Theoretical and experimental studies of cationized uracil complexes in the gas phase

Cationized uracil clusters were generated in the gas phase by electrospray ionization (ESI). Mass spectrometry experiments showed that with particular experimental conditions, decameric uracil clusters are magic number clusters. MS/MS experiments demonstrated that the structure of these decameric uracil clusters depends substantially on the size and the charge of the cation. On the basis of the ab initio and density functional theory (DFT) quantum chemistry calculations, structures for these decameric clusters were proposed. These structures are in agreement with the experimental mass spectra of modified nucleobases. Theoretical calculations showed that complexes experimentally observed using ESI-MS techniques, are not naturally the most stable in the gas phase.     

Clustering of nucleosides in the presence of alkali metals: Biologically relevant quartets of guanosine,deoxyguanosine and uridine observed by ESI-MS/MS

Electrospray ionization (ESI) mass spectra of nucleosides, recorded in the presence of alkali metals, display alkali metal ion-bound quartets and other clusters that may have implications for understanding non-covalent interactions in DNA and RNA. The tetramers of guanosine and deoxyguanosine and also their metaclusters (clusters of clusters), cationized by alkali metals, were observed as unusually abundant magic number clusters. The observation of these species in the gas phase parallels previous condensed-phase studies, which show that guanine derivatives can form quartets and metaclusters of quartets in solution in the presence of metal cations. This parallel behavior and also internal evidence suggest that bonding in the guanosine tetramers involves the bases rather than the sugar units. The nucleobases thymine and uracil are known to form magic number pentameric adducts with K+, Cs+ and NH4+ in the gas phase. In sharp contrast, we now show that the nucleosides uridine and deoxythymidine do not form the pentameric clusters characteristic of the corresponding bases. More subtle effects of the sugars are evident in the fact that adenosine and cytidine form numerous higher order clusters with alkali metals, whereas deoxyadenosine and deoxycytidine show no clustering. It is suggested that hydrogen bonding between the bases in the tetramers of dG and rG are the dominant interactions in the clusters, hence changing the ribose group to deoxyribose (and vice versa) generally has little effect. However, the additional hydroxyl group of RNA nucleosides enhances the non-selective formation of higher-order aggregates for adenosine and cytidine and results in the lack of highly stable magic number clusters. Some clusters are the result of aggregation in the course of ionization (ESI) whereas others appear to be intrinsic to the solution being examined.     

Large mixed complexes involving uracil,cytosine, thymine and/or 1‐methyl uracil around Ca2+ ions: an electrospray ionization/MS study

We investigated the possible formation of mixed B_nB′_n′Ca²⁺ complexes where B and B′ are two different nucleobases. Electrospray ionization (ESI) mass spectrometric experiments from solutions containing two different kinds of nucleobases and calcium ions were carried out to investigate the formation of magic number clusters that may be relevant in a biological point of view. The results presented here clearly show that mixed complexes can be formed and are stable in the gas phase. This represents an important step toward more complex solutions in which several nucleobases are present simultaneously and may compete in the formation of cationized clusters. We believe that thorough investigations on such systems may help understanding biological processes that may effect the tridimensional structure of the DNA macromolecule. The formation of mixed hexamers, decamers, dodecamers and tetradecamers are clearly favored from solution containing uracil (Ura), thymine (Thy) and Ca²⁺, whereas mixed octamers are preferred from 1‐methyl uracil (MeU), uracil and Ca²⁺ mixtures. Cytosine (Cyto) can form mixed complexes with either uracil or 1‐methyl uracil or thymine. On the other hand, the main species formed in these latter cases are mixed tetramers. Copyright © 2013 John Wiley & Sons, Ltd.     

