Mechanism of the OH Radical Addition to Adenine from Quantum-Chemistry Determinations of Reaction Paths and Spectroscopic Tracking of the Intermediates.

The OH radical is a well-known mediator in the oxidation of biological structures like DNA. Over the past decades, the precise events taking place after reaction of DNA nucleobases with OH radical have been widely investigated by the scientific community. Thirty years after the proposal of the main routes for the reaction of •OH with adenine ( Vieira , A. ; Steenken , S. J. Am. Chem. Soc. 1990 , 112 , 6986 - 6994 ), the present work demonstrates that the OH radical addition to C4 position is a minor pathway. Instead, the dehydration process is mediated by the A5OH adduct. Conclusions are based on density functional theory calculations for the ground-state reactivity and highly accurate multiconfigurational computations for the excited states of the radical intermediates. The methodology has been also used to study the mechanism giving rise to the mutagens 8-oxoA and FAPyA. Taking into account the agreement between the experimental data and the theoretical results, it is concluded that addition to the C5 and C8 positions accounts for at least ∼44.5% of the total •OH reaction in water solution. Finally, the current findings suggest that hydrophobicity in the DNA/RNA surroundings facilitates the formation of 8-oxoA and FAPyA.

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2.

The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted ¹(ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected.

Complete-active-space second-order perturbation theory (CASPT2//CASSCF) study of the dissociative electron attachment in canonical DNA nucleobases caused by low-energy electrons (0-3 eV).

Low-energy (0-3 eV) ballistic electrons originated during the irradiation of biological material can interact with DNA/RNA nucleobases yielding transient-anion species which undergo decompositions. Since the discovery that these reactions can eventually lead to strand breaking of the DNA chains, great efforts have been dedicated to their study. The main fragmentation at the 0-3 eV energy range is the ejection of a hydrogen atom from the specific nitrogen positions. In the present study, the methodological approach introduced in a previous work on uracil [I. González-Ramírez et al., J. Chem. Theory Comput. 8, 2769-2776 (2012)] is employed to study the DNA canonical nucleobases fragmentations of N-H bonds induced by low-energy electrons. The approach is based on minimum energy path and linear interpolation of internal coordinates computations along the N-H dissociation channels carried out at the complete-active-space self-consistent field//complete-active-space second-order perturbation theory level. On the basis of the calculated theoretical quantities, new assignations for the adenine and cytosine anion yield curves are provided. In addition, the π1 (-) and π2 (-) states of the pyrimidine nucleobases are expected to produce the temporary anions at electron energies close to 1 and 2 eV, respectively. Finally, the present theoretical results do not allow to discard neither the dipole-bound nor the valence-bound mechanisms in the range of energies explored, suggesting that both possibilities may coexist in the experiments carried out with the isolated nucleobases.

Excitation of nucleobases from a computational perspective I: reaction paths.

The main intrinsic photochemical events in nucleobases can be described on theoretical grounds within the realm of non-adiabatic computational photochemistry. From a static standpoint, the photochemical reaction path approach (PRPA), through the computation of the respective minimum energy path (MEP), can be regarded as the most suitable strategy in order to explore the electronically excited isolated nucleobases. Unfortunately, the PRPA does not appear widely in the studies reported in the last decade. The main ultrafast decay observed experimentally for the gas-phase excited nucleobases is related to the computed barrierless MEPs from the bright excited state connecting the initial Franck-Condon region and a conical intersection involving the ground state. At the highest level of theory currently available (CASPT2//CASPT2), the lowest excited (1)(ππ*) hypersurface for cytosine has a shallow minimum along the MEP deactivation pathway. In any case, the internal conversion processes in all the natural nucleobases are attained by means of interstate crossings, a self-protection mechanism that prevents the occurrence of photoinduced damage of nucleobases by ultraviolet radiation. Many alternative and secondary paths have been proposed in the literature, which ultimately provide a rich and constructive interplay between experimentally and theoretically oriented research.

Theoretical study of the hydroxyl radical addition to uracil and photochemistry of the formed U6OH• adduct.

