A theoretical study on the ionization of OCS with an analysis of vibrational structures of the photoelectron spectrum

 Ab initio calculations have been performed to study the molecular structures and vibrational levels of the four low-lying ionic states (1, 2²Π, and 1, 2²Σ⁺) of carbonyl sulfide. The global regions of the potential-energy surfaces have been obtained by multireference single and double excitation configuration interaction calculations. Vibrational calculations using explicit vibrational Hamiltonians have been used for vibrational analysis. The equilibrium molecular structures and a vibrational analysis of the four ionic states are presented. The theoretical ionization intensity curves including the vibrational structures of the ionic states are also presented and are compared with the photoelectron spectrum. Received: 20 January 2001 / Accepted: 22 August 2001 / Published online: 30 October 2001     

Long RNA dangling end has large energetic contribution to duplex stability

Long terminal unpaired nucleotides known as dangling ends play interesting roles in biological systems. Previous studies, however, only dealt with the energy contributions of single dangling bases. The energy contributions of long dangling ends on the stability of duplexes have not been systematically studied. We now report a quantitative increase in stability of RNA-RNA and DNA-DNA duplexes containing a long dangling end. We found a larger enhancement of the stability by the long RNA dangling end of the RNA-RNA duplex than has been observed for the DNA duplexes. It is also found that structural stabilizations by long dangling ends seem to originate from the single-stranded stacking interactions of nucleotides. These results indicate that RNA stability can be achieved by increasing the length of the dangling end. The thermodynamic parameters of the long dangling ends are useful for designing ribozymes and antisense oligonucleotides, and for the prediction of the RNA secondary structure like the pseudoknot.     

Applications of the model potential method to transition metal compounds

Model potential parameters and basis sets, presented previously for the transition metal atoms Sc through Hg, are tested in calculations of the transition metal compounds (CuF, CuCl, Cu₂, TiCl₄, ZrCl₄, CoF₆^3?, CoF₆^2?, AgH, AuH, CrF₆, ScO, ZrO, Cr₂, Mo₂). Calculated values of the bond distances, vibrational frequencies, and some transition energies (for Cu₂ and CoF₆^2?) are compared with those given by all-electron calculations with basis sets of high quality. Singlet-triplet splittings in Cu₂ and correlation energies in CrF₆^n? (n = 0, 1, and 2) are also examined. The satisfactory results obtained by these calculations strongly support the contention that the model potential method is a reliable and economical alternative to the ab initio Hartree-Fock-Roothaan method.     

Role of methyl radicals in the growth of PAHs

The role of methyl radicals in the networking of sp² carbons has been explored through kinetic analysis of mass spectra of the gas-phase products of the pyrolysis of toluene and toluene/acetone mixtures. Pyrolytic reactions were performed in a flow tube reactor at temperatures of 1140–1320 K and a constant total pressure of 10.38 Torr with a residence time of 0.585 s. On addition of acetone, methyl substituted products and their derivatives were enhanced. Mass peaks were observed in several sequences at an interval of 14 mass units; these ions correspond to methyl substituted products formed as a result of hydrogen abstraction (−H) followed by methyl radical addition (+CH₃). Each major peak was usually preceded by a peak at two mass units lower, which was likely produced through dehydrogenation/dehydrocyclization (−H₂) of methyl substituted products. Detected species include a large number of alkyl, cyclotetrafused (CT), cyclopentafused (CP) mono-, di-, and polycyclic aromatic hydrocarbons (PAHs) along with primary PAHs. The analysis showed that MAC (methyl addition/cyclization) has a unique capacity to induce the sequential growth of hexagonal networks of sp² carbons from all fusing sites [1] of a PAH. Moreover, MAC was found capable of answering an important question in PAH growth, which is expansion of the CT → CP → hexagonal network for which other reported mechanisms are inefficient.     

Simultaneous determination of hydrophilic amino acid enantiomers in mammalian tissues and physiological fluids applying a fully automated micro-two-dimensional high-performance liquid chromatographic concept

A validated two-dimensional HPLC system combining a microbore-monolithic ODS column and a narrowbore-enantioselective column has been established for a sensitive and simultaneous analysis of hydrophilic amino acid enantiomers (His, Asn, Ser, Gln, Arg, Asp, allo-Thr, Glu and Thr) and the non-chiral amino acid, Gly, in biological samples. To accomplish this goal, the amino acids were first tagged with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F) to the respective fluorescent NBD derivatives which were separated in the first dimension by a micro-reversed-phase column. The automatically collected fractions of the target peaks were then transferred to the second dimension consisting of a Pirkle type enantioselective column generating separation factors higher than 1.13 for all the enantiomeric target analytes. The system was validated using standard amino acids and a rat plasma sample, and analytically satisfactory calibration and precision results were obtained. The present 2D-HPLC system enables the fully automated determination of hydrophilic amino acid enantiomers in mammalian samples. The d-isomers of all the investigated 9 amino acids were found in rat urine but at various enantiomeric ratios.     

Inner-valence states of N2+ and the dissociation dynamics studied by threshold photoelectron spectroscopy and configuration interaction calculation

The N2(+) states lying in the ionization region of 26-45 eV and the dissociation dynamics are investigated by high-resolution threshold photoelectron spectroscopy and threshold photoelectron-photoion coincidence spectroscopy. The threshold photoelectron spectrum exhibits several broad bands as well as sharp peaks. The band features are assigned to the N2(+) states associated with the removal of an inner-valence electron, by a comparison with a configuration interaction calculation. In contrast, most of the sharp peaks on the threshold photoelectron spectrum are allocated to ionic Rydberg states converging to N2(2+). Dissociation products formed from the inner-valence N2(+) states are determined by threshold photoelectron-photoion coincidence spectroscopy. The dissociation dynamics of the inner-valence ionic states is discussed with reference to the potential energy curves calculated.     

Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions

The effect of molecular crowding on the structure and stability of biomolecules has become a subject of increasing interest because it can clarify how biomolecules behave under cell-mimicking conditions. Here, we quantitatively analyzed the effects of molecular crowding on the thermodynamics of antiparallel G-quadruplex formation via Hoogsteen base pairs and of antiparallel hairpin-looped duplex (HP duplex) formation via Watson-Crick base pairs. The free energy change at 25 degrees C for G-quadruplex formation decreased from -3.5 to -5.5 kcal mol(-1) when the concentration of poly(ethylene glycol) 200 was increased from 0 to 40 wt %, whereas that of duplex formation increased from -9.8 to -6.9 kcal mol(-1). These results showed that the antiparallel G-quadruplex is stabilized under molecular crowding conditions, but that the HP duplex is destabilized. Moreover, plots of stability (ln K(obs)) of the DNA structures versus water activity (ln a(w)) demonstrated that the ln K(obs) for G-quadruplex formation decreased linearly as the ln a(w) increased, whereas that for duplex formation increased linearly with the increase in ln a(w), suggesting that the slope approximately equals the number of water molecules released or taken up during the formation of these structures. Thus, molecular crowding affects the thermodynamics of DNA structure formation by altering the hydration of the DNA. The stabilization of the DNA structures with Hoogsteen base pairs and destabilization of DNA structures with Watson-Crick base pairs under molecular crowding conditions lead to structural polymorphism of DNA sequences regulated by the state of hydration.