Jill K. Wolken

Proton affinity of uracil. A computational study of protonation sites.

Relative stabilities of uracil tautomers and cations formed by gas-phase protonation were studied computationally with the B3LYP, MP2, QCISD, and QCISD(T) methods and with basis sets expanding from 6–31G(d,p) to 6–311+G(3df,2p). In accordance with a previous density functional theory study, the dioxo tautomer 1a was the most stable uracil isomer in the gas phase. Gibbs free energy calculations using effective QCISD(T)/6-311+G(3df,2p) energies suggested >99.9% of 1a at equilibrium at 523 K. The most stable ion isomer corresponded to N-1 protonated 2,4-dihydroxypyrimidine, which however is not formed by direct protonation of 1a. The topical proton affinities in 1a followed the order O-8 > O-7 > C-5 > N-3 > N-1. The thermodynamic proton affinity of 1a was calculated as 858 kJ mol−1 at 298 K. A revision is suggested for the current estimate included in the ion thermochemistry database.

Distinction of isomeric pyridyl cations and radicals by neutralization-reionization mass spectrometry, ab initio and density functional theory calculations

Isomeric pyridyl radicals, 2-pyridyl (2), 3-pyridyl (3) and 4-pyridyl (4) were studied by neutralization-reionization mass spectrometry (NRMS) and a combination of ab initio PMP2/6-311G(2d,p) and density functional theory B3LYP/6-311G(2d,p) calculations. The experiment and theory agreed on the radicals being stable species in the gas phase. The order of 0 K relative enthalpies was established as 2 (most stable) < 4 (+17 kJ mol−1) < 3 (+22 kJ mol−1). This differed from the order of cation enthalpies which was 2+ (most stable) < 3+ (+90 kJ mol−1) < 4+ (+105 kJ mol−1). Metastable-ion spectra of 2+, 3+ and 4+ showed losses of hydrogen cyanide as the dominating dissociations, which were 273, 184 and 168 kJ mol−1 endothermic, respectively. Radical 2 underwent competitive dissociations by losses of acetylene and hydrogen cyanide for which comparable threshold energies, 292 and 290 kJ mol−1, respectively, were obtained computationally. Radicals 3 and 4 cannot eliminate acetylene via low-energy paths or intermediates as investigated by computations. The lowest-energy dissociation in 3 was cleavage of the N–C-2 bond and elimination of hydrogen cyanide to form the 3-buten-1-yn-3-yl radical (6), which required 272 kJ mol−1 at the thermochemical threshold at 0 K. The lowest-energy dissociation in 4 proceeded by cleavage of the C-2-C-3 bond and elimination of hydrogen cyanide to form 6, which required 273 kJ mol−1 at 0 K. The dissociations of pyridyl radicals observed upon collisional neutralization were, in general, consistent with the mechanisms of pyridine pyrolysis proposed earlier by Kiefer, Kern and coworkers and by Hore and Russell. The different energetics and dissociation mechanisms accounted for the difference in the NRMS spectra of 2+–4+ which allowed partial isomer differentiation.

Neutralization-Reionization of alkenylammonium cations: An experimental and ab initio study of intramolecular N-H … C=C interactions in cations and hypervalent ammonium radicals

A series of isomeric hexenylammonium and hexenyldimethylammonium cations were neutralized by collisional electron transfer in the gas phase in an attempt to generate hypervalent ammonium radicals. The radicals dissociated completely on the 4.8–5.4 µs time scale. Radicals in which the hexene double bond was in the 3-, 4-, and 5-positions dissociated by competitive N-H and N=C bond cleavages. Allylic 2-hexen-1-ylammonium and 2-hexen-1-yldimethylammonium radicals underwent predominant cleavages of allylic N-C bonds. Deuterium labeling experiments revealed no intramolecular hydrogen transfer from the hypervalent ammonium group to the hexene double bond. Ab initio and density functional theory calculations showed that alkenylammonium and alkenylmethyloxonium ions preferred hydrogen bonded structures in the gas phase. The stabilization through intramolecular H bonding in 3-buten-1-ylammonium and 3-buten-1-yl methyloxonium ions was calculated by B3LYP/6-311G(2d,p) at 26 and 18 kJ mol−1, respectively. No intramolecular hydrogen bonding was found for the allylammonium ion. The hypervalent 3-buten-1-yl-methyloxonium radical was calculated to be unbound and predicted to dissociate exothermically by O-H bond cleavage. This dissociation may provide kinetic energy for the hydrogen atom to overcome a small energy barrier for exothermic addition to the double bond. The 3-butten-1-ylammonium and allylammonium radicals were found to be bound and preferred gauche conformations without intramolecular hydrogen bonding. Vertical neutralization of alkenylammonium ions was accompanied by small Franck-Condon effects. The failure to detect stable or metastable hypervalent alkenylammonium radicals was ascribed to the low activation barriers to exothermic dissociations by N-H and N-C bond cleavages.

Bond dissociations in hypervalent ammonium radicals prepared by collisional neutralization of protonated six‐membered nitrogen heterocycles

Hypervalent organic ammonium radicals were generated by collisional neutralization with dimethyl disulfide of protonated 1,4-diazabicyclo[2.2.2]octane (1H+), N,N′-dimethylpiperazine (2H+) and N-methylpiperazine (3H+). The radicals dissociated completely on the 5.1 μs time-scale. Radical 1H• underwent competitive N−H and N−C bond dissociations producing 1,4-diazabicyclo[2.2.2]octane and small ring fragments. Dissociations of radical 2H• proceeded by N−H bond dissociation and ring cleavage, whereas N−CH3 bond cleavage was less frequent. Radical 3H• underwent N−H, N−CH3 and N−Cring bond cleavages followed by post-reionization dissociations of the formed cations. The pattern of bond dissociations in the hypervalent ammonium radicals derived from six-membered nitrogen heterocycles is similar to those of aliphatic ammonium radicals.