Interactions of nucleobases with alkali earth metal cations--electrospray ionization mass spectrometric study

Interactions of nucleobases with alkali earth metal cations have been studied by electrospray ionization mass spectrometry (ESI-MS). Nucleobases containing at least one oxygen atom form stable complexes with alkali earth metal cations. This phenomenon can be explained on the grounds of the well known theory of hard and soft acids and bases. Uracil and thymine make complexes only when in their deprotonoted forms. The cations of great radii (Sr(2+), Ba(2+)) are more prone to form complexes of stoichiometry 1:1 with uracil and thymine than the cations of small radii (Mg(2+), Ca(2+)). On the other hand, Mg(2+) forms complexes of stoichiometry 2:1 and 3:2 with uracil and thymine. Gas-phase stabilities of the 1:1 complexes are higher for the cations of small radii, in contrast to the solution stabilities. For cytosine and 9- methylhypoxantine the 1:1 complexes of their deprotonated forms are observed at higher cone voltage as a result of HCl molecule loss from the complexes containing the counter ion (Cl(-)). In solution, more stable complexes are formed with metal cations of low radii. Gas-phase stability of the complexes formed by deprotonated 9- methyl-hypoxantine increases with increasing metal cation radius.     

On the photoproduction of DNA/RNA cyclobutane pyrimidine dimers

The UV photoreactivity of different pyrimidine DNA/RNA nucleobases along the singlet manifold leading to the formation of cyclobutane pyrimidine dimers has been studied by using the CASPT2 level of theory. The initially irradiated singlet state promotes the formation of excimers between pairs of properly oriented nucleobases through the overlap between the ?? structures of two stacked nucleobases. The system evolves then to the formation of cyclobutane pyrimidine dimers via a shearing-type conical intersection activating a [2?+?2] photocycloaddition mechanism. The relative location of stable excimer conformations or alternative decay channels with respect to the reactive degeneracy region explains the differences in the photoproduction efficiency observed in the experiments for different nucleobases sequences. A comparative analysis of the main structural parameters and energetic profiles in the singlet manifold is carried out for thymine, uracil, cytosine, and 5-methylcytosine homodimers. Thymine and uracil dimers display the most favorable paths, in contrast to cytosine. Methylation of the nucleobases seems to increase the probability for dimerization.     

Helical supramolecular self-assembly by prolamide thymidine/uridine analogues

This report describes the syntheses of rationally designed non-sugar nucleoside as prolamide nucleosides which contain prolyl ring and pyrimidine nucleobases (uracil/thymine) via acetamide bonds. These nucleosides have propensity to form distinctive self-assembly supramolecular helical structures ubiquitously through Watson-Crick/reverse type of hydrogen bonding with nucleobases. Moreover, the prolyl acetamide backbone groups- carbonyl (-C = O) and hydroxyl (-OH) group, are also involved in strengthening of self-assembled helical structures. Importantly, both prolamide thymidine and prolamide uridine have shown two distinctive helical structural patterns, in spite of containing the same backbone. Hence thymine and uracil moieties of prolamide nucleosides are responsible for unique supramolecular helical structural architectures.     

Self-Assembling of cytosine nucleoside into triply-bound dimers in acid Media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry,X-rays diffractometry,and theoretical calculations

Electrospray tandem mass spectrometry (ESI-MS/MS) is used to evaluate the assembling of cytosine and thymine nucleosides in the gas phase, through the formation of hydrogen bonded supermolecules. Mixtures of cytidine analogues and homologues deliver in the gas phase proton-bound heterodimers stabilized by multiple interactions, as proven by the kinetics of their dissociation into the corresponding protonated monomers. Theoretical calculations, performed on initial structures of methylcytosine homodimers available in the literature, converged to a minimized structure whereby the two pyrimidine rings interact through the formation of three hydrogen bonds of similar energy. The crystallographic data here reported show the equivalency of the two interacting pyrimidines which is attributable to the presence of an inversion center. Thymine and uracil pyrimidyl nucleosides form, by ESI, gaseous proton-bound dimers. The kinetic of their dissociation into the related protonated monomers shows that the nucleobases are weekly interacting through a single hydrogen bond. The minimized structure of the protonated heterodimer formed by thymine and N-1-methylthymine confirmed the existence of mainly one hydrogen bond which links the two nucleobases through the O4 oxygens. No crystallographic data exists on thymine proton-bound species, nor have we been able to obtain these aggregates in the solid phase. The gaseous phase, under high vacuum conditions, seems therefore a suitable environment where vanishing structures produced by ESI can be studied with a good degree of approximation.     

