Jill Wolken - Academia.edu (original) (raw)

Papers by Jill Wolken

Research paper thumbnail of A neutralization-reionization mass spectrometry and computational analysis of 3-hydroxypyridine, 2-hydroxypyridine/2-(1H)pyridone, and uracil

Research paper thumbnail of A neutralization-reionization mass spectrometry and computational analysis of 3-hydroxypyridine, 2-hydroxypyridine/2-(1H)pyridone, and uracil

Thesis (Ph. D.)--University of Washington, 2000Free radical damage to DNA has been studied since ... more Thesis (Ph. D.)--University of Washington, 2000Free radical damage to DNA has been studied since the early years of radiobiology, when it became well established that DNA, and specifically the purine and pyrimidine bases are critical cellular target for radiation-induced damage. Cytosine and uracil are of key importance since the observation that cytosine deaminates to form uracil at a finite rate in vivo. Although a detailed mechanism has not been well established, it has been observed that radical damage increases mutations such as the C to A point mutation which occurs if uracil is left in the replicating DNA strand. This dissertation focuses on both modeling studies for the pyrimidine base radicals by examining the 3-Hydroxypyridine and the 2-Hydroxypyridine/2-(1H)Pyridone system as well as the more complicated uracil system by neutralization-reionization mass spectrometry.Neutralization - reionization mass spectrometry (NRMS) is a technique that allows the characterization of r...

Research paper thumbnail of A neutralization-reionization mass spectrometry and computational analysis of 3-hydroxypyridine, 2-hydroxypyridine/2-(1H)pyridone, and uracil

Research paper thumbnail of Abstract #LB-37: Characterization of both allosteric and ATP-Competitive kinase inhibitors with TR-FRET binding assays

Cancer Research, 2009

There is a great clinical need to develop selective, high affinity kinase inhibitors. While high ... more There is a great clinical need to develop selective, high affinity kinase inhibitors. While high throughput kinase activity assays have become readily available, easy to use and cost-effective, activity-based assays have significant limitations in terms of both the extent of target coverage and the type of information they can provide about compounds. We have developed a binding assay platform based on Alexa Fluor® 647 conjugated to kinase inhibitor scaffolds that does not require substrate or an activated kinase preparation. Binding of the conjugate to a kinase is detected by addition of a europium-labeled anti-tag antibody, which binds specifically to the kinase. Binding of the tracer and antibody to a kinase results in a high degree of FRET, whereas displacement of the tracer with a kinase inhibitor results in a loss of FRET. This assay can be utilized to explore activation-state binding selectivity, such as the case of Imatinib binding preferentially to the non-activated form of...

Research paper thumbnail of Modeling Nucleobase Radicals in the Gas Phase. Experimental and Computational Study of 2-Hydroxypyridinium and 2-(1H)Pyridone Radicals

The Journal of Physical Chemistry a, Jul 19, 1999

Isomeric radicals corresponding to hydrogen atom adducts to 2-hydroxypyridine (1) and 2-(1H)pyrid... more Isomeric radicals corresponding to hydrogen atom adducts to 2-hydroxypyridine (1) and 2-(1H)pyridone (2) were investigated by neutralization-reionization mass spectrometry and combined ab initio and density functional theory calculations. Gas-phase protonation of 1 and 2 occurred preferentially at the nitrogen and oxygen atoms, respectively, to give a single 2-hydroxypyridinium ion 3 +. The calculated topical proton affinities in 1 were 922, 602, 777, 649, 786, 694, and 746 kJ mol-1 for the N-1, C-2, C-3, C-4, C-5, C-6, and OH positions, respectively. The topical proton affinities in 2 were 756, 824, 815, 692, and 930 kJ mol-1 for the N-1, C-3, C-5, C-6, and carbonyl oxygen positions, respectively. The 2-hydroxy-(1H)pyridinium radical (3 •) was generated by collisional neutralization of ion 3 + and found to be stable on a 4.67 µs time scale. Radical 3 • dissociated by losses of the hydroxyl and amine hydrogen atoms and by ring cleavages. MP2 and B3LYP calculations with the 6-311G(2d,p) basis set established the 298 K relative energies of hydrogen atom adducts derived from 1 and 2 as 3-H-2 (11 • , most stable, 0) < 6-H-2 (14 • , +20) < 3H-1 (5 • ,+37) < 4H-2 (12 • ,+59) < 5H-2 (13 • ,+60) < 5H-1 (7 • ,+62) < 3 • (+67) < 6H-1 (8 • ,+76) < 4H-1 (6 • ,+86) < 2H-1 (4 • ,+107) < 1H-2 (10 • ,+139 kJ mol-1). Hydrogen atom adducts to C-2 in 2 and to the hydroxyl group in 1 were found to be unstable and dissociated by ring opening and loss of H, respectively. RRKM calculations on the effective QCISD(T)/6-311+G(2d,p) potential energy surface showed cleavages of the O-H and N-H bonds in 3 • to be the lowest energy dissociations occurring in a 10:1 ratio. 1 was calculated to be 4.7 kJ mol-1 more stable than 2 in the gas phase at 0 K. Fitting the experimental and calculated isotope effects on dissociations of deuteriumlabeled radicals yielded a distribution function for the internal energy in the ground electronic state of 3 • formed by collisional electron transfer. The maximum of the internal energy distribution in ground-state 3 • (129 kJ mol-1) was found to be expressed accurately by a combination of the internal energy of the precursor ion and the Franck-Condon energy gained on vertical electron transfer. The three lowest excited electronic states in 3 • were found by CIS/6-311G(2d,p) calculations to be outer states resulting from excitation of the unpaired electron in 3 • or electron capture by 3 +. The energetics and radiative lifetimes of the outer excited states of 3 • allowed interpretation of the highly endothermic ring-cleavage dissociations. The unimolecular chemistry of 3 can be explained by a bimodal energy distribution due to the formation of the ground and excited electronic states upon femtosecond collisional electron transfer.

