Computer-aided structure elucidation methods

Computer-aided structure elucidation methodology is discussed. Major processes involved in computer-aided structure elucidation systems are partial-structure elucidation, structure generation, and structure examination. For the three representative systems CONGEN, CASE, and CHEMICS, these processes are examined. There are four necessary conditions for automated chemical structure elucidation systems: reliability, width of application, ease of modification and portability.     

Enantioselective carbanion cyclization of 5-alkenyl carbamates induced by asymmetric lithiation with s-butyllithium/(−)-sparteine system

Treatment of (E)-6-phenyl-5-hexenyl carbamates with s-BuLi/(−)-sparteine is shown to afford the trans-1,2-disubstituted cyclopentane derivatives in high % ee, along with the bicyclo[3.1.0]hexanes (bicyclization products).     

Structural difference between a superconducting sodium cobalt oxide and its related phase

Monolayer hydrate (MLH) Na_xCoO₂·y′H₂O was obtained from superconducting bilayer hydrate (BLH) Na_xCoO₂·yH₂O by partial extraction of H₂O molecules between the CoO₂ layers. Magnetization measurements indicated that electron densities in the CoO₂ layer of the MLH phase remained unchanged after the water extraction. Nevertheless, superconductivity was completely suppressed in the MLH phase. This strongly suggests that the highly 2D nature in the BLH phase due to its thick insulating layers consisting of H₂O molecules and Na⁺ ions plays an important role for inducing superconductivity.     

High Molecular Orientation in Mono- and Trilayer Polydiacetylene Films Imaged by Atomic Force Microscopy

Atomically flat monolayer and trilayer films of polydiacetylenes have been prepared on mica and silicon using a horizontal deposition technique from a pure water subphase. Langmuir films of 10,12-pentacosadiynoic acid (I) and N-(2-ethanol)-10,12-pentacosadiynamide (II) were compressed to 20 mN/m and subsequently polymerized by UV irradiation at the air-water interface. Blue and red forms of the films were prepared by varying exposure times and incident power. Polymerization to the blue-phase films produced slight contractions of 2 and 5% for the films of II and I, respectively. Longer UV exposures yielded red-phase films with dramatic film contraction of 15 and 32% for II and I, respectively. The horizontal deposition technique provided transfer ratios of unity with minimal film stress or structure modification. Atomic force microscopy images revealed nearly complete coverage of the substrate with atomically flat films. Crystalline domains of up to 100 micrometers of highly oriented polydiacetylene molecules were observed. The results reported herein provide insight into the roles of molecular packing and chain orientations in converting the monomeric film to the polymerized blue and red phases. Copyright 2000 Academic Press.     

ESTIMATION OF AN INDEX OF HYDROPHOBICITY OF DNA INTERIOR USING 5-METHOXYPSORALEN AS A FLUORESCENT PROBE

The index of hydrophobicity of DNA interior was estimated by measuring fluorescence spectra of psoralen derivatives associated with DNA. The environment around 5-MOP associated with DNA was as hydrophobic (D_k = 34) as methanol, suggesting that the molecules reside at the space between the base-pairs in B-form DNA. This is also true for 8-MOP. Thus, planar and aromatic molecules of 5- and 8-MOP are more stable in the interior of DNA than in aqueous medium due to hydrophobic affinity.     

Mononuclear oxovanadium complexes of tris(2-pyridylmethyl)amine

Mononuclear oxovanadium(IV) and dioxovanadium(V) complexes of tris(2-pyridylmethyl)amine (tpa) have been prepared for the first time. Crystal structure determinations of three oxovanadium(IV) complexes, [VO(SO4)(tpa)], [VOCl(tpa)]PF6, or [VOBr(tpa)]PF6, and a dioxovanadium(v) complex [V(O)2(tpa)]PF6 disclosed that the tertiary nitrogen of the tpa ligand always occupies the trans-to-oxo site. The structures of an oxo-peroxo complex [VO(O2)(tpa)]Cl that was prepared previously and of a mu-oxo vanadium(III) complex [{VCl(tpa)}2(mu-O)](PF6)2 have also been determined. The tertiary nitrogen is located at a trans site to the peroxo and chloride ligands, respectively. The total sums of the four V-N bond lengths from the tpa ligand are remarkably similar among the six complexes, indicating that the vanadium oxidation states become less influential in tpa bonding due primarily to the coordination of electron-donating oxo ligand(s). Absorption spectra of [VOCl(tpa)]+ in acetonitrile showed a significant change upon addition of p-toluenesulfonic acid and HClO4, but not on addition of benzoic acid. Protonation at the oxo ligand by the former two acids is suggested. Cyclic voltammetric studies in acetonitrile verified the proton-coupled redox behavior of the V(III)/V(IV) process involving the oxo ligand for the first time. From the dependence of the added p-toluenesulfonic acid to the CV, redox potentials for the following species have been estimated: [V(IV)OCl(tpa)]+/[V(III)OCl(tpa)](E1/2=-1.59 V vs. Fc+/Fc), [V(IV)(OH)Cl(tpa)]2+/[V(III)(OH)Cl(tpa)]+(Epc=-1.34 V), [V(IV)(OH2)Cl(tpa)]3+/[V(III)(OH2)Cl(tpa)]2+(Epa=-0.49 V), and [V(IV)Cl2(tpa)]2+/[V(III)Cl2(tpa)]+(E1/2=-0.89 V). The reduction of [V(V)(O)2(tpa)]+ in 0.05 M [(n-Bu)4N]PF6 acetonitrile showed a major irreversible reduction wave V(V)/(IV) at -1.48 V. The metal reduction potentials of the oxovanadium(IV) and dioxovanadium(V) species are very close, reinforcing the significant influence of the oxo ligand(s).     