Desorption electrospray ionization mass spectrometry of DNA nucleobases: implications for a liquid film model

Desorption electrospray ionization (DESI) mass spectrometry has been implemented on a commercial ion‐trap mass spectrometer and used to optimize mass spectrometric conditions for DNA nucleobases: adenine, cytosine, thymine, and guanine. Experimental parameters including spray voltage, distance between mass spectrometer inlet and the sampled spot, and nebulizing gas inlet pressure were optimized. Cluster ions including some magic number clusters of nucleobases were observed for the first time using DESI mass spectrometry. The formation of the cluster species was found to vary with the nucleobases, acidification of the spray solvent, and the deposited sample amount. All the experimental results can be explained well using a liquid film model based on the two‐step droplet pick‐up mechanism. It is further suggested that solubility of the analytes in the spray solvent is an important factor to consider for their studies by using DESI. Copyright © 2009 John Wiley & Sons, Ltd.     

Theoretical and gas-phase studies of specific cationized purine base quartet

Guanine tetraplexes are biological non-covalent systems stabilized by alkali cations. Thus, self-clustering of guanine, xanthine and hypoxanthine with alkali cations (Na(+), K(+) and Li(+)) is investigated by electrospray ionization mass spectrometry (ESI-MS) in order to provide new insights into G-quartets, hydrogen-bonded complexes. ESI assays displayed magic numbers of tetramer adducts with Na(+), Li(+) and K(+), not only for guanine, but also for xanthine bases. The optimized structures of guanine and xanthine quartets have been determined by B3LYP hybrid density functional theory calculations. Complexes of metal ions with quartets are classified into different structure types. The optimized structures obtained for each quartet explain the gas-phase results. The gas-phase binding sequence between the monovalent cations and the xanthine quartet follows the order Li(+) > Na(+) > K(+), which is consistent with that obtained for the guanine quartet in the literature. The smallest stabilization energy of K(+) and its position versus the other alkali metal ions in guanine and xanthine quartets is consistent with the fact that the potassium cation can be located between two guanine or xanthine quartets, for providing a [gua(or (xan))(8)+K](+) octamer adduct. Even if an abundant octamer adduct with K(+) for xanthine was detected by ESI-MS, it was not the case for guanine.     

Electrospray ionization mass spectrometry of pyrimidine base-rubidium complexes

Nucleobases and alkali metal cations, under electrospray ionisation conditions, tend to form the so-called magic number clusters (unusually stable clusters in comparison with the neighbouring ones). The effect of the ion source parameters, namely cone voltage and desolvation temperature and relative concentrations of thymine and RbCl on the [T5+Rb]+ ion abundance has been studied.     

Adsorption of DNA/RNA nucleobases on hexagonal boron nitride sheet: an ab initio study

Our ab initio calculations indicate that the interaction of deoxyribonucleic/ribonucleic acid (DNA/RNA) nucleobases [guanine (G), adenine (A), thymine (T), cytosine (C), and uracil (U)] with the hexagonal boron nitride (h-BN) sheet, a polar but chemically inert surface, is governed by mutual polarization. Unlike the case of graphene, all nucleobases exhibit the same stacking arrangement on the h-BN sheet due to polarization effects: the anions (N and O atoms) of nucleobases prefer to stay on top of cations (B) of the substrate as far as possible, regardless of the biological properties of nucleobases. The adsorption energies, ranging from 0.5 eV to 0.69 eV, increase in the order of U, C, T, A and G, which can be attributed to different side groups or atoms of nucleobases. The fundamental nature of DNA/RNA nucleobases and h-BN sheet remains unchanged upon adsorption, suggesting that the h-BN sheet is a promising template for DNA/RNA-related research, such as self-assembly.     

