Hydrogen storage inside a toroidal carbon nanostructure C120: Density functional theory computer simulation

Ab initio density functional calculations were performed for a toroidal carbon C₁₂₀ nanostructure. Hydrogen molecules, n = 1–15, were added inside the nanotorus and for each one of these systems a geometry optimization was obtained. The cohesive energy shows that these structures are energetically stable. For example, the binding energies are ?34.95 and ?36.19 Hartrees and the interatomic distances H? H are 0.753 and 0.772 Å for 1 and 14 molecules, respectively. Considering only molecular hydrogen, we have always seen so far weak physisorption into the C₁₂₀ nanotorus. There is no chemisorption until the number oh hydrogen molecules are increased to 14. In this case, four hydrogen atoms are chemisorbed. With 15 molecules, there are 10 hydrogen atoms chemisorbed just at the inner nanotorus surface forming 10 H? C bondings with bond length close to that in methane. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2495–2508, 2010     

Dynamics of the nitroxide side chain in spin-labeled proteins

The dynamics of the tether linking methanethiosulfonate (MTSSL) spin probes to alpha-helices has been investigated with the purpose of rationalizing its effects on ESR line shapes. Torsional profiles for the chain bonds have been calculated ab initio, and steric interactions with the alpha-helix and the neighboring residues have been introduced at the excluded-volume level. As a consequence of the restrictions deriving from chain geometry and local constraints, a limited number of allowed conformers has been identified that undergo torsional oscillations and conformational jumps. Torsional fluctuations are described as damped oscillations, while transition rates between conformers are calculated according to the Langer multidimensional extension of the Kramers theory. The time scale and amplitude of the different motions are compared; the major role played by rotations of the outermost bonds of the side chain emerges, along with the effects of substituents in the pyrroline ring on the conformer distribution and dynamics. The extent and symmetry of magnetic tensor averaging produced by the side chain motions are estimated, the implications for the ESR spectra of spin-labeled proteins are discussed, and suggestions for the introduction of realistic features of the spin probe dynamics into the line shape simulation are presented.     

Hydrazone- and hydrazide-containing N-substituted glycines as peptoid surrogates for expedited library synthesis: application to the preparation of Tsg101-directed HIV-1 budding antagonists

Replacing the Pro6 in the p6(Gag)-derived 9-mer "P-E-P-T-A-P-P-E-E" with N-substituted glycine (NSG) residues is problematic. However, incorporation of hydrazone amides ("peptoid hydrazones") can be readily achieved in library fashion. Furthermore, reduction of these hydrazones to N-substituted "peptoid hydrazides" affords a facile route to library diversification. This approach is demonstrated by application to Tsg101-binding compounds designed as potential HIV budding antagonists. [reaction: see text]     

Modeling the effects of structure and dynamics of the nitroxide side chain on the ESR spectra of spin-labeled proteins

In the companion paper (J. Phys. Chem. B 2006, 110, jp0629487), a study of the conformational dynamics of methanethiosulfonate spin probes linked at a surface-exposed alpha-helix has been presented. Here, on the basis of this analysis, X-band ESR spectra of these spin labels are simulated within the framework of the Stochastic Liouville equation (SLE) methodology. Slow reorientations of the whole protein are superimposed on fast chain motions, which have been identified with conformational jumps and fluctuations in the minima of the chain torsional potential. Fast chain motions are introduced in the SLE for the protein reorientations through partially averaged magnetic tensors and relaxation times calculated according to the motional narrowing theory. The 72R1 and 72R2 mutants of T4 lysozyme, which bear the spin label at a solvent-exposed helix site, have been taken as test systems. For the side chain of the R2 spin label, only a few noninterconverting conformers are possible, whose mobility is limited to torsional fluctuations, yielding almost identical spectra, typical of slightly mobile nitroxides. In the case of R1, more complex spectra result from the simultaneous presence of constrained and mobile chain conformers, with relative weights that can depend on the local environment. The model provides an explanation for the experimentally observed dependence of the spectral line shapes on temperature, solvent, and pattern of substituents in the pyrroline ring. The relatively simple methodology presented here allows the introduction of realistic features of the spin probe dynamics into the simulation of ESR spectra of spin-labeled proteins; moreover, it provides suggestions for a proper account of such dynamics in more sophisticated approaches.     

