John J. Nash

A reinvestigation of singlet benzyne thermochemistry predicted by CASPT2, coupled-cluster and density functional calculations

Abstract Recent CASPT2 calculations of the heats of formation of the isomeric benzynes by R. Lindh and M. Schutz[Chem. Phys. Lett. 258 (1996) 409] are re-examined. The unrealistically low value reported for p -benzene (132.7 kcal/mol) is shown to be an artifact of the use of incorrect CASSCF and CASPT2 energies for p -benzene, as well as a flawed isodesmic reaction analysis. Use of correct energies and an appropriate isodesmic reaction leads to excellent agreement between the calculated and measured heats of formation for p -benzene. The performance of coupled-cluster methods and density functional theory in predicting benzyne thermochemistry and singlet-triplet splittings is also evaluated.

Mode‐selective photoisomerization in 5‐hydroxytropolone. II. Theory

Ab initio calculations are used to explore the ground‐state potential energy surface for the syn–anti photoisomerization reaction of 5‐hydroxytropolone (5‐HOTrOH). Two reaction coordinates are identified, involving 2‐OH tunneling and 5‐OH torsion. Hartree–Fock (HF) and perturbation theory (at the MP2 level) have been used to calculate the stationary points on the two‐dimensional surface associated with these coordinates. Similar calculations on the parent molecule tropolone are carried out for comparison. As observed in previous studies, the 2‐OH tunneling barrier drops dramatically at the MP2 level which includes electron correlation. Vibrational frequency calculations are carried out for both tropolone and 5‐HOTrOH at the HF/6‐31G** and MP2/6‐31G** levels in order to correlate the modes with those observed experimentally. A method is introduced for evaluating which normal coordinates should be most strongly coupled to a given reaction coordinate. Normalized, mass‐weighted intrinsic and direct reaction c...

Gas-phase reactivity of protonated 2-, 3-, and 4-dehydropyridine radicals toward organic reagents.

To explore the effects of the electronic nature of charged phenyl radicals on their reactivity, reactions of the three distonic isomers of n-dehydropyridinium cation (n = 2, 3, or 4) have been investigated in the gas phase by using Fourier-transform ion cyclotron resonance mass spectrometry. All three isomers react with cyclohexane, methanol, ethanol, and 1-pentanol exclusively via hydrogen atom abstraction and with allyl iodide mainly via iodine atom abstraction, with a reaction efficiency ordering of 2 > 3 > 4. The observed reactivity ordering correlates well with the calculated vertical electron affinities of the charged radicals (i.e., the higher the vertical electron affinity, the faster the reaction). Charged radicals 2 and 3 also react with tetrahydrofuran exclusively via hydrogen atom abstraction, but the reaction of 4 with tetrahydrofuran yields products arising from nonradical reactivity. The unusual reactivity of 4 is likely to result from the contribution of an ionized carbene-type resonance structure that facilitates nucleophilic addition to the most electrophilic carbon atom (C-4) in this charged radical. The influence of such a resonance structure on the reactivity of 2 is not obvious, and this may be due to stabilizing hydrogen-bonding interactions in the transition states for this molecule. Charged radicals 2 and 3 abstract a hydrogen atom from the substituent in both phenol and toluene, but 4 abstracts a hydrogen atom from the phenyl ring, a reaction that is unprecedented for phenyl radicals. Charged radical 4 reacts with tert-butyl isocyanide mainly by hydrogen cyanide (HCN) abstraction, whereas CN abstraction is the principal reaction for 2 and 3. The different reactivity observed for 4 (as compared to 2 and 3) is likely to result from different charge and spin distributions of the reaction intermediates for these charged radicals.

Phenyl radical-induced damage to dipeptides.

Laser-induced acoustic desorption (LIAD) incorporated with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR) has been utilized to investigate phenyl radical-induced damage to dipeptides in the gas phase. On the basis of the product branching ratios measured for the reactions of two different positively charged phenyl radicals with 17 different dipeptides, the overall order of susceptibility to attack of the different sites in the dipeptides was determined to be heteroaromatic side chain approximately = S atom in SCH(3) group > H atom in SH group > H atom in CH group > aromatic side chain > S atom in SH group > NH(2) in side chain > N-terminal NH(2) > COOH in side chain approximately = C-terminal COOH. The amino acid sequence also influences the selectivity of these reactions. As expected, the ability of a phenyl radical to damage dipeptides increases as the electrophilicity of the phenyl radical increases.