Research paper thumbnail of Bond dissociations in hypervalent ammonium radicals prepared by collisional neutralization of protonated six-membered nitrogen heterocycles

Journal of Mass Spectrometry, 1997

ABSTRACT Hypervalent organic ammonium radicals were generated by collisional neutralization with ... more ABSTRACT 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. © 1997 John Wiley &amp; Sons, Ltd.

Research paper thumbnail of Dissociation Energies and Kinetics of Aminopyrimidinium Radicals by ab Initio and Density Functional Theory

J Phys Chem a, 1999

A series of isomeric 4-aminopyrimidinium radicals were used to model hydrogen atom adducts of nuc... more A series of isomeric 4-aminopyrimidinium radicals were used to model hydrogen atom adducts of nucleobases containing the 4-aminopyrimidine structure motif. Relative stabilities and activation energies for dissociations by hydrogen atom loss have been calculated by density functional theory and ab initio methods up to effective QCISD(T)/6-311+G(2d,p) for 4-amino-N-1-H-(1), 2-H-(2), N-3-H-(3), 4-H-(4), 5-H-(5), and 6-H-(6) pyrimidinium radicals and the 4-pyrimidylammonium radical (7). All these radicals were found to be bound species existing in potential energy wells. The order of stabilities has been established as 5 (most stable) > 3 > 2 > 1 > 6 > 4. 7 (least stable). Dissociations of the N-H and C-H bonds in 1-7 required activation barriers above the dissociation thresholds. RRKM calculations of unimolecular rate constants for N-H bond dissociations in 1 and 3 predicted substantial stabilization of these radicals by kinetic shift in the gas phase. Additions of hydrogen atoms to the N-1, C-2, N-3, C-4, C-5, and C-6 ring positions in 4-aminopyrimidine were found to be exothermic by 68, 70, 76, 23, 91, and 62 kJ mol-1 at 0 K, respectively. Hydrogen atom addition to the NH 2 group was 58 kJ mol-1 endothermic. The activation barriers for the hydrogen atom additions to 4-aminopyrimidine were found to inversely correlate with the reaction enthalpies. The calculated rate constants predicted predominant (95%) hydrogen atom addition to C-5. The other positions were substantially less reactive, e.g., N-3 (2%), C-2 (1%), C-6 (0.8%), and N-1 (0.4%).

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

Eur Mass Spectrom, 1998

Isomeric pyridyl radicals, 2-pyridyl (2), 3-pyridyl (3) and 4-pyridyl (4) were studied by neutral... more 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 3buten-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.

Research paper thumbnail of Neutralization-Reionization of Alkenylammonium Cations: An Experimental and Ab Initio Study of Intramolecular N-H... Interactions in Cations and Hypervalent Ammonium Radicals

J Amer Soc Mass Spectrom, 1997

A series of isomeric hexenylammonium and hexenyldimethylammonium cations were neutralized by coll... more 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/~s 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-l-ylammonium and 2-hexen-l-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-1ylammonium and 3-buten-l-yl methyloxonium ions was calculated by B3LYP/6-311G(2d,p) at 26 and 18 kJ tool-1, respectively. No intramolecular hydrogen bonding was found for the allylammonium ion. The hypervalent 3-buten-l-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-buten-l-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 FranckM2ondon 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.

Research paper thumbnail of Fluorescence-Based Biochemical Assays for the Study of Pregnane X Receptor and Constitutive Androstane Receptor

Research paper thumbnail of Direct Observation of a Hydrogen Atom Adduct to O-4 in Uracil. Energetics and Kinetics of Uracil Radicals

The Journal of Physical Chemistry A, 2001

ABSTRACT The 4-hydroxy-3,4-dihydropyrimidine-2(1H)-on-4-yl radical (1), an elusive hydrogen atom ... more ABSTRACT The 4-hydroxy-3,4-dihydropyrimidine-2(1H)-on-4-yl radical (1), an elusive hydrogen atom adduct to the O-4 position in uracil, was generated in the gas phase by femtosecond collisional electron transfer to O-4 protonated uracil and investigated by neutralization−reionization mass spectrometry (NRMS). A fraction of radicals 1 was stable on the 5.1 μs time scale. The main unimolecular dissociations of 1 were ring cleavages and a specific loss of the hydrogen atom from O-4, as determined by deuterium labeling. Ab initio calculations up to effective QCISD(T)/6-311+G(3df,2p) and combined density functional theory and perturbational calculations up to B3-MP2/6-311+G(3df,2p) were used to obtain bond dissociation and transition state energies for several radical and ion dissociations. The energies were used for calculations of rate constants by RRKM and transition state theory. The dissociations observed by NRMS could not be explained by competitive reactions occurring on the potential energy surface of the ground doublet state of 1 and must to a large part originate from excited electronic states of 1 that are formed by vertical electron capture. The adiabatic ionization energy of 1 was calculated as 5.55 eV. Activation energies for hydrogen atom additions to uracil were found to inversely correlate with the addition exothermicities. The most reactive position in uracil was C-5 which was calculated to account for &gt;95% hydrogen atom additions, followed by C-6 (&lt;5% additions), while additions to O-2 and O-4 were kinetically negligible.

