UV-Vis Photodissociation Action Spectroscopy on Thermo LTQ-XL ETD and Bruker amaZon Ion Trap Mass Spectrometers: a Practical Guide.

We report automated procedures for multiple tandem mass spectra acquisition allowing UV-Vis photodissociation action spectroscopy measurements of ions and radicals. The procedures were developed for two commercial ion trap mass spectrometers and applied to collision-induced and electron-transfer dissociation tandem mass spectrometry modes of ion generation.

Hydrogen-Rich Cation Radicals of DNA Dinucleotides: Generation and Structure Elucidation by UV-Vis Action Spectroscopy.

Hydrogen-rich DNA dinucleotide cation radicals (dGG + 2H)+•, (dCG + 2H)+•, and (dGC + 2H)+• represent transient species comprising protonated and hydrogen atom adducted nucleobase rings that serve as models for proton and radical migrations in ionized DNA. These DNA cation radicals were generated in the gas phase by electron-transfer dissociation of dinucleotide dication-crown-ether complexes and characterized by UV-vis photodissociation action spectra, ab initio calculations of structures and relative energies, and time-dependent density functional theory calculations of UV-vis absorption spectra. Theoretical calculations indicate that (dGG + 2H)+• cation radicals formed by electron transfer underwent an exothermic conformational collapse that was accompanied by guanine ring stacking and facile internucleobase hydrogen atom transfer, forming 3'-guanine C-8-H radicals. In contrast, exothermic hydrogen transfer from the 5'-cytosine radical onto the guanine ring in (dCG + 2H)+• was kinetically hampered, resulting in the formation of a mixture of 5'-cytosine and 3'-guanine radicals. Conformational folding and nucleobase stacking were energetically unfavorable in (dGC + 2H)+• that retained its structure of a 3'-cytosine radical, as formed by one-electron reduction of the dication. Hydrogen-rich guanine (G + H)• and cytosine (C + H)• radicals were calculated to have vastly different basicities in water, as illustrated by the respective p Ka values of 20.0 and 4.6, which is pertinent to their different abilities to undergo proton-transfer reactions in solution.

UV-Vis Action Spectroscopy Reveals a Conformational Collapse in Hydrogen-Rich Dinucleotide Cation Radicals.

We report the generation of deoxyriboadenosine dinucleotide cation radicals by gas-phase electron transfer to dinucleotide dications and their noncovalent complexes with crown ether ligands. Stable dinucleotide cation radicals of a novel hydrogen-rich type were generated and characterized by tandem mass spectrometry and UV-vis photodissociation (UVPD) action spectroscopy. Electron structure theory analysis indicated that upon electron attachment the dinucleotide dications underwent a conformational collapse followed by intramolecular proton migrations between the nucleobases to give species whose calculated UV-vis absorption spectra matched the UVPD action spectra. Hydrogen-rich cation radicals generated from chimeric riboadenosine 5'-diesters gave UVPD action spectra that pointed to novel zwitterionic structures consisting of aromatic π-electron anion radicals intercalated between stacked positively charged adenine rings. Analogies with DNA ionization are discussed.

Cytosine Radical Cations: A Gas-Phase Study Combining IRMPD Spectroscopy, UVPD Spectroscopy, Ion-Molecule Reactions, and Theoretical Calculations.

The radical cation of cytosine (Cyt.+ ) is generated by dissociative oxidation from a ternary CuII complex in the gas phase. The radical cation is characterized by infrared multiple photon dissociation (IRMPD) spectroscopy in the fingerprint region, UV/Vis photodissociation (UVPD) spectroscopy, ion-molecule reactions, and theoretical calculations (density functional theory and ab initio). The experimental IRMPD spectrum features diagnostic bands for two enol-amino and two keto-amino tautomers of Cyt.+ that are calculated to be among the lowest energy isomers, in agreement with a previous study. Although the UVPD action spectrum can also be matched to a combination of the four lowest energy tautomers, the presence of a nonclassical distonic radical cation cannot be ruled out. Its formation is, however, unlikely due to the high energy of this isomer and the respective ternary CuII complex. Gas-phase ion-molecule reactions showed that Cyt.+ undergoes hydrogen-atom abstraction from 1-propanethiol, radical recombination reactions with nitric oxide, and electron transfer from dimethyl disulfide.

Conformation-specific spectroscopy of alkyl benzyl radicals: Effects of a radical center on the CH stretch infrared spectrum of an alkyl chain.