Natural resonance structures and aromaticity of the nucleobases

Natural resonance theory (NRT) and nucleus- independent chemical shift (NICS) analyses have been applied to the standard nucleobases adenine, guanine, cytosine, uracil, and thymine. The molecular electron densities were obtained from density functional theory calculations at the B3LYP level and ab initio calculations at the HF, MP2, and CCD levels. Compared with the dominance of the two Kekulé structures in benzene, the structural modifications in the forms of endocyclic heteroatoms and exocyclic substituents introduce various degrees of charge separation in nucleobases. As a result, the leading resonance structures for cytosine, uracil, and thymine are found to be covalent structures, but their weightings decrease to ~30% in the NRT expansion. For adenine and guanine, the covalent structures have weightings of ~20%, and the leading ionic resonance structures have weightings of as high as about 8%. Methods that include electron correlation effects, B3LYP, MP2, and CCD, give smaller weightings for the covalent structures than HF. However, MP2 and CCD results often include “strange” resonance structures with connections between unbonded vicinal atoms, making DFT at the B3LYP level the better choice for calculating these molecules’ electron density. The NICS at the ring center shows that the six-membered rings in cytosine, uracil, thymine, and guanine are nonaromatic with NICS within − 3 to − 1 ppm, while it is − 7.3 ppm for the six-membered ring in adenine. The NICS of the five-membered rings of adenine and guanine is around − 12 ppm, a slight decrease from the value of − 15.0 ppm for pyrrole.     

Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.     

Prebiotic Route to Thymine from Formamide—A Combined Experimental–Theoretical Study

Synthesis of RNA nucleobases from formamide is one of the recurring topics of prebiotic chemistry research. Earlier reports suggest that thymine, the substitute for uracil in DNA, may also be synthesized from formamide in the presence of catalysts enabling conversion of formamide to formaldehyde. In the current paper, we show that to a lesser extent conversion of uracil to thymine may occur even in the absence of catalysts. This is enabled by the presence of formic acid in the reaction mixture that forms as the hydrolysis product of formamide. Under the reaction conditions of our study, the disproportionation of formic acid may produce formaldehyde that hydroxymethylates uracil in the first step of the conversion process. The experiments are supplemented by quantum chemical modeling of the reaction pathway, supporting the plausibility of the mechanism suggested by Saladino and coworkers.     

Ab initio determination of the ionization potentials of DNA and RNA nucleobases

Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron spectra.     

X-ray absorption spectroscopy of the nucleotide bases at the carbon, nitrogen, and oxygen K-edges

Near-edge X-ray absorption fine structure spectra of three pyrimidine (viz., cytosine, uracil, and thymine) and two purine (viz., adenine and guanine) nucleobases, which are the key constituents of DNA and RNA, were measured at the C, N, and O K-edges using the self-absorption-free partial electron yield mode. The nucleobase samples were prepared as highly pure native polycrystalline powder films. The spectra are analyzed in terms of the electronic structure of the nucleobases. Subtle chemical effects related to the molecular structures of these heterocyclic compounds with extended pi-electron systems are considered and discussed.     

DNA Nucleobase under Ionizing Radiation: Unexpected Proton Transfer by Thymine Cation in Water Nanodroplets

The effect of ionizing radiation on DNA constituents is a widely studied fundamental process using experimental and computational techniques. In particular, radiation effects on nucleobases are usually tackled by mass spectrometry in which the nucleobase is embedded in a water nanodroplet. Here, we present a multiscale theoretical study revealing the effects and the dynamics of water droplets towards neutral and ionized thymine. In particular, by using both hybrid quantum mechanics/molecular mechanics and full ab initio molecular dynamics, we reveal an unexpected proton transfer from thymine cation to a nearby water molecule. This leads to the formation of a neutral radical thymine and a Zundel structure, while the hydrated proton localizes at the interface between the deprotonated thymine and the water droplet. This observation opens entirely novel perspectives concerning the reactivity and further fragmentation of ionized nucleobases.     