Research paper thumbnail of Hydroxyl Radical Adducts to Pyridine. The Generation and Properties of the Elusive N -Hydroxypyridyl Radical

The Journal of Physical Chemistry A, 2001

The elusive N-hydroxypyridyl radical 1 has been generated transiently in the gas phase by collisi... more The elusive N-hydroxypyridyl radical 1 has been generated transiently in the gas phase by collisional neutralization of the stable cation 1 +. The radical underwent extensive dissociation by specific losses of H, OH, and ring-cleavage reactions, as elucidated by neutralization-reionization mass spectrometry aided by deuterium labeling. Effective QCISD(T)/6-311+G(3df,2p) and combined Møller-Plesset and density functional theory calculations indicated that loss of OH from 1 was 49 kJ mol-1 exothermic and proceeded on the potential energy surface of the ground doublet electronic state of the radical. The loss of H and ring-cleavage dissociations were initiated by the formation of excited electronic states in 1 that provided the internal energy for these endothermic reactions. OH radical addition to pyridine was predicted by transition-state theory calculations to occur mainly (82%) in the C-3 and C-5 positions. Hydrogen atom addition to pyridine-Noxide (2) was predicted to occur selectively at the oxygen atom and trigger a reaction sequence that can result in a highly exothermic catalytic isomerization of 2 to hydroxypyridines.

Research paper thumbnail of Dissociation Energies and Kinetics of Aminopyrimidinium Radicals by ab Initio and Density Functional Theory

The Journal of Physical Chemistry A, 1999

A series of isomeric 4-aminopyrimidinium radicals were used to model hydrogen atom adducts of nuc... more A series of isomeric 4-aminopyrimidinium radicals were used to model hydrogen atom adducts of nucleobases containing the 4-aminopyrimidine structure motif. Relative stabilities and activation energies for dissociations by hydrogen atom loss have been calculated by density functional theory and ab initio methods up to effective QCISD(T)/6-311+G(2d,p) for 4-amino-N-1-H-(1), 2-H-(2), N-3-H-(3), 4-H-(4), 5-H-(5), and 6-H-(6) pyrimidinium radicals and the 4-pyrimidylammonium radical (7). All these radicals were found to be bound species existing in potential energy wells. The order of stabilities has been established as 5 (most stable) > 3 > 2 > 1 > 6 > 4. 7 (least stable). Dissociations of the N-H and C-H bonds in 1-7 required activation barriers above the dissociation thresholds. RRKM calculations of unimolecular rate constants for N-H bond dissociations in 1 and 3 predicted substantial stabilization of these radicals by kinetic shift in the gas phase. Additions of hydrogen atoms to the N-1, C-2, N-3, C-4, C-5, and C-6 ring positions in 4-aminopyrimidine were found to be exothermic by 68, 70, 76, 23, 91, and 62 kJ mol-1 at 0 K, respectively. Hydrogen atom addition to the NH 2 group was 58 kJ mol-1 endothermic. The activation barriers for the hydrogen atom additions to 4-aminopyrimidine were found to inversely correlate with the reaction enthalpies. The calculated rate constants predicted predominant (95%) hydrogen atom addition to C-5. The other positions were substantially less reactive, e.g., N-3 (2%), C-2 (1%), C-6 (0.8%), and N-1 (0.4%).

Research paper thumbnail of Energetics of Uracil Cation Radical and Anion Radical Ion−Molecule Reactions in the Gas Phase

The Journal of Physical Chemistry A, 2001

The uracil cation radical was calculated to exist predominantly as the 1,3-dioxo tautomer 1 • + ,... more The uracil cation radical was calculated to exist predominantly as the 1,3-dioxo tautomer 1 • + , similar to the most stable tautomer of neutral uracil (1). The enol forms of 1 • + were found to be 10-173 kJ mol-1 less stable than 1 • + and should not be significantly populated at 298 K thermal equilibrium. Cation radical 1 • + is a moderately strong gas-phase acid of topical acidities ∆H acid) 829, 921, 916, and 879 kJ mol-1 for the H-1, H-3, H-5, and H-6 protons, respectively. Ion 1 • + is capable of exothermic protonation of adenine, guanine, and cytosine, and of the arginine, lysine, histidine, and tryptophan amino acid residues in proteins. The hydrogen atom affinities of 1 • + were-∆H rxn) 432, 371, and 360 kJ mol-1 for H-atom additions to O-4, O-2, and C-5, respectively. 1 • + was calculated to exothermically abstract the thiol hydrogen atom from CH 3 SH, the hydroxyl hydrogen from phenol, and an R-hydrogen atom from glycine N-methylamide. Uracil radicals formed by deprotonation of 1 • + were calculated to have large hydrogen atom affinities that should allow for exothermic abstraction of H-atoms from thiol groups, phenolic hydroxyls, and amino acid backbone R-methylene and methine groups. Protonation by a uracil cation radical followed by hydrogen atom abstraction can propagate radiation damage from the initial ionization site. In contrast to the highly reactive uracil cation radicals and radicals, the weakly bound uracil anion radical (1 •-) was predicted to be much less reactive in the gas phase. Ion-molecule reactions of 1 •by proton and hydrogen atom abstractions from thiols, phenol, and R-positions of amino acids were calculated to be endothermic and thus very slow in the gas phase. 1 •can selectively deprotonate carboxylic groups as calculated for the reaction with glycine.

