Biomedical subjects

Mark S Gordon

Publications and source records attributed to Mark S Gordon.

40 records · Page 3Linked to original sources

PubMed2003

Alpha,2-, alpha,3-, and alpha,4-dehydrophenol radical anions: formation, reactivity, and energetics leading to the heats of formation of alpha,2-, alpha,3-, and alpha,4-oxocyclohexadienylidene.

We have regiospecifically generated the alpha,2-, alpha,3-, and alpha,4-dehydrophenoxide anions by collisional activation of o-, m-, and p-nitrobenzoate. The alpha,2 and alpha,4 isomers also were synthesized by reacting o-benzyne radical anion with carbon dioxide and electron ionization of p-diazophenol. All three dehydrophenol radical anions were differentiated from each other and identified by probing their chemical reactivity with several reagents. Each isomer was converted to phenoxide and its corresponding quinone as well. Thermochemical measurements were carried out on all three radical anions and their hydrogen-atom affinities, proton affinities, and electron binding energies are reported. These measured quantities are combined in thermodynamic cycles to derive the heats of formation of each of the radical anions and their corresponding carbenes (i.e., alpha,2-, alpha,3-, and alpha,4-dehydrophenol). These results are compared to MCQDPT2, G3, G2+(MP2), and B3LYP calculations and experimental data for appropriate reference compounds.

Journal Article↗

PubMed2002

Passive and active oxidation of Si(100) by atomic oxygen: a theoretical study of possible reaction mechanisms.

Reaction mechanisms for oxidation of the Si(100) surface by atomic oxygen were studied with high-level quantum mechanical methods in combination with a hybrid QM/MM (Quantum mechanics/Molecular Mechanics) method. Consistent with previous experimental and theoretical results, three structures, "back-bond", "on-dimer", and "dimer-bridge", are found to be the most stable initial surface products for O adsorption (and in the formation of SiO(2) films, i.e., passive oxidation). All of these structures have significant diradical character. In particular, the "dimer-bridge" is a singlet diradical. Although the ground state of the separated reactants, O+Si(100), is a triplet, once the O atom makes a chemical bond with the surface, the singlet potential energy surface is the ground state. With mild activation energy, these three surface products can be interconverted, illustrating the possibility of the thermal redistribution among the initial surface products. Two channels for SiO desorption (leading to etching, i.e., active oxidation) have been found, both of which start from the back-bond structure. These are referred to as the silicon-first (SF) and oxygen-first (OF) mechanisms. Both mechanisms require an 89.8 kcal/mol desorption barrier, in good agreement with the experimental estimates of 80-90 kcal/mol. "Secondary etching" channels occurring after initial etching may account for other lower experimental desorption barriers. The calculated 52.2 kcal/mol desorption barrier for one such secondary etching channel suggests that the great variation in reported experimental barriers for active oxidation may be due to these different active oxidation channels.

Journal Article↗

PubMed2002

Structure and thermodynamics of carbon and carbon/silicon precursors to nanostructures.

The structures at the Hartree-Fock level, as well as the energetics, are reported for the unsaturated system C(36)H(16), its Si-doped analogue C(32)Si(4)H(16), and several smaller, unsaturated fragments. Structural effects on the electronic distribution are discussed in terms of a localized orbital energy decomposition. The standard heats of formation are calculated based on homodesmic and isodesmic reactions and the G2(MP2,SVP) method with a valence double-zeta plus polarization basis. The origin of the observed explosion of the all-carbon system (C(36)H(16)) to form carbon nanotubes was investigated by exploring a possible initial reactive channel (dimerization), which could lead to the formation of the observed onion-type nanostructures.

Journal Article↗

PubMed2002

Cycloaddition reactions of acrylonitrile on the Si(100)-2 x 1 surface.

Multi-reference as well as single-reference quantum mechanical methods were adopted to study the potential energy surface along three possible surface reaction mechanisms of acrylonitrile on the Si(100)-2 x 1 surface. All three reactions occur via stepwise radical mechanisms. According to the computed potential energy surfaces, both [4+2] and [2+2](CN) cycloaddition products resulting from the reactions of surface dimers with the C[triple bond]N of acrylonitrile are expected, due to the negligible activation barriers at the surface. Another possible surface product, [2+2](CC), requires a 16.7 kcal/mol activation energy barrier. The large barrier makes this route much less favorable kinetically, even though this route produces the thermodynamically most stable products. Isomerization reactions among the surface products are very unlikely due to the predicted large activation barriers preventing thermal redistributions of the surface products. As a result, the distribution of the final surface products is kinetically controlled leading to a reinterpretation of recent experiments. An intermediate Lewis acid-base type complex appears in both the [4+2] and [2+2](CN) cycloadditions entrance channels, indicating that the surface may act as an electrophile/Lewis acid toward a strong Lewis base substrate.

Acrylonitrile↗