Electron Attachment to the (O2···CO2) van der Waals Complex Results in a Monomeric Anion (O2-CO2)-, a Possible Form of CO4.

We found that electron attachment to the van der Waals complex (O2···CO2) turns the weak intermolecular bond into a pseudochemical bond of significant strength. The resulting monomeric molecular anion (O2-CO2)- may be a form of CO4-, the gaseous anionic species suspected to be present in Earth's ionosphere whose chemical characteristics have not been comprehensively identified since its existence was first predicted by Conway in 1962. The measured vertical detachment energy of CO4- is very large (4.56 ± 0.05 eV), while the known electron affinity of its component species is much smaller (0.448 eV, O2) or even negative (-0.6 eV, CO2). These characteristics are correctly borne out by theoretical calculations that show that electron attachment transforms the van der Waals complex to a single contiguous molecular anion, with the formation of a pseudochemical bond between O2 and CO2 through an extended π-orbital system.

Site-dependent effects of methylation on the electronic spectra of jet-cooled methylated xanthine compounds.

We obtained the electronic spectra of various methylated xanthine compounds including caffeine in a supersonic jet by resonant two-photon ionization spectroscopy. The methyl group in the tested methylated xanthine compounds has a distinct, site-dependent effect on the electronic spectrum. Methylation at the N3 position causes a significant red shift of the ππ* state, whereas methylation at the N1 position has only minimal effects on the electronic spectrum. The notably broad spectra of theobromine and caffeine result from methyl substitution at the N7 position, which causes a large displacement between the potential energy surfaces of the S0 and S1 states, and a strong vibronic coupling. We also investigated the internal rotation of the methyl group and its effect on the electronic spectrum of the methylated xanthine compounds. We found that the barrier height for the torsional motion in the ground state is significantly affected by a carbonyl or methyl group that lies close to the methyl group of interest. In contrast, the torsional barrier in the excited state is governed by the hyperconjugation interaction in the lowest unoccupied molecular orbital. The agreement between the experimental and simulated spectra of torsional vibronic bands suggested that the low frequency torsional vibrations arising from the tunneling splitting and the coupling between the torsional and molecular motions give theobromine and theophylline the multiplet nature of their origin bands. This study provides a new level of understanding for the methyl substitution effects on the electronically excited states of xanthine compounds, which may very well be applicable to many other methyl substituted biomolecules including DNAs and proteins.

Protein NMR structures refined without NOE data.

The refinement of low-quality structures is an important challenge in protein structure prediction. Many studies have been conducted on protein structure refinement; the refinement of structures derived from NMR spectroscopy has been especially intensively studied. In this study, we generated flat-bottom distance potential instead of NOE data because NOE data have ambiguity and uncertainty. The potential was derived from distance information from given structures and prevented structural dislocation during the refinement process. A simulated annealing protocol was used to minimize the potential energy of the structure. The protocol was tested on 134 NMR structures in the Protein Data Bank (PDB) that also have X-ray structures. Among them, 50 structures were used as a training set to find the optimal "width" parameter in the flat-bottom distance potential functions. In the validation set (the other 84 structures), most of the 12 quality assessment scores of the refined structures were significantly improved (total score increased from 1.215 to 2.044). Moreover, the secondary structure similarity of the refined structure was improved over that of the original structure. Finally, we demonstrate that the combination of two energy potentials, statistical torsion angle potential (STAP) and the flat-bottom distance potential, can drive the refinement of NMR structures.

Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach.

A set of grid type knowledge-based energy functions is introduced for ϕ-χ1 , ψ-χ1 , ϕ-ψ, and χ1 -χ2 torsion angle combinations. Boltzmann distribution is assumed for the torsion angle populations from protein X-ray structures, and the functions are named as statistical torsion angle potential energy functions. The grid points around periodic boundaries are duplicated to force periodicity, and the remedy relieves the derivative discontinuity problem. The devised functions rapidly improve the quality of model structures. The potential bias in the functions and the usefulness of additional secondary structure information are also investigated. The proposed guiding functions are expected to facilitate protein structure modeling, such as protein structure prediction, protein design, and structure refinement.

The effect of Zn(2+) on Pelodiscus sinensis creatine kinase: unfolding and aggregation studies.

We studied the effects of Zn(2+) on creatine kinase from the Chinese soft-shelled turtle, Pelodiscus sinensis (PSCK). Zn(2+) inactivated the activity of PSCK (IC(50) = .079 ± .004 mM) following first-order kinetics consistent with multiple phases. The spectrofluorimetry results showed that Zn(2+) induced significant tertiary structural changes of PSCK with exposure to hydrophobic surfaces and that Zn(2+) directly induced PSCK aggregation. The addition of osmolytes such as glycine, proline, and liquaemin successfully blocked PSCK aggregation, recovering the conformation and activity of PSCK. We measured the ORF gene sequence of PSCK by rapid amplification of cDNA end and simulated the 3D structure of PSCK. The results of molecular dynamics simulations showed that eight Zn(2+) bind to PSCK and one Zn(2+) is predicted to bind in a plausible active site of creatine and ATP. The interaction of Zn(2+) with the active site could mostly block the activity of PSCK. Our study provides important insight into the action of Zn(2+) on PSCK as well as more insights into the PSCK folding and ligand-binding mechanisms, which could provide important insight into the metabolic enzymes of P. sinensis.

A simplified homology-model builder toward highly protein-like structures: an inspection of restraining potentials.

A homology model builder using simple restraining potentials based on spline-interpolated quadratic functions is developed and interfaced with CHARMM package. The continuity and stability of the potential function were validated, and the parameters were optimized using the CASP7 targets. The performance of the model builder was benchmarked to the Modeller program using the template-based modeling targets in CASP9. The benchmark results show that, while our builder yields the structures with slightly lower packing, backbone, and template modeling scores, our models show much better protein-like scores in terms of normalized discrete optimized protein energy, dipolar distance-scaled finite-ideal gas reference, Molprobity clash, Ramachandran appearance Z-score, and rotamer Z-score. As our model builder is interfaced with CHARMM, it is advantageous to directly use other CHARMM functionality and energy functions to refine the model structures or to use the models for other computational studies using CHARMM.

Relativistic potential energy surfaces of initial oxidations of Si(100) by atomic oxygen: the importance of surface dimer triplet state.

The non-relativistic and relativistic potential energy surfaces (PESs) of the symmetric and asymmetric reaction paths of Si(100)-2×1 oxidations by atomic oxygen were theoretically explored. Although only the singlet PES turned out to exist as a major channel leading to "on-dimer" product, both the singlet and triplet PESs leading to "on-top" products are attractive. The singlet PESs leading to the two surface products were found to be the singlet combinations (open-shell singlet) of the low-lying triplet state of surface silicon dimer and the ground (3)P state of atomic oxygen. The triplet state of the "on-top" product can also be formed by the ground singlet state of the surface silicon dimer and the same (3)P oxygen. The attractive singlet PESs leading to the "on-dimer" and "on-top" products made neither the intersystem crossings from triplet to singlet PES nor high energy (1)D of atomic oxygen necessary. Rather, the low-lying triplet state of surface silicon dimer plays an important role in the initial oxidations of silicon surface.

Efficient chirality transfer in the SmI2-mediated cyclization of aldehydo beta-alkoxyvinyl sulfoxides: asymmetric synthesis of 3-hydroxyoxanes.

Stereoselective syntheses of 3-hydroxyoxanes were achieved via efficient chirality transfer in the SmI2-mediated cyclization reactions of aldehydo beta-alkoxyvinyl sulfoxides.