Research paper thumbnail of Modeling Nucleobase Radicals in the Gas Phase. Experimental and Computational Study of 2-Hydroxypyridinium and 2-(1H)Pyridone Radicals

The Journal of Physical Chemistry A, 1999

Isomeric radicals corresponding to hydrogen atom adducts to 2-hydroxypyridine (1) and 2-(1H)pyrid... more Isomeric radicals corresponding to hydrogen atom adducts to 2-hydroxypyridine (1) and 2-(1H)pyridone (2) were investigated by neutralization-reionization mass spectrometry and combined ab initio and density functional theory calculations. Gas-phase protonation of 1 and 2 occurred preferentially at the nitrogen and oxygen atoms, respectively, to give a single 2-hydroxypyridinium ion 3 +. The calculated topical proton affinities in 1 were 922, 602, 777, 649, 786, 694, and 746 kJ mol-1 for the N-1, C-2, C-3, C-4, C-5, C-6, and OH positions, respectively. The topical proton affinities in 2 were 756, 824, 815, 692, and 930 kJ mol-1 for the N-1, C-3, C-5, C-6, and carbonyl oxygen positions, respectively. The 2-hydroxy-(1H)pyridinium radical (3 •) was generated by collisional neutralization of ion 3 + and found to be stable on a 4.67 µs time scale. Radical 3 • dissociated by losses of the hydroxyl and amine hydrogen atoms and by ring cleavages. MP2 and B3LYP calculations with the 6-311G(2d,p) basis set established the 298 K relative energies of hydrogen atom adducts derived from 1 and 2 as 3-H-2 (11 • , most stable, 0) < 6-H-2 (14 • , +20) < 3H-1 (5 • ,+37) < 4H-2 (12 • ,+59) < 5H-2 (13 • ,+60) < 5H-1 (7 • ,+62) < 3 • (+67) < 6H-1 (8 • ,+76) < 4H-1 (6 • ,+86) < 2H-1 (4 • ,+107) < 1H-2 (10 • ,+139 kJ mol-1). Hydrogen atom adducts to C-2 in 2 and to the hydroxyl group in 1 were found to be unstable and dissociated by ring opening and loss of H, respectively. RRKM calculations on the effective QCISD(T)/6-311+G(2d,p) potential energy surface showed cleavages of the O-H and N-H bonds in 3 • to be the lowest energy dissociations occurring in a 10:1 ratio. 1 was calculated to be 4.7 kJ mol-1 more stable than 2 in the gas phase at 0 K. Fitting the experimental and calculated isotope effects on dissociations of deuteriumlabeled radicals yielded a distribution function for the internal energy in the ground electronic state of 3 • formed by collisional electron transfer. The maximum of the internal energy distribution in ground-state 3 • (129 kJ mol-1) was found to be expressed accurately by a combination of the internal energy of the precursor ion and the Franck-Condon energy gained on vertical electron transfer. The three lowest excited electronic states in 3 • were found by CIS/6-311G(2d,p) calculations to be outer states resulting from excitation of the unpaired electron in 3 • or electron capture by 3 +. The energetics and radiative lifetimes of the outer excited states of 3 • allowed interpretation of the highly endothermic ring-cleavage dissociations. The unimolecular chemistry of 3 can be explained by a bimodal energy distribution due to the formation of the ground and excited electronic states upon femtosecond collisional electron transfer.

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

Journal of the American Society for Mass Spectrometry, 1997

A series of isomeric hexenylammonium and hexenyldimethylammonium cations were neutralized by coll... more 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/~s 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-l-ylammonium and 2-hexen-l-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-1ylammonium and 3-buten-l-yl methyloxonium ions was calculated by B3LYP/6-311G(2d,p) at 26 and 18 kJ tool-1, respectively. No intramolecular hydrogen bonding was found for the allylammonium ion. The hypervalent 3-buten-l-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-buten-l-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 FranckM2ondon 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.

Research paper thumbnail of Proton affinity of uracil. A computational study of protonation sites

Journal of the American Society for Mass Spectrometry, 2000

Relative stabilities of uracil tautomers and cations formed by gas-phase protonation were studied... more 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 6-311ϩG(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)/6-311ϩG(3df,2p) energies suggested Ͼ99.9% 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 Ͼ O-7 Ͼ C-5 Ͼ N-3 Ͼ N-1. The thermodynamic proton affinity of 1a was calculated as 858 kJ mol Ϫ1 at 298 K. A revision is suggested for the current estimate included in the ion thermochemistry database.

Research paper thumbnail of Uracil Radicals in the Gas Phase:  Specific Generation and Energetics

Journal of the American Chemical Society, 2001

... (18) Details of labeling experiments and calculations will be reported in full papers, see: W... more ... (18) Details of labeling experiments and calculations will be reported in full papers, see: Wolken, JK; Ture ek, F. J. Phys. Chem. A, submitted for publication, April 2001, and Syrstad, EA;Vivekananda, S. Ture ek, F. J. Phys. Chem. A, submitted for publication, April 2001. ...

Research paper thumbnail of Heterocyclic Radicals in the Gas Phase. An Experimental and Computational Study of 3-Hydroxypyridinium Radicals and Cations

Journal of the American Chemical Society, 1999

... the precursor ion beam. The reported spectra are averages of 30-40 consecutive scans taken at... more ... the precursor ion beam. The reported spectra are averages of 30-40 consecutive scans taken at a scan rate of 1 mass unit/s. The spectra were reproduced over the period of several weeks. Variable-time measurements were ...

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

Journal of Mass Spectrometry, 1997

ABSTRACT Hypervalent organic ammonium radicals were generated by collisional neutralization with ... more ABSTRACT 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. © 1997 John Wiley &amp; Sons, Ltd.