Photochemical Hydrogen Abstraction and Electron Transfer Reactions of Tetrachlorobenzoquinone with Pyrimidine Nucleobases

Pentachlorophenol, a widespread environmental pollutant that is possibly carcinogenic to humans, is metabolically oxidized to tetrachloroquinone (TCBQ) which can result in DNA damage. We have investigated the photochemical reaction dynamics of TCBQ with two pyrimidine type nucleobases (thymine and uracil) upon UVA (355 nm) excitation using the technique of nanosecond time-resolved laser flash photolysis. It has been found that 355 nm excitation populates TCBQ molecules to their triplet state ³TCBQ^*, which are highly reactive towards thymine or uracil and undergo two parallel reactions, the hydrogen abstraction and electron transfer, leading to the observed photoproducts of TCBQH· and TCBQ·^- in transient absorption spectra. The concomitantly produced nucleobase radicals and radical cations are expected to induce a series of oxidative or strand cleavage damage to DNA afterwards. By characterizing the photochemical hydrogen abstraction and electron transfer reactions, our results provide potentially important molecular reaction mechanisms for understanding the carcinogenic effects of pentachlorophenol and its metabolites TCBQ.     

Quinone sensitized electron transfer photooxidation of nucleic acids: chemistry of thymine and thymidine radical cations in aqueous solution

The 2-methyl-1,4-naphthoquinone (MQ) sensitized photooxidation of nucleic acid derivatives has been studied by laser flash photolysis and steady state methods. Thymine and thymidine, as well as other DNA model compounds, quench triplet MQ by electron transfer to give MQ radical anions and pyrimidine or purine radical cations. Although the pyrimidine radical cations cannot be directly observed by flash photolysis, the addition of N,N,N',N'-tetramethyl-1,4-phenylenediamine (TMPD) results in the formation of the TMPD radical cation via scavenging of the pyrimidine radical cation. The photooxidation products for thymine and thymidine are shown to result from subsequent chemical reactions of the radical cations in oxygenated aqueous solution. The quantum yield for substrate loss at limiting substrate concentrations is 0.38 for thymine and 0.66 for thymidine. The chemistry of the radical cations involves hydration by water leading to C(6)-OH adduct radicals of the pyrimidine and deprotonation from the N(1) position in thymine and the C(5) methyl group for thymidine. Superoxide ions produced via quenching of the quinone radical anion with oxygen appear to be involved in the formation of thymine and thymidine hydroperoxides and in the reaction with N(1)-thyminyl radicals to regenerate thymine. The effects of pH were examined in the range pH 5-8 in both the presence and absence of superoxide dismutase. Initial C(6)-OH thymine adducts are suggested to dehydrate to give N(1)-thyminyl radicals.     

Application of chromium‐doped fullerene as a carrier for thymine and uracil nucleotides: Comprehensive density functional theory calculations

The interactions of the nucleobases thymine (C₅H₆N₂O₂) and uracil (C₄H₄N₂O₂) with Cr‐doped C₂₀ fullerene (C₁₉Cr) are investigated by performing density functional theory calculations. The adsorption of these nucleobases on C₁₉Cr leads to two distinct geometries (P1 and P2) differing in the orientation of the nucleobases. The interaction of the nucleobases with the C₁₉Cr nanocluster is highly exothermic, revealing that they are chemically adsorbed on C₁₉Cr. The results show that the binding energy of the thymine–C₁₉Cr complex is slightly higher than that of the uracil–C₁₉Cr complex. In addition, the P2 geometry is more stable compared to P1 due to the higher binding energy in the former configuration. However, based on the results of natural bond orbital and frontier molecular orbitals analyses, the C₁₉Cr nanocage has higher reactivity with the nucleobases in P1 geometry in comparison with P2 due to the larger charge transfer and orbital hybridization in the former geometry. Moreover, the band gap of the C₁₉Cr nanocage decreases after interaction with the nucleobases, and interestingly the impact is more pronounced for P1 geometry, confirming the higher sensitivity of C₁₉Cr to the nucleobases in P1 geometry. Our findings reveal the promising potential of C₁₉Cr as an organometallic carrier for nucleobases thymine and uracil.