An important initial step in the combustion of gasoline and diesel fuels is the abstraction of hydrogen from alkylbenzenes to form resonance-stabilized alkyl benzyl radicals. This work uses, for the first time, double resonance spectroscopy methods to explore the conformation-specific vibronic and infrared spectroscopy of the α-ethylbenzyl (αEtBz) and α-propylbenzyl (αPrBz) radicals. Local mode Hamiltonian modeling enables assignment of the alkyl CH stretch IR spectra, accounting for Fermi resonance that complicates aliphatic alkyl CH stretch IR spectroscopy. The ground state conformational preferences of the ethyl and propyl chains are changed from those in the alkylbenzenes themselves, with global minima occurring for an in-plane orientation of the alkyl chain (trans) about its first dihedral angle (ϕf123, numbers are alkyl C atoms. C1 is CH radical site). This in-plane structure is the only observed conformer for the α-EtBz radical, while two conformers, tt and tg' share this orientation at the first dihedral, but differ in the second (ϕ1234) for the αPrBz radical. The in-plane orientation lowers the local site frequencies of the CH2 group stretches immediately adjacent to the benzylic radical site by about 50 cm-1 relative to those in pure alkyl chains or alkylbenzenes. This effect of the radical site is localized on the first CH2 group, with little effect on subsequent members of the alkyl chain. In the D1 excited electronic state, an out-of-plane orientation is preferred for the alkyl chains, leading to torsional mode Franck-Condon activity in the D0-D1 spectra that is both conformer-specific and diagnostic of the conformational change.

Infrared and Electronic Spectroscopy of the Jet-Cooled 5-Methyl-2-furanylmethyl Radical Derived from the Biofuel 2,5-Dimethylfuran.

The electronic and infrared spectra of the 5-methyl-2-furanylmethyl (MFM) radical have been characterized under jet-cooled conditions in the gas phase. This resonance-stabilized radical is formed by H atom loss from one of the methyl groups of 2,5-dimethylfuran (DMF), a promising second-generation biofuel. As a resonance-stabilized radical, it plays an important role in the flame chemistry of DMF. The D0-D1 transition was studied using two-color resonant two-photon ionization (2C-R2PI) spectroscopy. The electronic origin is in the middle of the visible spectrum (21934 cm(-1) = 455.9 nm) and is accompanied by Franck-Condon activity involving the hindered methyl rotor. The frequencies and intensities are fit to a one-dimensional methyl rotor potential, using the calculated form of the ground state potential. The methyl rotor reports sensitively on the local electronic environment and how it changes with electronic excitation, shifting from a preferred ground state orientation with one CH in-plane and anti to the furan oxygen, to an orientation in the excited state in which one CH group is axial to the plane of the furan ring. Ground and excited state alkyl CH stretch infrared spectra are recorded using resonant ion-dip infrared (RIDIR) spectroscopy, offering a complementary view of the methyl group and its response to electronic excitation. Dramatic changes in the CH stretch transitions with electronic state reflect the changing preference for the methyl group orientation.

Anharmonic modeling of the conformation-specific IR spectra of ethyl, n-propyl, and n-butylbenzene.

Conformation-specific UV-IR double resonance spectra are presented for ethyl, n-propyl, and n-butylbenzene. With the aid of a local mode Hamiltonian that includes the effects of stretch-scissor Fermi resonance, the spectra can be accurately modeled for specific conformers. These molecules allow for further development of a first principles method for calculating alkyl stretch spectra. Across all chain lengths, certain dihedral patterns impart particular spectral motifs at the quadratic level. However, the anharmonic contributions are consistent from molecule to molecule and conformer to conformer. This transferability of anharmonicities allows for the Hamiltonian to be constructed from only a harmonic frequency calculation, reducing the cost of the model. The phenyl ring alters the frequencies of the CH2 stretches by about 15 cm(-1) compared to their n-alkane counterparts in trans configurations. Conformational changes in the chain can lead to shifts in frequency of up to 30 cm(-1).

The spectroscopy and photochemistry of quinioline structural isomers: (E)- and (Z)-phenylvinylnitrile.

In Titan's atmosphere, photochemical pathways that lead to nitrogen heteroaromatics may incorporate photoisomerization of their structural isomers as a final step. (E)- and (Z)-phenylvinylnitrile ((E)- and (Z)-PVN, C6H5-CH=CHCN) are structural isomers of quinoline that themselves possess extensive absorptions in the ultraviolet, and thus may engage in such photoisomerization pathways. The present study explores the vibronic spectroscopy and photo-induced isomerization of gas-phase (E)- and (Z)-PVN in the 33,600-35,850 cm(-1) region under jet-cooled conditions. The S0-S1 origins for (E)- and (Z)-PVN have been identified at 33 827 cm(-1) and 33 707 cm(-1), respectively. Isomer-specific UV-UV hole-burning and UV depletion spectra reveal sharp vibronic structure that extends over almost 2000 cm(-1), with thresholds for fast non-radiative decay identified by a comparison between hole-burning and UV depletion spectra. Dispersed fluorescence spectra of the two isomers enable the assignment of many low frequency transitions in both molecules, aided by harmonic frequency calculations (B3LYP/6-311++G(d,p)) and a comparison with the established spectroscopy of phenylvinylacetylene, the ethynyl counterpart to PVN. Both isomers are proven to be planar in both the S0 ground and S1 electronic excited states. (E)-PVN exhibits extensive Duschinsky mixing involving out-of-plane modes whose frequencies and character change significantly in the ππ* transition, which modulates the degree of single- and double-bond character along the vinylnitrile substituent. This same mixing is much less evident in (Z)-PVN. The spectroscopic characterization of (E)- and (Z)-PVN served as the basis for photoisomerization experiments using ultraviolet hole-filling spectroscopy carried out in a reaction tube affixed to the pulsed valve. Successful interconversion between (E) and (Z)-PVN was demonstrated via ultraviolet hole-filling experiments. Photoexcitation of (E)- and (Z)-PVN at their respective S0-S1 origins failed to produce quinoline, a simple polycyclic aromatic nitrogen heterocylcle, within the detection sensitivity of our experiments. Stationary points along the potential energy surface associated with (Z)-PVN → quinoline isomerization showed a barrier of 93 kcal/mol associated with the first step in the isomerization process, slowing the interconversion process at the excitation energies used (96 kcal/mol) to timescales beyond those probed in the present experiment.