Research paper thumbnail of A neutralization-reionization mass spectrometry and computational analysis of 3-hydroxypyridine, 2-hydroxypyridine/2-(1H)pyridone, and uracil

Research paper thumbnail of A neutralization-reionization mass spectrometry and computational analysis of 3-hydroxypyridine, 2-hydroxypyridine/2-(1H)pyridone, and uracil

Thesis (Ph. D.)--University of Washington, 2000Free radical damage to DNA has been studied since ... more Thesis (Ph. D.)--University of Washington, 2000Free radical damage to DNA has been studied since the early years of radiobiology, when it became well established that DNA, and specifically the purine and pyrimidine bases are critical cellular target for radiation-induced damage. Cytosine and uracil are of key importance since the observation that cytosine deaminates to form uracil at a finite rate in vivo. Although a detailed mechanism has not been well established, it has been observed that radical damage increases mutations such as the C to A point mutation which occurs if uracil is left in the replicating DNA strand. This dissertation focuses on both modeling studies for the pyrimidine base radicals by examining the 3-Hydroxypyridine and the 2-Hydroxypyridine/2-(1H)Pyridone system as well as the more complicated uracil system by neutralization-reionization mass spectrometry.Neutralization - reionization mass spectrometry (NRMS) is a technique that allows the characterization of r...

Research paper thumbnail of A neutralization-reionization mass spectrometry and computational analysis of 3-hydroxypyridine, 2-hydroxypyridine/2-(1H)pyridone, and uracil

Research paper thumbnail of Abstract #LB-37: Characterization of both allosteric and ATP-Competitive kinase inhibitors with TR-FRET binding assays

Cancer Research, 2009

There is a great clinical need to develop selective, high affinity kinase inhibitors. While high ... more There is a great clinical need to develop selective, high affinity kinase inhibitors. While high throughput kinase activity assays have become readily available, easy to use and cost-effective, activity-based assays have significant limitations in terms of both the extent of target coverage and the type of information they can provide about compounds. We have developed a binding assay platform based on Alexa Fluor® 647 conjugated to kinase inhibitor scaffolds that does not require substrate or an activated kinase preparation. Binding of the conjugate to a kinase is detected by addition of a europium-labeled anti-tag antibody, which binds specifically to the kinase. Binding of the tracer and antibody to a kinase results in a high degree of FRET, whereas displacement of the tracer with a kinase inhibitor results in a loss of FRET. This assay can be utilized to explore activation-state binding selectivity, such as the case of Imatinib binding preferentially to the non-activated form of...

Research paper thumbnail of Modeling Nucleobase Radicals in the Gas Phase. Experimental and Computational Study of 2-Hydroxypyridinium and 2-(1H)Pyridone Radicals

The Journal of Physical Chemistry a, Jul 19, 1999

Isomeric radicals corresponding to hydrogen atom adducts to 2-hydroxypyridine (1) and 2-(1H)pyrid... more Isomeric radicals corresponding to hydrogen atom adducts to 2-hydroxypyridine (1) and 2-(1H)pyridone (2) were investigated by neutralization-reionization mass spectrometry and combined ab initio and density functional theory calculations. Gas-phase protonation of 1 and 2 occurred preferentially at the nitrogen and oxygen atoms, respectively, to give a single 2-hydroxypyridinium ion 3 +. The calculated topical proton affinities in 1 were 922, 602, 777, 649, 786, 694, and 746 kJ mol-1 for the N-1, C-2, C-3, C-4, C-5, C-6, and OH positions, respectively. The topical proton affinities in 2 were 756, 824, 815, 692, and 930 kJ mol-1 for the N-1, C-3, C-5, C-6, and carbonyl oxygen positions, respectively. The 2-hydroxy-(1H)pyridinium radical (3 •) was generated by collisional neutralization of ion 3 + and found to be stable on a 4.67 µs time scale. Radical 3 • dissociated by losses of the hydroxyl and amine hydrogen atoms and by ring cleavages. MP2 and B3LYP calculations with the 6-311G(2d,p) basis set established the 298 K relative energies of hydrogen atom adducts derived from 1 and 2 as 3-H-2 (11 • , most stable, 0) < 6-H-2 (14 • , +20) < 3H-1 (5 • ,+37) < 4H-2 (12 • ,+59) < 5H-2 (13 • ,+60) < 5H-1 (7 • ,+62) < 3 • (+67) < 6H-1 (8 • ,+76) < 4H-1 (6 • ,+86) < 2H-1 (4 • ,+107) < 1H-2 (10 • ,+139 kJ mol-1). Hydrogen atom adducts to C-2 in 2 and to the hydroxyl group in 1 were found to be unstable and dissociated by ring opening and loss of H, respectively. RRKM calculations on the effective QCISD(T)/6-311+G(2d,p) potential energy surface showed cleavages of the O-H and N-H bonds in 3 • to be the lowest energy dissociations occurring in a 10:1 ratio. 1 was calculated to be 4.7 kJ mol-1 more stable than 2 in the gas phase at 0 K. Fitting the experimental and calculated isotope effects on dissociations of deuteriumlabeled radicals yielded a distribution function for the internal energy in the ground electronic state of 3 • formed by collisional electron transfer. The maximum of the internal energy distribution in ground-state 3 • (129 kJ mol-1) was found to be expressed accurately by a combination of the internal energy of the precursor ion and the Franck-Condon energy gained on vertical electron transfer. The three lowest excited electronic states in 3 • were found by CIS/6-311G(2d,p) calculations to be outer states resulting from excitation of the unpaired electron in 3 • or electron capture by 3 +. The energetics and radiative lifetimes of the outer excited states of 3 • allowed interpretation of the highly endothermic ring-cleavage dissociations. The unimolecular chemistry of 3 can be explained by a bimodal energy distribution due to the formation of the ground and excited electronic states upon femtosecond collisional electron transfer.

