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.     

Synthesis, characterization, and photochemical properties of azobenzene-conjugated Ru(II) and Rh(III) bis(terpyridine) complexes

We synthesized azobenzene-conjugated bis(terpyridine) Ru(II) and Rh(III) mononuclear and dinuclear complexes and investigated their photochemical properties on excitation of the azo pi-pi band upon 366 nm light irradiation. The Ru mononuclear complex underwent trans-to-cis photoisomerization to reach the photostationary state with only 20% of the cis form, while the Ru dinuclear complex did not isomerize at all photochemically. On the other hand, the mononuclear and dinuclear Rh complexes showed almost complete trans-to-cis photoisomerization behavior. Cis forms of the Rh complexes thermally returned to the trans form at a much slower rate than those of organic azobenzenes, but they did not isomerize photochemically. The reduction potential of the cis forms was 80 mV more negative than that of the trans forms. The photoisomerization quantum yields of the Rh complexes were strongly dependent on the polarity, viscosity, and donor site of the solvents as well as the size of the counterions. We investigated the photoisomerization process of these complexes using femtosecond absorption spectroscopy. For the Rh complexes, we observed S(n) <-- S(2) and S(n) <-- S(1) absorption bands similar to those of organic azobenzenes. For the Ru complexes, we observed very fast bleaching of the MLCT band of the Ru complex, which indicated that the energy transfer pathway to the MLCT was the primary cause of the depressed photoisomerization. The electronic structures, which were estimated from ZINDO molecular orbital calculation, supported the different photochemical reaction behavior between the Ru and Rh complexes.     

Preconcentration of palladium(II) from water with thionalide loaded on silica gel

2-Mercapto-N-2-naphthylacetamide (thionalide) on silica gel is used for rapid preconcentration of μg l^?1 levels of palladium(II) from aqueous solution, followed by atomic absorption spectrometric measurement. In batch experiments, palladium was quantitatively retained on the gel from solutions 5 M in acid to pH 8; equilibrium was achieved within 10 s. The chelating capacity of the gel was 7.5 μmol Pd g^?1 at pH < 4. The effect of flow rate on retention was studied. Palladium retained on the column was completely eluted with 20 ml of 0.2 M thiourea in 0.1 M hydrochloric acid. The palladium concentration in sea water is shown to be < 0.3 μg l^?1.     

Supramolecular assembly based on π-π stacking and π-cation interactions between thiacalix[6]arene and DMF

The molecular assembly of thiacalix[6]arene was formed by π-π stacking and π-DMF interactions between thiacalix[6]arene and adjoining thiacalix[6]arene and between thiacalix[6]arene and DMF, respectively. The X-ray crystal analysis also revealed that hydroxyl groups of thiacalix[6]arene adopted novel two sets of hydrogen bond with two DMF and intramolecular hydrogen bond between phenolic units, which cause to make 1,2,3-alternate configuration structure of thiacalix[6]arene.     

Fragmentation study of peptides using Fourier transform ion cyclotron resonance with infrared multiphoton dissociation: experiment and simulation

In this study, the fragmentation of gas-phase protonated Angiotensin II is investigated using electrospray ionization (ESI), Fourier-transform ion cyclotron resonance (FT-ICR), and mass spectrometry (MS) with a laser cleavage infrared multiphoton dissociation (IRMPD) technique. The experimental results show that the spectra peaks for the photoproducts are y2/b6- and y7-type ions, corresponding to the cleavage of His-Pro and Asp-Arg in the parent amino acid sequence. The fragmentation of the peptide under collision-free vacuum conditions is modeled using molecular dynamics simulations (MD). The binding energy for the peptide bonds (C'-N bond) of Angiotensin II is estimated from ab initio calculations. The calculations are directed at predicting experimental measurements of the product ions from the photodissociation of the peptide. The product distributions simulated by the MD dissociation trajectories include predominantly y7/b1 and y2/b6 pair ions.     

Reactive oligomers. II. Polymerization of glycol bis(allyl phthalate)s and glycol bis(allyl succinate)s

Seven glycol bis(allyl phthalate)s (GBAP) and four glycol bis(allyl succinate)s (GBASu) as reactive oligomers were prepared and their polymerization behaviors were investigated in detail in terms of cyclopolymerization and gelation as compared with diallyl dicarboxylates. Thus, the rates of polymerization of GBAPs were reduced compared to diallyl phthalate, being attributed to the steric effect on the intermolecular propagation of the uncyclized radical, whereas those of GBASus were enhanced as a consequence of intermolecular association by dipole–dipole interaction in polar GBASu monomers. Cyclization was enhanced in the following order: diallyl aliphatic dicarboxylates series < GBASu series < GBAP series. Gelation was discussed according to Gordon's theory; the actual gel-point conversions increased with an increase in the molecular weight of monomers, although the discrepancy between actual and theoretical gel-point conversion inversely tended to be decreased. The decreased delay in gelation with an increase of the molecular weight of monomers is ascribed to the reduction of excluded volume effects on crosslinking.     

