Impact of Sodium Cationization on Gas-Phase Conformations of DNA and RNA Cytidine Mononucleotides

Structural Characterization of the Metalized Radical Cations of Adenosine ([Ade+Li-H]•+ and [Ade+Na-H]•+) by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Studies

Nucleoside radicals are key intermediates in the process of DNA damage, and alkali metal ions are a common group of ions in living organisms. However, so far, there has been a significant lack of research on the structural effects of alkali metal ions on nucleoside free radicals. In this study, we report a new method for generating metalized nucleoside radical cations in the gas phase. The radical cations [Ade+M-H]•+ (M = Li, Na) are generated by the 280 nm ultraviolet photodissociation (UVPD) of the precursor ions of lithiated and sodiated ions of 2-iodoadenine in a Fourier transform ion cyclotron resonance (FT ICR) cell. Further infrared multiphoton dissociation (IRMPD) spectra of both radical cations were recorded in the region of 2750-3750 cm-1. By combining these results with theoretical calculations, the most stable isomers of both radicals can be identified, which share the common characteristics of triple coordination patterns of the metal ions. For both radical species, the lowest-energy isomers undergo hydrogen transfer. Although the sugar ring in the most stable isomer of [Ade+Li-H]•+ is in a (South, syn) conformation similar to that of [Ado+Na]+, [Ade+Na-H]•+ is distinguished by the unexpected opening of the sugar ring. Their theoretical spectra are in good agreement with experimental spectra. However, due to the flexibility of the structures and the complexity of their potential energy surfaces, the hydrogen transfer pathways still need to be further studied. Considering that the free radicals formed directly after C-I cleavage have some similar spectral characteristics, the existence of these corresponding isomers cannot be ruled out. The findings imply that the structures of nucleoside radicals may be significantly influenced by the attached alkali metal ions. More detailed experiments and theoretical calculations are still crucial.

Molecular and Structural Characterization of Isomeric Compounds in Atmospheric Organic Aerosol Using Ion Mobility-Mass Spectrometry

Secondary organic aerosol (SOA) formed through multiphase atmospheric chemistry makes up a large fraction of airborne particles. The chemical composition and molecular structures of SOA constituents vary between different emission sources and aging processes in the atmosphere, which complicates their identification. In this work, we employ drift tube ion mobility spectrometry with quadrupole time-of-flight mass spectrometry (IM-MS) detection for rapid gas-phase separation and multidimensional characterization of isomers in two biogenic SOAs produced from ozonolysis of isomeric monoterpenes, d-limonene (LSOA) and α-pinene (PSOA). SOA samples were ionized using electrospray ionization (ESI) and characterized using IM-MS in both positive and negative ionization modes. The IM-derived collision cross sections in nitrogen gas (^DTCCS_N2 ) for individual SOA components were obtained using multifield and single-field measurements. A novel application of IM multiplexing/high-resolution demultiplexing methodology was employed to increase sensitivity, improve peak shapes, and augment mobility baseline resolution, which revealed several isomeric structures for the measured ions. For LSOA and PSOA samples, we report significant structural differences of the isomer structures. Molecular structural calculations using density functional theory combined with the theoretical modeling of CCS values provide insights into the structural differences between LSOA and PSOA constituents. The average ^DTCCS_N2 values for monomeric SOA components observed as [M + Na]⁺ ions are 3-6% higher than those of their [M - H]^- counterparts. Meanwhile, dimeric and trimeric isomer components in both samples showed an inverse trend with the relevant values of [M - H]^- ions being 3-7% higher than their [M + Na]⁺ counterparts, respectively. The results indicate that the structures of Na⁺-coordinated oligomeric ions are more compact than those of the corresponding deprotonated species. The coordination with Na⁺ occurs on the oxygen atoms of the carbonyl groups leading to a compact configuration. Meanwhile, deprotonated molecules have higher ^DTCCS_N2 values due to their elongated structures in the gas phase. Therefore, ^DTCCS_N2 values of isomers in SOA mixtures depend strongly on the mode of ionization in ESI. Additionally, PSOA monomers and dimers exhibit larger ^DTCCS_N2 values (1-4%) than their LSOA counterparts owing to more rigid structures. A cyclobutane ring is present with functional groups pointing in opposite directions in PSOA compounds, as compared to noncyclic flexible LSOA structures, forming more compact ions in the gas phase. Lastly, we investigated the effects of direct photolysis on the chemical transformations of selected individual PSOA components. We use IM-MS to reveal structural changes associated with aerosol aging by photolysis. This study illustrates the detailed molecular and structural descriptors for the detection and annotation of structural isomers in complex SOA mixtures.

Sodium Cationization Enables Exotic Deprotonation Sites on Gaseous Mononucleotides

We report observation and photoelectron spectroscopic characterization of sodium cationization on four doubly deprotonated mononucleotide dianions Na⁺·[dNMP-2H]^2- (N = A, G, C, or T) in the gas phase. Multiple tautomers with distinct deprotonated sites are identified, in which Na⁺ enables novel double deprotonation patterns and folds the resultant mononucleotide dianions. The most stable isomer for the whole family is derived from detaching one proton from the phosphate and the other from the nucleobase (amino group for N = A, G, and C, but nitrogen atom for T), whereas high-lying isomers with protons detached separately from the phosphate and the hydroxy group of sugar coexist. Particularly, an exotic deprotomer with both protons deprived from guanosine is populated as well. This work thus displays a remarkably diverse binding landscape enabled by sodium cationization, a potentially critical element in developing a general formulism to better model metal cation and nucleotide interactions.