Research paper thumbnail of Bond dissociations in hypervalent ammonium radicals prepared by collisional neutralization of protonated six-membered nitrogen heterocycles

Journal of Mass Spectrometry, 1997

ABSTRACT Hypervalent organic ammonium radicals were generated by collisional neutralization with ... more ABSTRACT 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. © 1997 John Wiley &amp; Sons, Ltd.

Research paper thumbnail of Dissociation Energies and Kinetics of Aminopyrimidinium Radicals by ab Initio and Density Functional Theory

J Phys Chem a, 1999

A series of isomeric 4-aminopyrimidinium radicals were used to model hydrogen atom adducts of nuc... more A series of isomeric 4-aminopyrimidinium radicals were used to model hydrogen atom adducts of nucleobases containing the 4-aminopyrimidine structure motif. Relative stabilities and activation energies for dissociations by hydrogen atom loss have been calculated by density functional theory and ab initio methods up to effective QCISD(T)/6-311+G(2d,p) for 4-amino-N-1-H-(1), 2-H-(2), N-3-H-(3), 4-H-(4), 5-H-(5), and 6-H-(6) pyrimidinium radicals and the 4-pyrimidylammonium radical (7). All these radicals were found to be bound species existing in potential energy wells. The order of stabilities has been established as 5 (most stable) > 3 > 2 > 1 > 6 > 4. 7 (least stable). Dissociations of the N-H and C-H bonds in 1-7 required activation barriers above the dissociation thresholds. RRKM calculations of unimolecular rate constants for N-H bond dissociations in 1 and 3 predicted substantial stabilization of these radicals by kinetic shift in the gas phase. Additions of hydrogen atoms to the N-1, C-2, N-3, C-4, C-5, and C-6 ring positions in 4-aminopyrimidine were found to be exothermic by 68, 70, 76, 23, 91, and 62 kJ mol-1 at 0 K, respectively. Hydrogen atom addition to the NH 2 group was 58 kJ mol-1 endothermic. The activation barriers for the hydrogen atom additions to 4-aminopyrimidine were found to inversely correlate with the reaction enthalpies. The calculated rate constants predicted predominant (95%) hydrogen atom addition to C-5. The other positions were substantially less reactive, e.g., N-3 (2%), C-2 (1%), C-6 (0.8%), and N-1 (0.4%).

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

Eur Mass Spectrom, 1998

Isomeric pyridyl radicals, 2-pyridyl (2), 3-pyridyl (3) and 4-pyridyl (4) were studied by neutral... more 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 3buten-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.

Research paper thumbnail of Neutralization-Reionization of Alkenylammonium Cations: An Experimental and Ab Initio Study of Intramolecular N-H... Interactions in Cations and Hypervalent Ammonium Radicals

J Amer Soc Mass Spectrom, 1997

A series of isomeric hexenylammonium and hexenyldimethylammonium cations were neutralized by coll... more 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/~s 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-l-ylammonium and 2-hexen-l-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-1ylammonium and 3-buten-l-yl methyloxonium ions was calculated by B3LYP/6-311G(2d,p) at 26 and 18 kJ tool-1, respectively. No intramolecular hydrogen bonding was found for the allylammonium ion. The hypervalent 3-buten-l-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-buten-l-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 FranckM2ondon 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.

Research paper thumbnail of Fluorescence-Based Biochemical Assays for the Study of Pregnane X Receptor and Constitutive Androstane Receptor

Research paper thumbnail of Direct Observation of a Hydrogen Atom Adduct to O-4 in Uracil. Energetics and Kinetics of Uracil Radicals

The Journal of Physical Chemistry A, 2001

ABSTRACT The 4-hydroxy-3,4-dihydropyrimidine-2(1H)-on-4-yl radical (1), an elusive hydrogen atom ... more ABSTRACT The 4-hydroxy-3,4-dihydropyrimidine-2(1H)-on-4-yl radical (1), an elusive hydrogen atom adduct to the O-4 position in uracil, was generated in the gas phase by femtosecond collisional electron transfer to O-4 protonated uracil and investigated by neutralization−reionization mass spectrometry (NRMS). A fraction of radicals 1 was stable on the 5.1 μs time scale. The main unimolecular dissociations of 1 were ring cleavages and a specific loss of the hydrogen atom from O-4, as determined by deuterium labeling. Ab initio calculations up to effective QCISD(T)/6-311+G(3df,2p) and combined density functional theory and perturbational calculations up to B3-MP2/6-311+G(3df,2p) were used to obtain bond dissociation and transition state energies for several radical and ion dissociations. The energies were used for calculations of rate constants by RRKM and transition state theory. The dissociations observed by NRMS could not be explained by competitive reactions occurring on the potential energy surface of the ground doublet state of 1 and must to a large part originate from excited electronic states of 1 that are formed by vertical electron capture. The adiabatic ionization energy of 1 was calculated as 5.55 eV. Activation energies for hydrogen atom additions to uracil were found to inversely correlate with the addition exothermicities. The most reactive position in uracil was C-5 which was calculated to account for &gt;95% hydrogen atom additions, followed by C-6 (&lt;5% additions), while additions to O-2 and O-4 were kinetically negligible.