Vibronic spectroscopy of a nitrile/isonitrile isoelectronic pair: para-diisocyanobenzene and para-isocyanobenzonitrile.

The ultraviolet spectroscopy of isoelectronic pair para-diisocyanobenzene (pDIB) and para-isocyanobenzonitrile (pIBN) has been studied under gas-phase, jet-cooled conditions. These molecules complete a sequence of mono and disubstituted nitrile/isonitrile benzene derivatives, enabling a comparison of the electronic effects of such substitution. Utilizing laser-induced fluorescence (LIF) and resonant two-photon ionization (R2PI) spectroscopy, the S0-S1 electronic origins of pDIB and pIBN have been identified at 35,566 and 35,443 cm(-1), respectively. In pDIB, the S0-S1 origin is very weak, with b(3g) fundamentals induced by vibronic coupling to the S2 state dominating the spectrum at 501 cm(-1) (ν17, isocyano bend) and 650 cm(-1) (ν16, ring distortion). The spectrum extends over 5000 cm(-1), remaining sharp and relatively uncongested over much of this range. Dispersed fluorescence (DFL) spectra confirm the dominating role played by vibronic coupling and identify Franck-Condon active ring modes built off the vibronically-induced bands. In pDIB, the S2 state has been tentatively observed at about 6100 cm(-1) above the S0-S1 origin. In pIBN, the S0-S1 origin is considerably stronger, but vibronic coupling still plays an important role, involving fundamentals of b2 symmetry. The bending mode of the nitrile group dominates the vibronically-induced activity. Calculations carried out at the TD-DFT B3LYP/6-31+G(d) level of theory account for the extremely weak S0-S1 oscillator strength of pDIB and the larger intensity of the S0-S1 origins of pIBN and pDCB (para-dicyanobenzene) as nitrile groups are substituted for isonitrile groups. In pDIB, a nearly perfect cancellation of transition dipoles occurs due to two one-electron transitions that contribute nearly equally to the S0-S1 transition. The spectra of both molecules show no clear evidence of charge-transfer interactions that play such an important role in some cyanobenzene derivatives.

Ground and excited state infrared spectroscopy of jet-cooled radicals: exploring the photophysics of trihydronaphthyl and inden-2-ylmethyl.

The alkyl and aromatic CH stretch infrared spectra of inden-2-ylmethyl (I2M, C10H9) and trihydronaphthyl (THN, C10H11) radicals have been recorded under jet-cooled conditions in the ground (D0) and first electronically excited (D1) states using resonant ion-dip infrared (RIDIR) spectroscopy. Previously, the vibronic spectroscopy of a series of C10H9 and C10H11 hydronaphthyl radicals were investigated and their thermochemical properties were evaluated with isomer specificity [J. A. Sebree et al., J. Phys. Chem. A 11, 6255-6262 (2010)]. We show here that one of the m/z 129 spectral carriers characterized in that work was misidentified as 2-hydronaphthyl (2-HN) radical, appearing in a discharge of 1,2-dihydronaphthalene in close proximity to 1-hydronaphthyl radical. The D0-RIDIR spectrum in the alkyl CH stretch region positively identifies the m/z 129 isomer as I2M, whose two-color resonant two-photon ionization (2C-R2PI) spectrum was recently reported by Schmidt and co-workers [T. P. Troy et al., Chem. Sci. 2, 1755-1765 (2011)]. Here, we further characterize the I2M and THN radicals by recording their gas phase IR spectra in the alkyl and aromatic CH stretch regions, and explore the spectroscopic consequences of electronic excitation on the CH stretch absorptions. A local-mode CH stretch Hamiltonian incorporating cubic stretch-bend coupling between anharmonic CH stretches and CH2 scissor modes is utilized to describe their Fermi resonance interactions. Excellent agreement between the experimental and theoretical results facilitates the interpretation of the D0- and D1-state RIDIR spectra of I2M, revealing that upon excitation the alkyl CH stretches decrease in frequency by 70 cm(-1), while the allyl-like CH stretches experience a modest blueshift. In comparison, the photophysics of THN are strikingly different in that the IR transitions that possess vibrational motion along the CßH and CδH bonds are absent in the D1-RIDIR spectrum yet are predicted to be present from the theoretical model. Several hypotheses are considered to account for the perturbations to these vibrations.