Reactions of An Aromatic σ,σ-Biradical with Amino Acids and Dipeptides in the Gas Phase

Gas-phase reactivity of a positively charged aromatic σ,σ-biradical (N-methyl-6,8-didehydroquinolinium) was examined toward six aliphatic amino acids and 15 dipeptides by using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR) and laser-induced acoustic desorption (LIAD). While previous studies have revealed that H-atom and NH2 abstractions dominate the reactions of related monoradicals with aliphatic amino acids and small peptides, several additional, unprecedented reaction pathways were observed for the reactions of the biradical. For amino acids, these are 2H-atom abstraction, H2O abstraction, addition — CO2, addition — HCOOH, and formation of a stable adduct. The biradical reacts with aliphatic dipeptides similarly as with aliphatic amino acids, but undergoes also one additional reaction pathway, addition/C-terminal amino acid elimination (addition — CO — NHCHRC). These reactions are initiated by H-atom abstraction by the biradical from the amino acid or peptide, or nucleophilic addition of an NH2 or a HO group of the amino acid or peptide at the radical site at C-6 in the biradical. Reactions of the unquenched C-8 radical site then yield the products not observed for related monoradicals. The biradical reacts with aromatic dipeptides with an aromatic ring in N-terminus (i.e., Tyr-Leu, Phe-Val, and Phe-Pro) similarly as with aliphatic dipeptides. However, for those aromatic dipeptides that contain an aromatic ring in the C-terminus (i.e., Leu-Tyr and Ala-Phe), one additional pathway, addition/N-terminal amino acid elimination (addition — CO — NHCHRN), was observed. This reaction is likely initiated by radical addition of the biradical at the aromatic ring in the C-terminus. Related monoradicals add to aromatic amino acids and small peptides, which is followed by Cα-Cβ bond cleavage, resulting in side-chain abstraction by the radical. For biradicals, with one unquenched radical site after the initial addition, the reaction ultimately results in the loss of the N-terminal amino acid. Similar to monoradicals, the C-S bond in amino acids and dipeptides was found to be especially susceptible to biradical attack.

Fast pyrolysis of 13C-labeled cellobioses: gaining insights into the mechanisms of fast pyrolysis of carbohydrates.

A fast-pyrolysis probe/tandem mass spectrometer combination was utilized to determine the initial fast-pyrolysis products for four different selectively (13)C-labeled cellobiose molecules. Several products are shown to result entirely from fragmentation of the reducing end of cellobiose, leaving the nonreducing end intact in these products. These findings are in disagreement with mechanisms proposed previously. Quantum chemical calculations were used to identify feasible low-energy pathways for several products. These results provide insights into the mechanisms of fast pyrolysis of cellulose.

Reactivity and selectivity of charged phenyl radicals toward amino acids in a Fourier transform ion cyclotron resonance mass spectrometer.

The reactivity of 10 charged phenyl radicals toward several amino acids was examined in the gas phase in a dual-cell Fourier transform ion cyclotron resonance mass spectrometer. All radicals abstract a hydrogen atom from the amino acids, as expected. The most electrophilic radicals (with the greatest calculated vertical electron affinities (EA) at the radical site) also react with these amino acids via NH(2) abstraction (a nonradical nucleophilic addition-elimination reaction). Both the radical (hydrogen atom abstraction) and nonradical (NH(2) abstraction) reaction efficiencies were found to increase with the electrophilicity (EA) of the radical. However, NH(2) abstraction is more strongly influenced by EA. In contrast to an earlier report, the ionization energies of the amino acids do not appear to play a general reactivity-controlling role. Studies using several partially deuterium-labeled amino acids revealed that abstraction of a hydrogen atom from the α-carbon is only preferred for glycine; for the other amino acids, a hydrogen atom is preferentially abstracted from the side chain. The electrophilicity of the radicals does not appear to have a major influence on the site from which the hydrogen atom is abstracted. Hence, the regioselectivity of hydrogen atom abstraction appears to be independent of the structure of the radical but dependent on the structure of the amino acid. Surprisingly, abstraction of two hydrogen atoms was observed for the N-(3-nitro-5-dehydrophenyl)pyridinium radical, indicating that substituents on the radical not only influence the EA of the radical but also can be involved in the reaction. In disagreement with an earlier report, proline was found to display several unprecedented reaction pathways that likely do not proceed via a radical mechanism but rather by a nucleophilic addition-elimination mechanism. Both NH(2) and (15)NH(2) groups were abstracted from lysine labeled with (15)N on the side chain, indicating that NH(2) abstraction occurs both from the amino terminus and from the side chain. Quantum chemical calculations were employed to obtain insights into some of the reaction mechanisms.

