Theoretical and experimental study of the fragmentation of protonated uracil

Mechanism of Prebiotic Uracil Synthesis from Urea and HC3O+ in Space

The potential energy surface for the formation of protonated uracil (UH⁺) from urea and HC₃O⁺ was explored by performing quantum chemical complete basis set-QB3 calculations. A barrierless pathway was found for the formation of UH⁺, which was estimated to occur in the interstellar medium (ISM) much faster than the timescale of chemical revolution of typical dense interstellar clouds. Investigation of further reactions of UH⁺ formed through the obtained pathway led to the conclusion that uracil could be produced on icy grain surfaces but not in the gas phase of the ISM.

A TD-DFT-Based Study on the Attack of the OH· Radical on a Guanine Nucleotide

Heavy charged particles induce severe damage in DNA, which is a radiobiological advantage when treating radioresistant tumors. However, these particles can also induce cancer in humans exposed to them, such as astronauts in space missions. This damage can be directly induced by the radiation or indirectly by the attack of free radicals mainly produced by water radiolysis. We previously studied the impact of a proton on a DNA base pair, using the Time Dependent-Density Functional Theory (TD-DFT). In this work, we go a step further and study the attack of the OH· radical on the Guanine nucleotide to unveil how this molecule subsequently dissociates. The OH· attack on the H1', H2', H3', and H5' atoms in the guanine was investigated using the Ehrenfest dynamics within the TD-DFT framework. In all cases, the hydrogen abstraction succeeded, and the subsequent base pair dissociation was observed. The DNA dissociates in three major fragments: the phosphate group, the deoxyribose sugar, and the nitrogenous base, with slight differences, no matter which hydrogen atom was attacked. Hydrogen abstraction occurs at about 6 fs, and the nucleotide dissociation at about 100 fs, which agrees with our previous result for the direct proton impact on the DNA. These calculations may be a reference for adjusting reactive force fields so that more complex DNA structures can be studied using classical molecular dynamics, including both direct and indirect DNA damage.

Nucleic Acids under Stress: Understanding and Simulating Nucleobase Fragmentation Pathways

The effects of radiations on nucleic acids and their constituents is widely studied across several research fields using different experimental and theoretical protocols. While a large number of studies were performed in this context, many fundamental physical and chemical effects are still being investigated, particularly involving the effect of the biological environment. As an example, the interpretation of experimental nucleic acid bases mass spectra, and hence inferring their reactivity in complex environment still poses great challenge. This Minireview summarizes recent theoretical advancements aiming to predict and interpret the reactivity of nucleic acid bases. We focus not only on the understanding of the inherent fragmentation pathways of isolated nucleobases but also on the modeling of a realistic nano-environments highlighting the importance of molecular dynamics simulations and the non-innocent role of the environment and also the possibility to open novel fragmentation pathways.

Thermal desorption effects on fragment ion production from multi-photon ionized uridine and selected analogues

Experiments on neutral gas-phase nucleosides are often complicated by thermal lability. Previous mass spectrometry studies of nucleosides have identified enhanced relative production of nucleobase ions (e.g. uracil⁺ from uridine) as a function of desorption temperature to be the critical indicator of thermal decomposition. On this basis, the present multi-photon ionization (MPI) experiments demonstrate that laser-based thermal desorption is effective for producing uridine, 5-methyluridine, and 2′-deoxyuridine targets without thermal decomposition. Our experiments also revealed one notable thermal dependence: the relative production of the sugar ion C₅H₉O₄⁺ from intact uridine increased substantially with the desorption laser power and this only occurred at MPI wavelengths below 250 nm (full range studied 222–265 nm). We argue that this effect can only be rationalized plausibly in terms of changing populations of different isomers, tautomers, or conformers in the target as a function of the thermal desorption conditions. Furthermore, the wavelength threshold behavior of this thermally-sensitive MPI channel indicates a critical dependence on neutral excited state dynamics between the absorption of the first and second photons. The experimental results are complemented by density functional theory (DFT) optimizations of the lowest-energy structure of uridine and two further conformers distinguished by different orientations of the hydroxymethyl group on the sugar part of the molecule. The energies of the transitions states between these three conformers are low compared with the energy required for decomposition.

This work reveals the first experimental evidence supporting isomer-dependence in the radiation response of a nucleoside.

Chemical Bonding by the Chemical Orthogonal Space of Reactivity

The fashionable Parr-Pearson (PP) atoms-in-molecule/bonding (AIM/AIB) approach for determining the exchanged charge necessary for acquiring an equalized electronegativity within a chemical bond is refined and generalized here by introducing the concepts of chemical power within the chemical orthogonal space (COS) in terms of electronegativity and chemical hardness. Electronegativity and chemical hardness are conceptually orthogonal, since there are opposite tendencies in bonding, i.e., reactivity vs. stability or the HOMO-LUMO middy level vs. the HOMO-LUMO interval (gap). Thus, atoms-in-molecule/bond electronegativity and chemical hardness are provided for in orthogonal space (COS), along with a generalized analytical expression of the exchanged electrons in bonding. Moreover, the present formalism surpasses the earlier Parr-Pearson limitation to the context of hetero-bonding molecules so as to also include the important case of covalent homo-bonding. The connections of the present COS analysis with PP formalism is analytically revealed, while a numerical illustration regarding the patterning and fragmentation of chemical benchmarking bondings is also presented and fundamental open questions are critically discussed.

Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces

In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.