Research paper thumbnail of Hydroxyl Radical Adducts to Pyridine. The Generation and Properties of the Elusive N -Hydroxypyridyl Radical

The Journal of Physical Chemistry A, 2001

The elusive N-hydroxypyridyl radical 1 has been generated transiently in the gas phase by collisi... more The elusive N-hydroxypyridyl radical 1 has been generated transiently in the gas phase by collisional neutralization of the stable cation 1 +. The radical underwent extensive dissociation by specific losses of H, OH, and ring-cleavage reactions, as elucidated by neutralization-reionization mass spectrometry aided by deuterium labeling. Effective QCISD(T)/6-311+G(3df,2p) and combined Møller-Plesset and density functional theory calculations indicated that loss of OH from 1 was 49 kJ mol-1 exothermic and proceeded on the potential energy surface of the ground doublet electronic state of the radical. The loss of H and ring-cleavage dissociations were initiated by the formation of excited electronic states in 1 that provided the internal energy for these endothermic reactions. OH radical addition to pyridine was predicted by transition-state theory calculations to occur mainly (82%) in the C-3 and C-5 positions. Hydrogen atom addition to pyridine-Noxide (2) was predicted to occur selectively at the oxygen atom and trigger a reaction sequence that can result in a highly exothermic catalytic isomerization of 2 to hydroxypyridines.

Research paper thumbnail of Dissociation Energies and Kinetics of Aminopyrimidinium Radicals by ab Initio and Density Functional Theory

The Journal of Physical Chemistry A, 1999

A series of isomeric 4-aminopyrimidinium radicals were used to model hydrogen atom adducts of nuc... more A series of isomeric 4-aminopyrimidinium radicals were used to model hydrogen atom adducts of nucleobases containing the 4-aminopyrimidine structure motif. Relative stabilities and activation energies for dissociations by hydrogen atom loss have been calculated by density functional theory and ab initio methods up to effective QCISD(T)/6-311+G(2d,p) for 4-amino-N-1-H-(1), 2-H-(2), N-3-H-(3), 4-H-(4), 5-H-(5), and 6-H-(6) pyrimidinium radicals and the 4-pyrimidylammonium radical (7). All these radicals were found to be bound species existing in potential energy wells. The order of stabilities has been established as 5 (most stable) > 3 > 2 > 1 > 6 > 4. 7 (least stable). Dissociations of the N-H and C-H bonds in 1-7 required activation barriers above the dissociation thresholds. RRKM calculations of unimolecular rate constants for N-H bond dissociations in 1 and 3 predicted substantial stabilization of these radicals by kinetic shift in the gas phase. Additions of hydrogen atoms to the N-1, C-2, N-3, C-4, C-5, and C-6 ring positions in 4-aminopyrimidine were found to be exothermic by 68, 70, 76, 23, 91, and 62 kJ mol-1 at 0 K, respectively. Hydrogen atom addition to the NH 2 group was 58 kJ mol-1 endothermic. The activation barriers for the hydrogen atom additions to 4-aminopyrimidine were found to inversely correlate with the reaction enthalpies. The calculated rate constants predicted predominant (95%) hydrogen atom addition to C-5. The other positions were substantially less reactive, e.g., N-3 (2%), C-2 (1%), C-6 (0.8%), and N-1 (0.4%).

Research paper thumbnail of Energetics of Uracil Cation Radical and Anion Radical Ion−Molecule Reactions in the Gas Phase

The Journal of Physical Chemistry A, 2001

The uracil cation radical was calculated to exist predominantly as the 1,3-dioxo tautomer 1 • + ,... more The uracil cation radical was calculated to exist predominantly as the 1,3-dioxo tautomer 1 • + , similar to the most stable tautomer of neutral uracil (1). The enol forms of 1 • + were found to be 10-173 kJ mol-1 less stable than 1 • + and should not be significantly populated at 298 K thermal equilibrium. Cation radical 1 • + is a moderately strong gas-phase acid of topical acidities ∆H acid) 829, 921, 916, and 879 kJ mol-1 for the H-1, H-3, H-5, and H-6 protons, respectively. Ion 1 • + is capable of exothermic protonation of adenine, guanine, and cytosine, and of the arginine, lysine, histidine, and tryptophan amino acid residues in proteins. The hydrogen atom affinities of 1 • + were-∆H rxn) 432, 371, and 360 kJ mol-1 for H-atom additions to O-4, O-2, and C-5, respectively. 1 • + was calculated to exothermically abstract the thiol hydrogen atom from CH 3 SH, the hydroxyl hydrogen from phenol, and an R-hydrogen atom from glycine N-methylamide. Uracil radicals formed by deprotonation of 1 • + were calculated to have large hydrogen atom affinities that should allow for exothermic abstraction of H-atoms from thiol groups, phenolic hydroxyls, and amino acid backbone R-methylene and methine groups. Protonation by a uracil cation radical followed by hydrogen atom abstraction can propagate radiation damage from the initial ionization site. In contrast to the highly reactive uracil cation radicals and radicals, the weakly bound uracil anion radical (1 •-) was predicted to be much less reactive in the gas phase. Ion-molecule reactions of 1 •by proton and hydrogen atom abstractions from thiols, phenol, and R-positions of amino acids were calculated to be endothermic and thus very slow in the gas phase. 1 •can selectively deprotonate carboxylic groups as calculated for the reaction with glycine.