The spectroscopic and photophysical effects of the position of methyl substitution. I. 4‐ and 5‐methylpyrimidine

Laser-induced fluorescence excitation and dispersed fluorescence spectra of the first n-?r* transition of jet-cooled 2-methylpyrimidine have been recorded and analyzed. This work extends our earlier study of the spectroscopic and photophysical effects of methyl substitution in 4and 5methylpyrimidine. An unusual Fermi resonance involving the 6~2: progression forms the focus of the present study. The 6~2: vibronic transition is observed to be split into a triad of transitions. Dispersed fluorescence spectra are used to identify the dark background state responsible for the Fermi resonance coupling as the 166 ’ (3~;‘) vibration/internal rotation combination level. This level is selectively coupled by symmetry constraints to 6a’ (0~; ), leaving the 6~2’ ( le” ) level unperturbed. The positions and intensities of the triad of peaks in the excitation spectrum allow a quantitative determination of the 6a’ (0~; )++16b ’ (3a;‘) coupling matrix element of V = 4.1 cm ‘. This vibration/internal rotation Fermi resonance is thus typical of the new types of routes to vibrational state mixing which are opened by methyl substitution. Higher members of the 6~2: progression are also involved in Fermi resonance mixing. However, in addition, these levels experience weaker, less state-specific coupling to a bath of same-symmetry states at that energy. The excitation spectrum provides an estimate of the average coupling matrix element of this second tier coupling of 1 cm ‘.

Direct comparison of solution and gas-phase reactions of the three distonic isomers of the pyridine radical cation with methanol.

To directly compare the reactivity of positively charged carbon-centered aromatic σ-radicals toward methanol in solution and in the gas phase, the 2-, 3-, and 4-dehydropyridinium cations (distonic isomers of the pyridine radical cation) were generated by ultraviolet photolysis of the corresponding iodo precursors in a mixture of water and methanol at varying pH. The reaction mixtures were analyzed by using liquid chromatography/mass spectrometry. Hydrogen atom abstraction was the only reaction observed for the 3- and 4-dehydropyridinium cations (and pyridines) in solution. This also was the major reaction observed earlier in the gas phase. Depending on the pH, the hydrogen atom can be abstracted from different molecules (i.e., methanol or water) and from different sites (in methanol) by the 3- and 4-dehydropyridinium cations/pyridines in solution. In the pH range 1-4, the methyl group of methanol is the main hydrogen atom donor site for both 3- and 4-dehydropyridinium cations (just like in the gas phase). At higher pH, the hydroxyl groups of water and methanol also act as hydrogen atom donors. This finding is rationalized by a greater abundance of the unprotonated radicals that preferentially abstract hydrogen atoms from the polar hydroxyl groups. The percentage yield of hydrogen atom abstraction by these radicals was found to increase with lowering the pH in the pH range 1.0-3.2. This pH effect is rationalized by polar effects: the lower the pH, the greater the fraction of protonated (more polar) radicals in the solution. This finding is consistent with previous results obtained in the gas phase and suggests that gas-phase studies can be used to predict solution reactivity, but only as long as the same reactive species is studied in both experiments. This was found not to be the case for the 2-iodopyridinium cation. Photolysis of this precursor in solution resulted in the formation of two major addition products, 2-hydroxy- and 2-methoxypyridinium cations, in addition to the hydrogen atom abstraction product. These addition products were not observed in the earlier gas-phase studies on 2-dehydropyridinium cation. Their observation in solution is explained by the formation of another reactive intermediate, the 2-pyridylcation, upon photolysis of 2-iodopyridinium cation (and 2-iodopyridine). The same intermediate was observed in the gas phase but it was removed before examining the reactions of the desired radical, 2-dehydropyridinium cation (which cannot be done in solution).

Gas-phase reactivity of aromatic sigma,sigma-biradicals toward dinucleoside phosphates.

In order to improve the understanding of the interactions of aromatic sigma,sigma-biradicals with DNA, the reactivity of three isomeric sigma,sigma-biradicals toward four dinucleoside phosphates was studied in a mass spectrometer. The dinucleoside phosphates were evaporated into the mass spectrometer by using laser-induced acoustic desorption (LIAD). The results demonstrate that the structure of the sigma,sigma-biradical and the base sequence of the dinucleoside phosphate can have a major influence on these reactions.