Application of infrared data analysis based on symbolic logic in automated structure elucidation by chemics

A computer program, IRASSL, is described for processing infrared (IR) data. The program, based on symbolic logic, is used to formulate complex relationships between substructures and their characteristic wavenumber regions. The program yields sets of substructures inferred from a correlation table prepared from accumulated IR data. The procedure is applied as an ancillary to the automated structure elucidation system CHEMICS. The introduction of the substructural information provided by IRASSL into CHEMICS as restrictions in the elucidation process produces a significant decrease in the number of candidate structures. Some examples of the application are given.     

Low temperature synthesis and characterization of porous anatase TiO2 nanoparticles

An ethanol solution of Ti-peroxy compounds was prepared from the ethanol solution of titanium isopropoxide (Ti(O-iPr)4) and H2O2. Heating of the ethanol solution of the Ti-peroxy compounds at 348 K formed a Ti-peroxy gel, and heat treatment of the gel at 348 K for more than 6 h formed gels that consisted of anatase nanoparticles. The diameter of the anatase nanoparticles increased from 9 to 15 nm as the heating time increased from 6 to 48 h. According to the results of the N2 adsorption measurement, the anatase nanoparticles had micropores, and the specific surface area (SBET) was in the range of 254 to 438 m2/g. The particle size, lattice strain, specific surface area, and photocatalytic activity of the anatase nanoparticles can be regulated by the heating time of the Ti-peroxy gel at 348 K.     

Sensitive determination of bisphenol A and alkylphenols by high performance liquid chromatography with pre-column derivatization with 2-(4-carboxyphenyl)-5,6-dimethylbenzimidazole

A new and sensitive high-performance chromatographic method for the determination of bisphenol A and 8 alkylphenols with fluorescence detection is reported. Each phenol was derivatized by reaction with 2-(4-carboxyphenyl)-5,6-dimethylbenzimidazole at 40 degrees C for 60 min. The fluorescence derivatives were separated on a Wakosil 5C18 column (4.0 i.d. x 300 mm, 5 microm) with methanol:water (10:90) as mobile phase (detection wavelength: lambda(ex) 336 nm, lambda(em) 440 nm). The detection limits were in the range of 0.1-10.0 pg/mL in serum. The calibration graphs were linear to 1.0 microg/mL. The relative standard deviations were 7.2-8.9%, respectively. The proposed method was applied to the determination of bisphenol A in mother and infant rat serum.     

Search for a simpler synthetic model system for intramolecular 1,3-dipolar cycloaddition to the 5,6-double bond of a pyrimidine nucleoside

In search for a simpler model system for the study of intramolecular thermal reactions between the base and 5'-functionalized sugar moiety in nucleosides, 1-(3-azidopropyl)uracil (2), 1-(4-azidobutyl) pyrimidines (12 and 13) and 1-(5-azidopentyl)-uracil (14) was synthesized through the corresponding ω-benzoyloxy-(6,7 and 8) and ω-hydroxyalkyl-pyrimidines (9,10 and 11). Heating 2 gave 1,N⁶-trimethylene-6-aminouracil (4), while heating 12 and 13 gave N¹-C₆ cleaved addition products. 15 and 16, respectively. 15 was regiospecifically transformed to 1,2,3-triazole derivatives, 17,18 and 19. Heating 1-(4-azidobutyl)-5-bromouracil (20) yielded 3,9-tetramethylene-8-azaxanthine (22). 9 with NBA gave 1,0⁶-tetramethylene-5-bromo-6-hydroxy-5,6-dihydrouracil (24) and the 5-brominated analog of 9 (25). The 4-functionalized butyl side chain proved to serve as a substitute for the 5'-functionalized sugar moiety in pyrimidine ribonucleosides.