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Rearrangement of hydrogen bonds in the protonated methanol−water cluster ion H⁺(CH3OH)4H2O is analyzed. The analysis, based on ab initio calculations performed at the B3LYP/aug-cc-pVTZ//6-31+G* and MP4/ 6-311+G*//B3LYP/6-31+G* levels of computation, provides information about potential minima, transition states, and pathways for the hydrogen bond rearrangement processes. Results of the analysis are compared systematically to the experimental measurements for H⁺(CH3OH)4H2O, where two distinct charge-centered (H3O⁺ and CH3OH2⁺) isomers have been identified in a supersonic expansion by fragment-dependent vibrational predissociation spectroscopy (Chaudhuri et al. J. Chem. Phys. 2000, 112, 7279). Revealed by the calculations, the lowest energy pathway for the transition from an open noncyclic hydronium-centered isomer [H3O⁺(CH3OH)4] to a linear methyloxoium-centered isomer [CH3OH2⁺(CH3OH)3H2O] involves three stable intermediates and four transition states. The transition can go through either all four-membered ring isomers or a mixture of four-membered and five-membered ring intermediates. The latter is an energetically more favorable process because of less strain involved in the five-membered ring formation. A barrier height of <2.5 kcal/mol (after zero-point energy corrections) is predicted, suggesting that rapid interconversions among different isomers can occur at room temperature for this particular cluster cation.

Structures of the solvation shells of O-protonated formamide (H⁺FA) have been characterized by infrared spectroscopy and ab initio calculations at varying stages of hydration. A few isomeric structures, including both H⁺FA- and H3O⁺-centered forms, were identified from a close examination of the hydrogen-bonded and non-hydrogen-bonded NH and OH stretching spectra of H⁺FA(H2O)n (n = 3 and 4) produced by a supersonic expansion. Theoretical investigations of H⁺FA(H2O)1-3 indicate that filling of the first hydration shell of the protonated formamide cation with three water molecules is not an energetically favorable process. The process is hampered by the hydrogen bond anticooperative effect, which prohibits both NH bonds to be involved in hydrogen bonding. Further increasing the cluster size to n = 4 results in grouping of the water molecules on one side of the formamide, rather than forming a filled first solvation shell of H⁺FA. The grouping, in effect, enhances the proton affinity of the water molecule in direct contact with the excess proton and progressively moves the proton away from H⁺FA, producing an H3O⁺ ion core. Detailed analysis of the results, both qualitatively and quantitatively, reveals the existence of a low-barrier proton transfer process, which is expected to occur similarly in aqueous solutions during acid-catalyzed amide hydrolysis. In this work, we also successfully identified a shell-filled isomer for H⁺(FA)3H2O for the first time. It is demonstrated that a combined investigation of cluster ions by infrared spectroscopy and ab initio calculations allows for an unambiguous determination of both the protonation sites and hydration structures of biomolecules in the gas phase.

Characterization of protonated formamide clusters by vibrational predissociation spectroscopy confirms theoretical predictions that O-protonation occurs in preference to N-protonation in formamide. The confirmation is made from a close comparison of the infrared spectra of H⁺[HC(O)NH2]3 and NH4⁺[HC(O)NH2]3 produced by a supersonic expansion with the spectra produced by ab initio calculations. For NH4⁺[HC(O)NH2]3, prominent and well-resolved vibrational features are observed at 3436 and 3554 cm^-1. They derive, respectively, from the symmetric and asymmetric NH2 stretching motions of the three formamide molecules linked separately to the NH4⁺ ion core via three N−H⁺···O hydrogen bonds. Similarly distinct absorption features are also found for H⁺[HC(O)NH2]3; moreover, they differ in frequency from the corresponding vibrational modes of NH4⁺[HC(O)NH2]3 by less than 10 cm^-1. The result is consistent with a picture of proton attachment to the oxygen atom, rather than the nitrogen atom in H⁺[HC(O)NH2]3. We provide in this work both spectroscopic and computational evidence for the O-protonation of formamide and its clusters in the gas phase.

Comparative vertebrate genome sequencing offers a powerful method for detecting conserved regulatory sequences. We propose that the compact genome of the teleost Fugu rubripes is well suited for this purpose. The evolutionary distance of teleosts from other vertebrates offers the maximum stringency for such evolutionary comparisons. To illustrate the comparative genome approach for F. rubripes, we use sequence comparisons between mouse and Fugu Hoxb-4 noncoding regions to identify conserved sequence blocks. We have used two approaches to test the function of these conserved blocks. In the first, homologous sequences were deleted from a mouse enhancer, resulting in a tissue-specific loss of activity when assayed in transgenic mice. In the second approach, Fugu DNA sequences showing homology to mouse sequences were tested for enhancer activity in transgenic mice. This strategy identified a neural element that mediates a subset of Hoxb-4 expression that is conserved between mammals and teleosts. The comparison of noncoding vertebrate sequences with those of Fugu, coupled to a transgenic bioassay, represents a general approach suitable for many genome projects.

In this preliminary work, using a 3-state diabatic molecular expansion without any excited channels, we have studied within the semiclassical impact parameter approximation the single charge transfer process He2++He(1s2)→He+(1s)+He+(1s). Our results agree very well with experiment, which demonstrates the usefulness of this type of diabatic molecular basis in doubly charged ion-atom collision systems.

The ability of several species of birds to synthesize L-ascorbic acid is correlated with their phylogeny. In the more primitive species, synthesis of L-ascorbic acid occurs in the kidney. Among the highly evolved passeriform species, kidney and liver can synthesize L-ascorbic acid in some, whereas in others synthesis occurs in the liver. In still others, the capacity for the synthesis of L-ascorbic acid is apparently lost. The pattern of evolution of the ascorbic acid pathway among birds is thus similar to that among mammals.