State-Dependent Fragmentation of Protonated Uracil and Uridine

Action spectroscopy using photon excitation in the VUV range (photon energy 4.5-9 eV) was performed on protonated uracil (UraH⁺) and uridine (UrdH⁺). The precursor ions with m/ z 113 and m/ z 245, respectively, were produced by an electrospray ionization source and accumulated inside a quadrupole ion trap mass spectrometer. After irradiation with tunable synchrotron radiation, product ion mass spectra were obtained. Fragment yields as a function of excitation energy show several maxima that can be attributed to the photoexcitation into different electronic states. For uracil, vertically excited states were calculated using the equation-of-motion coupled cluster approach and compared to the observed maxima. This allows to establish correlations between electronic states and the resulting fragment masses and can thus help to disentangle the complex de-excitation and fragmentation pathways of nucleic acid building blocks. Photofragmentation of the nucleoside uridine shows a significantly lower variety of fragments, indicating stabilization of the nucleobase by the attached sugar.

Gas-Phase Oxidation of the Protonated Uracil-5-yl Radical Cation

This study targets the kinetics and product detection of the gas-phase oxidation reaction of the protonated 5-dehydrouracil (uracil-5-yl) distonic radical cation using ion-trap mass spectrometry. Protonated 5-dehydrouracil radical ions (5-dehydrouracilH⁺ radical ion, m/z 112) are produced within an ion trap by laser photolysis of protonated 5-iodouracil. Storage of the 5-dehydrouracilH⁺ radical ion in the presence of controlled concentration of O₂ reveals two main products. The major reaction product pathway is assigned as the formation of protonated 2-hydroxypyrimidine-4,5-dione (m/z 127) + ^•OH. A second product ion (m/z 99), putatively assigned as a five-member-ring ketone structure, is tentatively explained as arising from the decarbonylation (-CO) of protonated 2-hydroxypyrimidine-4,5-dione. Because protonation of the 5-dehydrouracil radical likely forms a dienol structure, the O₂ reaction at the 5 position is ortho to an -OH group. Following this addition of O₂, the peroxyl-radical intermediate isomerizes by H atom transfer from the -OH group. The ensuing hydroperoxide then decomposes to eliminate ^•OH radical. It is shown that this elimination of ^•OH radical (-17 Da) is evidence for the presence of an -OH group ortho to the initial phenyl radical site, in good accord with calculations. The subsequent CO loss mechanism, to form the aforementioned five-member-ring structure, is unclear, but some pathways are discussed. By following the kinetics of the reaction, the room temperature second-order rate coefficient of the 5-dehydrouracilH⁺ distonic radical cation with molecular oxygen is measured at 7.2 × 10^-11 cm³ molecule^-1 s^-1, Φ = 12% (with ±50% total accuracy). For aryl radical reactions with O₂, the presence of the ^•OH elimination product pathway, following the peroxyl-radical formation, is an indicator of an -OH group ortho to the radical site.

Fragmentation of pure and hydrated clusters of 5Br-uracil by low energy carbon ions: observation of hydrated fragments

The fragmentation of the isolated 5-bromouracil (5BrU) molecule and pure and nano-hydrated 5BrU clusters induced by low energy ¹²C⁴⁺ ions has been studied.

Influence of microhydration on the structures and proton-induced charge transfer in RNA intermediates

Solvation effects are of major interest in the context of radiation damage, due to their potential applications in cancer therapy. Reliable modeling of the solvent is, however, quite challenging, and numerous studies have been devoted to isolated biomolecules and stepwise-hydrated molecules in which the amount of solvent is controlled one molecule at a time. The influence of stepwise hydration on radiation damage is investigated here using the example of proton-induced charge transfer in two biomolecular targets. Uracil has been widely investigated both experimentally and theoretically in this context, and 2-aminooxazole was recently shown to be a potentially important intermediate in prebiotic chemistry. Focusing here on doubly hydrated biomolecules, stable structures and infrared spectra were obtained by combining the results of molecular dynamics simulations with those of quantum chemistry calculations performed at the density-functional theory level with the double hybrid M06-2X functional. The charge-transfer cross-sections upon proton impact were obtained from ab initio molecular calculations and after applying a semi-classical approach to investigate the collision. Our results suggest a significant relationship between the detailed hydration structure and the efficacy of proton-induced charge transfer, highlighting the competing roles of inter- and intramolecular hydrogen bonding.

The role of the environment in the ion induced fragmentation of uracil

The fragmentation of uracil molecules and pure and nano-hydrated uracil clusters by ¹²C⁴⁺ ion impact is investigated.

On the gas phase fragmentation of protonated uracil: a statistical perspective

The major fragmentation pathways of protonated uracil calculated in this work using statistical methods agree with mass spectrometry experiments.

Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments

In this study we have coupled mixed quantum-classical (quantum mechanics/molecular mechanics) direct chemical dynamics simulations with electrospray ionization/tandem mass spectrometry experiments in order to achieve a deeper understanding of the fragmentation mechanisms occurring during the collision induced dissociation of gaseous protonated uracil. Using this approach, we were able to successfully characterize the fragmentation pathways corresponding to ammonia loss (m/z 96), water loss (m/z 95) and cyanic or isocyanic acid loss (m/z 70). Furthermore, we also performed experiments with isotopic labeling completing the fragmentation picture. Remarkably, fragmentation mechanisms obtained from chemical dynamics simulations are consistent with those deduced from isotopic labeling.

Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine

The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.

Proton irradiation of DNA nucleosides in the gas phase

Charge localization within nucleosides after proton irradiation is strongly influenced by the ionization energy of the base.