Sub-microsecond photodissociation pathways of gas phase adenosine 5'-monophosphate nucleotide ions

Hydrogen-Deuterium-Exchange-Based Mass Distribution Shifts in High-Resolution Cyclic Ion Mobility Separations

The mass distribution of ions influences separations in ion mobility spectrometry-mass spectrometry (IMS-MS). Herein, we introduce a method to induce mass distribution shifts for various analytes using hydrogen-deuterium exchange (HDX) immediately prior to ionization using a dual syringe approach. By replacing labile hydrogens on analytes with deuteriums, we were able to differentiate isomers using separations of isotopologues. For each analyte studied, every possible level of deuteration (from undeuterated to fully deuterated) was generated and then separated using cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS). The information gained from such separations (relative arrival times; t_Rel. values) was found to be orthogonal to conventional IMS-MS separations. Additionally, the observed shifts were linearly additive with increasing deuteration, suggesting that this methodology could be extended to analytes with a larger number of labile hydrogens. For one isomer pair, as few as two deuteriums were able to produce a large enough mass distribution shift to differentiate isomers. In another experiment, we found that the mass distribution shift was large enough to overcome the reduced mass contribution, resulting in a "flipped" arrival time where the heavier deuterated isotopologue arrived before the lighter one. In this work, we present a proof-of-concept demonstration that mass-distribution-based shifts, t_Rel. values, could potentially act as an added dimension to characterize molecules in IMS-MS. We anticipate, along with future work in this area, that mass-distribution-based shifts could enable the identification of unknown molecules through a database-driven approach in an analogous fashion to collision cross section (CCS) measurements.

Triplet Mediated C-N Dissociation versus Internal Conversion in Electronically Excited N-Methylpyrrole

The photochemical and photophysical pathways operative in N-methylpyrrole, after excitation in the near part of its ultraviolet absorption spectrum, have been investigated by the combination of time-resolved total ion yield and photoelectron spectroscopies with high-level ab initio calculations. The results collected are remarkably different from the observations made for pyrrole and other aromatic systems, whose dynamics is dictated by the presence of πσ* excitations on X-H (X: N, O, S, ...) bonds. The presence of a barrier along the C-N dissociation coordinate that can not be tunneled triggers two alternative decay mechanisms for the S1 A″ πσ* state. While at low vibrational content the C-N dissociation occurs on the surface of a lower (3)ππ* state reached after efficient intersystem crossing, at higher excitation energies, the A″ πσ* directly internally converts to the ground state through a ring-twisted S1/S0 conical intersection. The findings explain previous observations on the molecule and may be relevant for more complex systems containing similar C-N bonds, such as the DNA nucleotides.

Energy-Dependent UV Photodissociation of Gas-Phase Adenosine Monophosphate Nucleotide Ions: The Role of a Single Solvent Molecule

The photodissociation of gaseous protonated adenosine 5'-monophosphate (AMP) and the same system hydrated with one water molecule has been investigated in the 4 to 13 eV photon energy range by coupling a linear quadrupole ion trap with a synchrotron radiation beamline. The dissociation of the bare AMP cation upon absorption of a single ultraviolet (UV) photon below the ionization energy (IE) almost exclusively produces the protonated adenine base, with a measured photodissociation yield showing spectroscopic features with dominant absorption bands located at 4.75 and 6.5 eV, found in agreement with TD-DFT calculations. Nevertheless, the addition of a single water molecule to the system modifies the dissociation energy dependence and strongly suppresses the cleavage of the glycosidic CN bond below the IE. Both the experimental and theoretical results suggest that a single solvent molecule can intrinsically influence the structure and physicochemical properties of the AMP cation, including its UV induced dissociation pattern, beyond the simple water evaporation.

Electronic coupling between photo-excited stacked bases in DNA and RNA strands with emphasis on the bright states initially populated

In biology the interplay between multiple light-absorbers gives rise to complex quantum effects such as superposition states that are of extreme importance for life, both for harvesting solar energy and likely protecting nucleic acids from radiation damage. Still the characteristics of these states and their quantum dynamics are a much debated issue. While the electronic properties of single bases are fairly well understood, the situation for strands is complicated by the fact that stacked bases electronically couple when photoexcited. These newly arising states are denoted as exciton states and are simply linear combinations of localised wavefunctions that involve N - 1 ground-state bases and one base in its excited state (cf. the Frenkel exciton model). There is disagreement over the number of bases, N, that coherently couple, i.e., the spatial extent of the exciton, and how electronic deexcitation back to the ground state occurs. The importance of dark charge-transfer states has been inferred both from time-resolved fluorescence and transient absorption experiments. These states were suggested to be responsible for long deexcitation times but it is unclear whether 'long' is tens of picoseconds or nanoseconds. In this review paper, we focus on the bright states initially populated and discuss their nature based on information obtained from systematic absorption and circular dichroism experiments on single strands of different lengths. Our results from the last five years are compared with those from other groups, and are discussed in the context of successive deexcitation schemes. Pieces to the puzzle have come from different experiments and theory but a complete description has yet to emerge. As such the story about DNA/RNA photophysical decay mechanisms resembles the tale about the blind men and the elephant where all see the beast in different, correct but incomplete ways.