Hydroxyl radical ((•)OH) is produced in biological systems by external or endogenous agents. It can damage DNA/RNA by attacking pyrimidine nucleobases through the addition to the C5═C6 double bond. The adduct resulting from the attachment at the C5 position prevails in the experimental measurements, although the reasons for this preference remain unclear. The first aim of this work is therefore to shed light on the comprehension of this important process. Thus, the thermal (•)OH addition to the C5═C6 double bond of uracil has been studied theoretically by using DFT, MP2, and the multiconfigurational CASPT2//CASSCF methodologies. The in-vacuo results obtained with the latter protocol plus the analysis of solvent effects support the experimental observation. A significant lower barrier height is predicted for the C5 pathway with respect to that of the C6 route. In contrast to the C5 adduct, the C6 adduct is able to absorb visible light. Hence, the second aim of the work is to study the photochemistry of this species using the CASPT2//CASSCF methodology within the framework of the photochemical reaction path approach (PRPA). The nonradiative decay to the ground state of this compound has been characterized. A photoreactive character is predicted for the C6 adduct in the excited states according to the presence of excited-state minima along the main decay channel. Finally, a new mechanism of photodissociation has been explored, which implies the photoinduced regeneration of the canonical nucleobase by irradiating with visible light, being therefore relevant in RNA protection against damage by reactive oxygen species.

Relaxation Mechanisms of 5-Azacytosine.

The photophysics and deactivation pathways of the noncanonical 5-azacytosine nucleobase were studied using the CASPT2//CASSCF protocol. One of the most significant differences with respect to the parent molecule cytosine is the presence of a dark (1)(nNπ*) excited state placed energetically below the bright excited state (1)(ππ*) at the Franck-Condon region. The main photoresponse of the system is a presumably efficient radiationless decay back to the original ground state, mediated by two accessible conical intersections involving a population transfer from the (1)(ππ*) and the (1)(nNπ*) states to the ground state. Therefore, a minor contribution of the triplet states in the photophysics of the system is expected, despite the presence of a deactivation path leading to the lowest (3)(ππ*) triplet state. The global scenario on the photophysics and photochemistry of the 5-azacytosine system gathered on theoretical grounds is consistent with the available experimental data, taking especially into account the low values of the singlet-triplet intersystem crossing and fluorescence quantum yields observed.

Communication: Electronic UV-Vis transient spectra of the ∙OH reaction products of uracil, thymine, cytosine, and 5,6-dihydrouracil by using the complete active space self-consistent field second-order perturbation (CASPT2//CASSCF) theory.

Addition of ∙OH radicals to pyrimidine nucleobases is a common reaction in DNA/RNA damage by reactive oxygen species. Among several experimental techniques, transient absorption spectroscopy has been during the last decades used to characterize such compounds. Discrepancies have however appeared in the assignment of the adduct or adducts responsible for the reported transient absorption UV-Vis spectra. In order to get an accurate assignment of the transient spectra and a unified description of the absorption properties of the ∙OH reaction products of pyrimidines, a systematic complete active space self-consistent field second-order perturbation (CASPT2//CASSCF) theory study has been carried out on the uracil, thymine, and cytosine ∙OH addition adducts, as well as on the 5,6-dihydrouracil hydrogen abstraction products. With the obtained findings, the C5OH contributions to the lowest-energy band can be finally discarded. Instead, a bright (2)(π2) state of the C6OH adducts is determined to be the main responsible in all compounds for the absorption band in the Vis range.

Tuning the photophysical properties of anti-B18H22: efficient intersystem crossing between excited singlet and triplet states in new 4,4'-(HS)2-anti-B18H20.

The tuning of the photophysical properties of the highly fluorescent boron hydride cluster anti-B18H22 (1), by straightforward chemical substitution to produce 4,4'-(HS)2-anti-B18H20 (2), facilitates intersystem crossing from excited singlet states to a triplet manifold. This subsequently enhances O2((1)Δg) singlet oxygen production from a quantum yield of ΦΔ âˆ¼ 0.008 in 1 to 0.59 in 2. This paper describes the synthesis and full structural characterization of the new compound 4,4'-(HS)2-anti-B18H20 (2) and uses UV-vis spectroscopy coupled with density functional theory (DFT) and ab initio computational studies to delineate and explain its photophysical properties.