THE SIMULATION AND OPTIMIZATION OF GRADIENT ELUTION HPLC

The movement of a particular component along an HPLC column is studied on the ba-sis of equilibrium equations. Numerical simulation of multi--step gradient elution HPLC isperformed by means o? a personal computer program. The location x, as a fraction of thecolumn length, for a given time t o? each compound is calculated, the velocity and corre-sponding acceleration are given as well. Diagrams for x,dx/dt and d~2x/dt~2 versus t display themovement process of the different components along the HPLC column during gradient elu-tion. The prediction of the retention time and peak width, and the optimization for the multi-step gradient elution HPLC are all based on such simulation and the molecular structure ofthe. components is separated as well.     

Response function theory of electron correlation

The full perturbation expansion for the response (or density—density correlation) function is examined in order to provide a useful general theory of excitation energies, oscillator strengths, dynamic polarizabilities, etc., that is more accurate than the random phase approximation. It is first shown how the formal partition of the diagrammatic version of the perturbation expansion into reducible and irreducible diagrams is generally useless as the latter category contains all the difficult terms which have heretofore resisted analysis in all but a haphazard form. It is then shown how the diagram for the response function can be partitioned into “correlated” and “uncorrelated” subsets. Restricting attention to the particle—hole blocks of the full response function, the “uncorrelated” diagrams desecribe the propagation of a particle—hole pair in an N-electron system where the particle and hole are each interacting with the remaining electrons but they are not interacting with each other. The “correlated” diagrams are those containing the hole—particle interactions, and, by defining a new class of reducible and irreducible diagrams, these are all summed to provide a perturbation expansion of the effective two-body hole—particle interaction that appears in the inverse of the response function. The “uncorrelated” diagrams are further partitioned into two sets, one of which is summed to all orders, while the other set is inverted in an order by order fashion. The final result presents a perturbation expansion for the inverse of the response function that is analogous to the Dyson equation for one-electron Green functions. Maintaining the perturbation expansion through first order for the inverse of the response function yields the eigenvalue equation of the familiar random phase approximation, while truncation at second order provides the most advanced theories that have been generated by the equations-of-motion method.     

Stochastic model for triplet yields

A stochastic model of triplet yields is considered where the singlet S₁ is initially excited and subsequently feeds the triplet T₁. Both S₁ and T₁ have Montroll—Shuler step ladder vibrational relaxation mechanisms and radiative and non-radiative decay rates that vary linearly with increasing vibrational energy. Assuming the S₁ → T₁ rates also have this linear variation, the kinetic model is exactly solved in terms of integrals of simple functions of hyperbolic functions. The predictions of the model are illustrated by application to naphthalene. The model parameters are chosen; wherever possible, from experimental data. The predictions are in gross qualitative agreement with available experiments on triplet yields, and they indicate more detailed future experiments to separate the S₁ → T₁ and S₁ → S₀ (ground singlet) decays (and their energy dependence) in aromatic hydrocarbons.     

PHOTOREACTIVATION IN THE EXTREME HALOPHILIC ARCHAEBACTERIUM Halobacterium cutirubrum

Abstract— Photoreactivation in the extreme halophilic archaebacterium Halobacterium cutirubrum was studied both in vivo and in vitro. Cells irradiated with ultraviolet (UV)-fluences up to 350 J/m² could be completely photoreactivated, indicating very efficient repair of pyrimidine dimers in UV-irradiated DNA. Dark repair is apparently absent in Halobacterium since liquid holding under non-growth conditions did not influence the survival of UV-irradiated cells, while cells remained completely photoreactivable with no change in the kinetics of photoreactivation. Experiments with Halobacterium isolates of different carotenoid content indicated that carotenoids do not influence either UV-inactivation or photoreactivation. Small differences in the rates of UV-inactivation and photoreactivation could be assigned to the occurrence of gas vesicles. Flash experiments and the temperature dependence of photoreactivation indicated an enzymatical reaction. This was confirmed by in vitro experiments with partially purified photoreactivating enzyme. The in vivo action spectrum of photoreactivation showed a main band in the 400-470 nm region with a maximum at 440 nm. Comparison with action spectra of other microorganisms classified the Halobacterium enzyme as a 8-hydroxy-5-deazaflavin type photoreactivating enzyme.