Assembly of Carbohydrates on a Nickel(II) Center by Utilizing N-Glycosidic Bond Formation with Tris(2-aminoethyl)amine (tren). Syntheses and Characterization of [Ni{N-(aldosyl)-tren}(H(2)O)](2+), [Ni{N,N'-bis(aldosyl)-tren}](2+) and [Ni{N,N',N"-tris(aldosyl)-tren}](2+)

Reactions of [Ni(tren)(H(2)O)(2)]X(2) (tren = tris(2-aminoethyl)amine; X = Cl (1a), Br (1b); X(2) = SO(4) (1c)) with mannose-type aldoses, having a 2,3-cis configuration (D-mannose and L-rhamnose), afforded {bis(N-aldosyl-2-aminoethyl)(2-aminoethyl)amine}nickel(II) complexes, [Ni(N,N'-(aldosyl)(2)-tren)]X(2) (aldosyl = D-mannosyl, X = Cl (2a), Br (2b), X(2) = SO(4) (2c); aldosyl = L-rhamnosyl, X(2) = SO(4) (3c)). The structure of 1c was confirmed by X-ray crystallography to be a mononuclear [Ni(II)N(4)O(2)] complex with the tren acting as a tetradentate ligand (1c.2H(2)O: orthorhombic, Pbca, a = 15.988(2) ?, b = 18.826(4) ?, c = 10.359(4) ?, V = 3118 ?(3), Z = 8, R = 0.047, and R(w) = 0.042). Complexes 2a,c and 3c were characterized by X-ray analyses to have a mononuclear octahedral Ni(II) structure ligated by a hexadentate N-glycoside ligand, bis(N-aldosyl-2-aminoethyl)(2-aminoethyl)amine (2a.CH(3)OH: orthorhombic, P2(1)2(1)2(1), a = 16.005(3) ?, b = 20.095(4) ?, c = 8.361(1) ?, V = 2689 ?(3), Z = 4, R = 0.040, and R(w) = 0.027. 2c.3CH(3)OH: orthorhombic, P2(1)2(1)2(1), a = 14.93(2) ?, b = 21.823(8) ?, c = 9.746(2) ?, V = 3176 ?(3), Z = 4, R = 0.075, and R(w) = 0.080. 3c.3CH(3)OH: orthorhombic, P2(1)2(1)2(1), a = 14.560(4) ?, b = 21.694(5) ?, c = 9.786(2) ?, V = 3091 ?(3), Z = 4, R = 0.072, and R(w) = 0.079). The sugar part of the complex involves novel intramolecular sugar-sugar hydrogen bondings around the metal center. The similar reaction with D-glucose, D-glucosamine, and D-galactosamine, having a 2,3-trans configuration, resulted in the formation of a mono(sugar) complex, [Ni(N-(aldosyl)-tren)(H(2)O)(2)]Cl(2) (aldosyl = D-glucosyl (4b), 2-amino-2-deoxy-D-glucosyl (5a), and 2-amino-2-deoxy-D-galactosyl (5b)), instead of a bis(sugar) complex. The hydrogen bondings between the sugar moieties as observed in 2 and 3 should be responsible for the assembly of two sugar molecules on the metal center. Reactions of tris(N-aldosyl-2-aminoethyl)amine with nickel(II) salts gave the tris(sugar) complexes, [Ni(N,N',N"-(aldosyl)(3)-tren)]X(2) (aldosyl = D-mannosyl, X = Cl (6a), Br (6b); L-rhamnosyl, X = Cl (7a), Br (7b); D-glucosyl, X = Cl (9); maltosyl, X = Br (10); and melibiosyl, X = Br (11)), which were assumed to have a shuttle-type C(3) symmetrical structure with Delta helical configuration for D-type aldoses on the basis of circular dichroism and (13)C NMR spectra. When tris(N-rhamnosyl)-tren was reacted with NiSO(4).6H(2)O at low temperature, a labile neutral complex, [Ni(N,N',N"-(L-rhamnosyl)(3)-tren)(SO(4))] (8), was successfully isolated and characterized by X-ray crystallography, in which three sugar moieties are anchored only at the N atom of the C-1 position (8.3CH(3)OH.H(2)O: orthorhombic, P2(1)2(1)2(1), a = 16.035(4) ?, b = 16.670(7) ?, c = 15.38(1) ?, V = 4111 ?(3), Z = 4, R = 0.084, and R(w) = 0.068). Complex 8 could be regarded as an intermediate species toward the C(3) symmetrical tris(sugar) complexes 7, and in fact, it was readily transformed to 7b by an action of BaBr(2).     

Catalytic oxygenative degradation of 4-chlorocatechol by a nonheme iron(III) complex—Mechanism and prevention of catechol ester formation

We examined the oxygenative degradation of 4-chlorocatechol and 4-tert-butylcatechol catalyzed by iron(III)-tris(pyridin-2-yl)amine complex from the standpoint of repressing the formation of 4-chlorocatechol esters of the oxygenated products that causes the incomplete degradation of 4-chlorocatechol. Analysis of the products revealed that 4-chlorocatechol esters are formed by the reaction of muconic anhydride, which is the monooxygenated product, with catechols. It was found that the use of MeOH as the solvent instead of MeCN completely suppressed the catechol ester formation through the methanolysis of muconic anhydride, which greatly improves the degradation efficiency of 4-chlorocatechol.