁻ complex formation was estimated to be (2.4±0.8)×10⁴ dm³ mol⁻¹ by fluorescence titration, which indicates that the [Calx-S8⁸⁻·Ru(bpy)₃²⁺]⁶⁻ complex is the main species in 1:1 molar ratio aqueous solution of Calx-S8 and Ru(bpy)₃²⁺. In situ UV-Vis spectroscopic measurements indicated that Ru(bpy)₃²⁺ complexes can be readily deposited onto ITO electrode through electrochemical polymerization of 3,4-ethylenedioxythiophene (EDOT) using [Calx-S8⁸⁻·Ru(bpy)₃²⁺]⁶⁻ host-guest complex as a dopant anion owing to the electrostatic interaction between the cationic conductive polymer and the anionic host-guest complex. The loading degree of the composite film with Ru(bpy)₃²⁺ can be determined by Lambert-Beer law modified for the two-dimensional concentration. The obtained composite film showed good photoelectric conversion properties in response to visible light irradiation. This is a novel photocurrent generation system in which the photoexcited state energy is efficiently collected by the conductive polymeric layer.     

Synthesis of bis(alk-3-en-1-ynyl)benzene with either E- or Z-configuration via a one-pot three-component coupling reaction and its optical properties

A convenient, efficient and stereoselective synthesis of a range of bis(alk-3-en-1-ynyl)benzenes with E- and Z-configuration is described. The protocol involves Cu-mediated cross-coupling reaction of (E)- and (Z)-alk-1-enyldisiamylboranes with (trimethylsilyl)ethynyl bromide and Pd/Cu-catalyzed cross-coupling reaction with diiodobenzene. The sequential cross-coupling reaction proceeds readily under extremely mild conditions in a one-pot manner to afford bis(alk-3-en-1-ynyl)benzenes in good to excellent yields. The optical properties of the products are also described.     

Synthesis, crystal structure and magnetic property of a new 1D molecular material [1-(4′-chlorobenzyl)-4-aminopyridinium](+) bis(maleonitriledithiolato)nickel(-)

A new ion-pair complex, [1-(4′-chlorobenzyl)-4-aminopyridinium](+)bis(maleonitrile-dithiolato)nickel(−),[ClbzPyNH₂][Ni(mnt)₂] (1), has been prepared and characterized. X-ray single crystal structure conforms that the Ni(mnt)₂⁻ anions and [ClbzPyNH₂]⁺ cations of 1 form completely segregated uniform stacking columns with the Ni?Ni distance 3.944 Å in the Ni(mnt)₂⁻ stacking column. The temperature dependence of the magnetic susceptibility reveals that 1 undergoes a magnetic transition, and exhibits ferromagnetic interaction in the high-temperature phase and spin gap system in the low-temperature phase.     

Spectroscopic and quantum chemical studies on the structure of 2-arylquinoline-4(1H)-thione derivatives

The geometries of the title compounds were probed in solution, solid and gas states using spectroscopic methods, X-ray crystallography and quantum chemical techniques. The exclusive existence of the NH-4-thiones in solution (NMR and PCM-B3LYP(MP2)/6-31+G(d) calculations) and solid state (FT-IR and X-ray) is also corroborated by comparison of their spectroscopic data with those of the corresponding 2-aryl-1-methylquinoline-4(1H)-thione derivatives. The co-existence of the quinoline-4-thione and quinoline-4-thiol (4-mercaptoquinoline) isomers in the gas phase is confirmed by mass spectrometry and the preponderance of the 4-thiol is supported by quantum chemical techniques (PM3, MP2 and B3LYP).     

Adsorption of<Emphasis Type="Italic"> N</Emphasis>-dodecyl-<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-dimethyl-3-ammonio-1-propanesulfonate (DDAPS), a model zwitterionic surfactant,on the Au(111) electrode surface

Electrochemical measurements including cyclic voltammetry, differential capacity, and chronocoulometry have been used to characterize the adsorption behaviors of the zwitterionic surfactant N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (DDAPS) on the Au(111) electrode surface. The thermodynamics of the ideally polarized electrode have been employed to determine the Gibbs excess and the Gibbs energy of adsorption. The results show that the adsorption of DDAPS has a multistate character. The first two states are observed at potentials close to zero charge. At low bulk DDAPS concentrations, it corresponds to the formation of a film of nearly flat adsorbed molecules. At higher concentrations it is converted into a hemimicellar state. The second state is formed at negative potentials and charge densities close to 0 C cm^–2. It corresponds to a film of tilted molecules oriented with the hydrocarbon tail towards the metal and the polar head toward the solution.Dedicated to Professor Zbigniew Galus on the occasion of his 70^th birthday and in recognition of his many contributions to electrochemistry.     

Action of HCl on 3-hydroxypyrazolo(iso)quinolines to give 1-chloropyrazoles: evidence for an addition–elimination mechanism by ab initio calculations in gas phase and water

 Addition–elimination reactions involving a nucleophile and a remote leaving group [S^H _N(AE)^tele] are well-known under basic conditions, especially amongst electron-poor six-membered heterocycles, but are less commonly encountered for five-membered heterocycles and are rare under acidic conditions. Concentrated HCl converts 1-hydroxy-1H-pyrazolo[3,4-c] isoquinoline and 1-hydroxy-1H-pyrazolo[3,4-c]quinoline into 3-chloro-1H-pyrazolo[3,4-c]isoquinoline and 3-chloro-1H-pyrazolo[3,4-c]quinoline, respectively. However, apparently neither the isomeric 1-hydroxy-1H-pyrazolo[4,3-c](iso)-quinolines nor the parent 1-hydroxypyrazole undergo this reaction. Additionally, all these systems are refractory under basic conditions. We present a plausible mechanism for the reaction, involving the 3-addition of Cl^- to the diprotonated heterocycle, followed by the elimination of water. Calculations of the initial transition states and intermediates, using optimisation at B3LYP/6-311+G(d,p), including thermochemistry [HF/6-31+G(d)], and single-point Poisson–Boltzmann self-consistent reaction field determination of the free energy of solvation (Jaguar Poisson–Boltzmann self-consistent reaction field), support this mechanism and reproduce the observed order of reactivity, the addition step being 2–4 kcal less favourable for the isomeric 1-hydroxy-1H-pyrazolo[4,3-c](iso)quinolines and provide a rationalisation for the role of strong acid. Received: 27 June 2002 / Accepted: 6 September 2002 / Published online: 14 February 2003     

毒蕈碱受体激动剂的三维定量构效关系研究

采用比较分子场分析法(CoMFA)研究了55个四氢吡啶类毒蕈碱受体激动剂的三维定量构效关系(3D-QSAR), 建立了具有较强预测能力的3D-QSAR模型. 所得模型的交叉验证相关系数(q²)为0.507, 常规相关系数(R²)为0.982 , 标准方差为0.218, 说明系列化合物分子周围立体场和静电场的分布与生物活性间存在良好的相关性. 模型不仅很好地预测了训练集和测试集化合物的活性, 而且为设计活性更高的受体激动剂提供了理论依据.