Photoinduced formation mechanism of the thymine-thymine (6-4) adduct.

The photoinduced mechanism leading to the formation of the thymine-thymine (6-4) photolesion has been studied by using the CASPT2//CASSCF approach over a dinucleotide model in vacuo. Following light absorption, localization of the excitation on a single thymine leads to fast singlet-triplet crossing that populates the triplet (3)(nπ*) state of thymine. This state, displaying an elongated C(4)═O bond, triggers (6-4) dimer formation by reaction with the C(5)═C(6) double bond of the adjacent thymine, followed by a second intersystem crossing, which acts as a gate between the excited state of the reactant and the ground state of the photoproduct. The requirement of localized excitation on just one thymine, whose main decay channel (by radiationless repopulation of its ground state) is nonphotochemical, can rationalize the experimentally observed low quantum yield of formation for the thymine-thymine (6-4) adduct.

Proton/Hydrogen Transfer Mechanisms in the Guanine-Cytosine Base Pair: Photostability and Tautomerism.

Proton/hydrogen-transfer processes have been broadly studied in the past 50 years to explain the photostability and the spontaneous tautomerism in the DNA base pairs. In the present study, the CASSCF/CASPT2 methodology is used to map the two-dimensional potential energy surfaces along the stretched NH reaction coordinates of the guanine-cytosine (GC) base pair. Concerted and stepwise pathways are explored initially in vacuo, and three mechanisms are studied: the stepwise double proton transfer, the stepwise double hydrogen transfer, and the concerted double proton transfer. The results are consistent with previous findings related to the photostability of the GC base pair, and a new contribution to tautomerism is provided. The C-based imino-oxo and imino-enol GC tautomers, which can be generated during the UV irradiation of the Watson-Crick base pair, have analogous radiationless energy-decay channels to those of the canonical base pair. In addition, the C-based imino-enol GC tautomer is thermally less stable. A study of the GC base pair is carried out subsequently taking into account the DNA surroundings in the biological environment. The most important stationary points are computed using the quantum mechanics/molecular mechanics (QM/MM) approach, suggesting a similar scenario for the proton/hydrogen-transfer phenomena in vacuo and in DNA. Finally, the static model is complemented by ab initio dynamic simulations, which show that vibrations at the hydrogen bonds can indeed originate hydrogen-transfer processes in the GC base pair. The relevance of the present findings for the rationalization of the preservation of the genetic code and mutagenesis is discussed.

Ab initio determination of the ionization potentials of water clusters (H2O)n (n = 2-6).

High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic ionization potentials of several water clusters: dimer, trimer, tetramer, pentamer, hexamer book, hexamer ring, hexamer cage, and hexamer prism. The present results establish reference values at a level not reported before for these systems, calibrating different computational strategies and helping to discard less reliable theoretical and experimental data. The systematic study with the increasing size of the water cluster allows obtaining some clues on the structure and reductive properties of liquid water.

On the deactivation mechanisms of adenine-thymine base pair.

In this contribution, the multiconfigurational second-order perturbation theory method based on a complete active space reference wave function (CASSCF/CASPT2) is applied to study all possible single and double proton/hydrogen transfers between the nucleobases in the adenine-thymine (AT) base pair, analyzing the role of excited states with different nature [localized (LE) and charge transfer (CT)], and considering concerted as well as step-wise mechanisms. According to the findings, once the lowest excited states, localized in adenine, are populated during UV irradiation of the Watson-Crick base pair, the proton transfer in the N-O bridge does not require high energy in order to populate a CT state. The latter state will immediately relax toward a crossing with the ground state, which will funnel the system to either the canonical structure or the imino-enol tautomer. The base pair is also capable of repairing itself easily since the imino-enol species is unstable to thermal conversion.

On the photophysics and photochemistry of the water dimer.

The photochemistry of the water dimer irradiated by UV light is studied by means of the complete active space perturbation theory//complete active space self-consistent field (CASPT2//CASSCF) method and accurate computational approaches like as minimum energy paths. