Resonance-stabilized hydrocarbon-radical chain reactions may explain soot inception and growth.

Mystery surrounds the transition from gas-phase hydrocarbon precursors to terrestrial soot and interstellar dust, which are carbonaceous particles formed under similar conditions. Although polycyclic aromatic hydrocarbons (PAHs) are known precursors to high-temperature carbonaceous-particle formation, the molecular pathways that initiate particle formation are unknown. We present experimental and theoretical evidence for rapid molecular clustering-reaction pathways involving radicals with extended conjugation. These radicals react with other hydrocarbon species to form covalently bound complexes that promote further growth and clustering by regenerating resonance-stabilized radicals through low-barrier hydrogen-abstraction and hydrogen-ejection reactions. Such radical-chain reaction pathways may lead to covalently bound clusters of PAHs and other hydrocarbons that would otherwise be too small to condense at high temperatures, thus providing the key mechanistic steps for rapid particle formation and surface growth by hydrocarbon chemisorption.

Steric modulations in the reversible dimerizations of phenalenyl radicals via unusually weak carbon-centered pi- and sigma-bonds.

[reaction: see text] Spontaneous self-associations of various tricyclic phenalenyl radicals lead reversibly to either pi- or sigma-dimers, depending on alkyl-substitution patterns at the alpha- and beta-positions. Thus, the sterically encumbered all-beta-substituted tri-tert-butylphenalenyl radical (2*) affords only the long-bonded pi-dimer in dichloromethane solutions, under conditions in which the parent phenalenyl radical (1*) leads to only the sigma-dimer. Further encumbrances of 1* with a pair of alpha, beta- or beta, beta- tert-butyl substituents and additional methyl and ethyl groups (as in sterically hindered phenalenyl radicals 3* - 6*) do not inhibit sigma-dimerization. ESR spectroscopy is successfully employed to monitor the formation of both diamagnetic (2-electron) dimers; and UV-vis spectroscopy specifically identifies the pi-dimer by its intense near-IR band. The different temperature-dependent spectral (ESR and UV-vis) behaviors of these phenalenyl radicals allow the quantitative evaluation of the bond enthalpy of 12 +/- 2 kcal mol(-1) for sigma-dimers, in which the unusually low value has been theoretically accounted for by the large loss of phenalenyl (aromatic) pi-resonance energy attendant upon such bond formation.

Decay behavior of least-squares coefficients in auxiliary basis expansions.

Many quantum chemical methods, both wave function and density based, rely on an expansion of elements of the electron density in an auxiliary basis. However, little is known about the analytical behavior of the expansion coefficients and, in particular, about their rate of decay with distance. We discuss an exactly solvable model system and characterize the expansion coefficients for various fitting metrics and various dimensionalities of the auxiliary basis. In the case of Coulomb fitting, we find that the decay rate depends critically on the effective dimensionality D of the auxiliary basis, varying from O(r(-1)) to O(r(-3)) to O(e(-zetar)) for D = 1, 2, or 3.

Role of electron-transfer quenching of chlorophyll fluorescence by carotenoids in non-photochemical quenching of green plants.

NPQ (non-photochemical quenching) is a fundamental photosynthetic mechanism by which plants protect themselves against excess excitation energy and the resulting photodamage. A discussed molecular mechanism of the so-called feedback de-excitation component (qE) of NPQ involves the formation of a quenching complex. Recently, we have studied the influence of formation of a zeaxanthin-chlorophyll complex on the excited states of the pigments using high-level quantum chemical methodology. In the case of complex formation, electron-transfer quenching of chlorophyll-excited states by carotenoids is a relevant quenching mechanism. Furthermore, additionally occurring charge-transfer excited states can be exploited experimentally to prove the existence of the quenching complex during NPQ.

Origin of substituent effects in the absorption spectra of peroxy radicals: time dependent density functional theory calculations.

We investigate the assignment of electronic transitions in alkyl peroxy radicals. Past experimental work has shown that the phenyl peroxy radical exhibits a transition in the visible region; however, previous high level calculations have not reproduced this observed absorption. We use time dependent density functional theory (TDDFT) to characterize the electronic excitations of the phenyl peroxy radical as well as other hydrocarbon substituted peroxy radicals. TDDFT calculations of the phenyl peroxy radical support an excitation in the visible spectrum. Further, we investigate the nature of this visible absorption using electron attachment/detachment density diagrams of the peroxy radicals and present a qualitative picture of the origin of the visible absorption based on molecular orbital perturbations. The peroxy radical substituent is also compared against isoelectronic radical groups. The visible absorption is determined to be dependent on mixing of the alkyl and radical substituent orbitals.

Electronic spectra and ionization potentials of a stable class of closed shell polycyclic aromatic hydrocarbon cations.

Due to their stability, closed shell polycyclic aromatic hydrocarbon (PAH) cations are possible candidates as carriers for some of the diffuse interstellar bands (DIBs). The electronic absorption spectra and ionization potentials of several closed shell PAH cations are determined in this study. We use density functional theory (DFT) at the BLYP/6-31G* level to determine the ionization potentials and thus confirm the stability of the PAH cations of interest. We use time-dependent density functional theory (TDDFT), again at the BLYP/6-31G* level, to calculate the vertical excitation energies and oscillator strengths of the PAH cations. We observe dominant single absorptions within the DIB spectral region of interest in all of the PAH cation spectra except for the smallest member of the series.

Absolute and relative energies from polarized atomic orbital self-consistent field calculations and a second order correction. Convergence with size and composition of the secondary basis

Polarized atomic orbitals (PAO's) are molecule-adapted minimal basis functions that are variationally obtained as an atom-blocked transformation from a conventional extended basis set, as a Hartree-Fock calculation is performed in the PAO basis. This approximation yields a higher energy than a HF calculation performed in the extended basis, although the two results converge to the same limit as the extended basis approaches completeness on each atom. To test the rate of convergence, PAO-HF calculations were performed using cc-pVXZ and aug-cc-pVXZ basis sets for the water monomer and dimer, and six substituted ethylenes. The results show that the quality of PAO calculations converges smoothly with X. The use of augmented functions is recommended. To correct a PAO-HF calculation for residual deficiencies, a noniterative second order correction is introduced. This correction corresponds to an energy-weighted steepest descent step, and substantially improves the quality of PAO energies.

The formation of HCS and HCSH molecules and their role in the collision of comet Shoemaker-Levy 9 with Jupiter.

The reaction of hydrogen sulfide with ground-state atomic carbon was examined with crossed molecular beams experiments and ab initio calculations. The thiohydroxycarbene molecule, HCSH, was the reactive intermediate, which fragmented into atomic hydrogen and the thioformyl radical HCS. This finding may account for the unassigned HCS source and an unidentified HCSH radical needed to match observed CS abundances from the collision of comet Shoemaker-Levy 9 into Jupiter. In the shocked jovian atmosphere, HCS could further decompose to H and CS, and CS could react with SH and OH to yield the observed CS2 and COS.

A combined experimental and theoretical study on the formation of interstellar C3H isomers.

The reaction of ground-state carbon atoms with acetylene was studied under single-collision conditions in crossed beam experiments to investigate the chemical dynamics of forming cyclic and linear C3H isomers (c-C3H and l-C3H, respectively) in interstellar environments via an atom-neutral reaction. Combined state-of-the-art ab initio calculations and experimental identification of the carbon-hydrogen exchange channel to both isomers classify this reaction as an important alternative to ion-molecule encounters to synthesize C3H radicals in the interstellar medium. These findings strongly correlate with astronomical observations and explain a higher [c-C3H]/[l-C3H] ratio in the dark cloud TMC-1 than in the carbon star IRC+10216.

The first solvation shell of magnesium ion in a model protein environment with formate, water, and X-NH3, H2S, imidazole, formaldehyde, and chloride as ligands: an Ab initio study.

The first coordination shell of an Mg(II) ion in a model protein environment is studied. Complexes containing a model carboxylate, an Mg(II) ion, various ligands (NH3, H2S, imidazole, and formaldehyde) and water of hydration about the divalent metal ion were geometry optimized. We find that for complexes with the same coordination number, the unidentate carboxylate-Mg(II) ion is greater than 10 kcal mol-1 more stable than the bidentate orientation. Imidazole was found to be the most stable ligand, followed in order by NH3, formaldehyde, H2O, and H2S.