Gas-phase spectroscopy of protonated adenine, adenosine 5'-monophosphate and monohydrated ions

Microsolvation of chromophore ions commonly has large effects on their electronic structure and as a result on their optical absorption spectra. Here spectroscopy of protonated adenine (AdeH(+)) and its complex with one water molecule isolated in vacuo was done using a home-built mass spectrometer in combination with a tuneable pulsed laser system. Experiments also included the protonated adenosine 5'-monophosphate nucleotide (AMPH(+)). In the case of bare AdeH(+) ions, one-photon absorption leads to four dominant fragment ions corresponding to ammonium and ions formed after loss of either NH3, HCN, or NH2CN. The yields of these were measured as a function of the wavelength of the light from 210 nm to 300 nm, and they were combined to obtain the total photoinduced dissociation at each wavelength (i.e., action spectrum). A broad band between 230 nm and 290 nm and the tail of a band with maximum below 210 nm (high-energy band) are seen. In the case of AdeH(+)(H2O), the dominant dissociation channel after photoexcitation in the low-energy band was simply loss of H2O while photodissociation of protonated AMP revealed two dominant dissociation channels associated with the formation of either AdeH(+) or loss of H3PO4. The action spectra of AdeH(+), AdeH(+)(H2O), and AMPH(+) are almost identical in the 230-290 nm region, and they resemble the absorption spectrum of protonated adenine in aqueous solution recorded at low pH. Hence from our work it is firmly established that the lowest-energy transitions are independent of the surroundings.

Infrared multiple photon dissociation action spectroscopy of deprotonated RNA mononucleotides: gas-phase conformations and energetics

The IRMPD action spectra of the deprotonated forms of the four common RNA mononucleotides, adenosine-5'-monophosphate (A5'p), guanosine-5'-monophosphate (G5'p), cytidine-5'-monophosphate (C5'p), and uridine-5'-monophosphate (U5'p), are measured to probe their gas-phase structures. The IRMPD action spectra of all four deprotonated RNA mononucleotides exhibit distinct IR signatures in the frequency region investigated, 570-1900 cm(-1), that allows these deprotonated mononucleotides to be easily differentiated from one other. Comparison of the measured IRMPD action spectra to the linear IR spectra calculated at the B3LYP/6-31+G(d,p) level of theory finds that the most stable conformations of the deprotonated forms of A5'p, C5'p, and U5'p are accessed in the experiments, and these conformers adopt the C3' endo conformation of the ribose moiety and the anti conformation of the nucleobase. In the case of deprotonated G5'p, the most stable conformer is also accessed in the experiments. However, the ground-state conformer differs from the other three deprotonated RNA mononucleotides in that it adopts the syn rather than anti conformation for the nucleobase. Present results are compared to results previously obtained for the deprotonated forms of the four common DNA mononucleotides to examine the fundamental conformational differences between these species, and thus elucidate the effects of the 2'-hydroxyl group on their structure, stability, and fragmentation behavior.

Base-specific ionization of deprotonated nucleotides by resonance enhanced two-photon detachment

The intrinsic ionization energy of a base in DNA plays a critical role in determining the energies at which damage mechanisms may emerge. Here, a two-photon resonance-enhanced ionization scheme is presented that utilizes the (1)ππ* transition, localized on the DNA base, to elucidate the base-specific ionization in a deprotonated nucleotide. In contrast to previous reports, the scheme is insensitive to competing ionization channels arising from the sugar-phosphate backbone. Using this approach, we demonstrate that for all bases except guanine, the lowest electron detachment energy corresponds to detachment from the sugar-phosphate backbone and allows us to determine the lowest adiabatic ionization energy for the other three bases for the first time in an isolated nucleotide.

UV photodissociation dynamics of deprotonated 2'-deoxyadenosine 5'-monophosphate [5'-dAMP-H]-

The UV photodissociation dynamics of deprotonated 2'-deoxyadenosine 5'-monophosphate ([5'-dAMP-H](-)) has been studied using a unique technique based on the coincident detection of the ion and the neutral fragments. The observed fragment ions are m/z 79 (PO(3)(-)), 97 (H(2)PO(4)(-)), 134 ([A-H](-)), 177 ([dAMP-H-A-H(2)O](-)), and 195 ([dAMP-H-A](-)), where "A" refers to a neutral adenine molecule. The relative abundances are comparable to that found in previous studies on [5'-dAMP-H](-) employing different excitation processes, i.e., collisions and UV photons. The fragmentation times of the major channels have been measured, and are all found to be on the microsecond time scale. The fragmentation mechanisms for all channels have been characterized using velocity correlation plots of the ion and neutral fragment(s). The findings show that none of the dissociation channels of [5'-dAMP-H](-) is UV specific and all proceed via statistical fragmentation on the ground state after internal conversion, a result similar to fragmentations induced by collisions.