Research paper thumbnail of Modeling Nucleobase Radicals in the Gas Phase. Experimental and Computational Study of 2-Hydroxypyridinium and 2-(1H)Pyridone Radicals

The Journal of Physical Chemistry A, 1999

Isomeric radicals corresponding to hydrogen atom adducts to 2-hydroxypyridine (1) and 2-(1H)pyrid... more Isomeric radicals corresponding to hydrogen atom adducts to 2-hydroxypyridine (1) and 2-(1H)pyridone (2) were investigated by neutralization-reionization mass spectrometry and combined ab initio and density functional theory calculations. Gas-phase protonation of 1 and 2 occurred preferentially at the nitrogen and oxygen atoms, respectively, to give a single 2-hydroxypyridinium ion 3 +. The calculated topical proton affinities in 1 were 922, 602, 777, 649, 786, 694, and 746 kJ mol-1 for the N-1, C-2, C-3, C-4, C-5, C-6, and OH positions, respectively. The topical proton affinities in 2 were 756, 824, 815, 692, and 930 kJ mol-1 for the N-1, C-3, C-5, C-6, and carbonyl oxygen positions, respectively. The 2-hydroxy-(1H)pyridinium radical (3 •) was generated by collisional neutralization of ion 3 + and found to be stable on a 4.67 µs time scale. Radical 3 • dissociated by losses of the hydroxyl and amine hydrogen atoms and by ring cleavages. MP2 and B3LYP calculations with the 6-311G(2d,p) basis set established the 298 K relative energies of hydrogen atom adducts derived from 1 and 2 as 3-H-2 (11 • , most stable, 0) < 6-H-2 (14 • , +20) < 3H-1 (5 • ,+37) < 4H-2 (12 • ,+59) < 5H-2 (13 • ,+60) < 5H-1 (7 • ,+62) < 3 • (+67) < 6H-1 (8 • ,+76) < 4H-1 (6 • ,+86) < 2H-1 (4 • ,+107) < 1H-2 (10 • ,+139 kJ mol-1). Hydrogen atom adducts to C-2 in 2 and to the hydroxyl group in 1 were found to be unstable and dissociated by ring opening and loss of H, respectively. RRKM calculations on the effective QCISD(T)/6-311+G(2d,p) potential energy surface showed cleavages of the O-H and N-H bonds in 3 • to be the lowest energy dissociations occurring in a 10:1 ratio. 1 was calculated to be 4.7 kJ mol-1 more stable than 2 in the gas phase at 0 K. Fitting the experimental and calculated isotope effects on dissociations of deuteriumlabeled radicals yielded a distribution function for the internal energy in the ground electronic state of 3 • formed by collisional electron transfer. The maximum of the internal energy distribution in ground-state 3 • (129 kJ mol-1) was found to be expressed accurately by a combination of the internal energy of the precursor ion and the Franck-Condon energy gained on vertical electron transfer. The three lowest excited electronic states in 3 • were found by CIS/6-311G(2d,p) calculations to be outer states resulting from excitation of the unpaired electron in 3 • or electron capture by 3 +. The energetics and radiative lifetimes of the outer excited states of 3 • allowed interpretation of the highly endothermic ring-cleavage dissociations. The unimolecular chemistry of 3 can be explained by a bimodal energy distribution due to the formation of the ground and excited electronic states upon femtosecond collisional electron transfer.

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

Journal of the American Society for Mass Spectrometry, 1997

A series of isomeric hexenylammonium and hexenyldimethylammonium cations were neutralized by coll... more 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/~s 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-l-ylammonium and 2-hexen-l-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-1ylammonium and 3-buten-l-yl methyloxonium ions was calculated by B3LYP/6-311G(2d,p) at 26 and 18 kJ tool-1, respectively. No intramolecular hydrogen bonding was found for the allylammonium ion. The hypervalent 3-buten-l-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-buten-l-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 FranckM2ondon 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.

Research paper thumbnail of Proton affinity of uracil. A computational study of protonation sites

Journal of the American Society for Mass Spectrometry, 2000

Relative stabilities of uracil tautomers and cations formed by gas-phase protonation were studied... more 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 6-311ϩG(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)/6-311ϩG(3df,2p) energies suggested Ͼ99.9% 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 Ͼ O-7 Ͼ C-5 Ͼ N-3 Ͼ N-1. The thermodynamic proton affinity of 1a was calculated as 858 kJ mol Ϫ1 at 298 K. A revision is suggested for the current estimate included in the ion thermochemistry database.

Research paper thumbnail of Uracil Radicals in the Gas Phase:  Specific Generation and Energetics

Journal of the American Chemical Society, 2001

... (18) Details of labeling experiments and calculations will be reported in full papers, see: W... more ... (18) Details of labeling experiments and calculations will be reported in full papers, see: Wolken, JK; Ture ek, F. J. Phys. Chem. A, submitted for publication, April 2001, and Syrstad, EA;Vivekananda, S. Ture ek, F. J. Phys. Chem. A, submitted for publication, April 2001. ...

Research paper thumbnail of Heterocyclic Radicals in the Gas Phase. An Experimental and Computational Study of 3-Hydroxypyridinium Radicals and Cations

Journal of the American Chemical Society, 1999

... the precursor ion beam. The reported spectra are averages of 30-40 consecutive scans taken at... more ... the precursor ion beam. The reported spectra are averages of 30-40 consecutive scans taken at a scan rate of 1 mass unit/s. The spectra were reproduced over the period of several weeks. Variable-time measurements were ...

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

Journal of Mass Spectrometry, 1997

ABSTRACT Hypervalent organic ammonium radicals were generated by collisional neutralization with ... more ABSTRACT 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. © 1997 John Wiley &amp; Sons, Ltd.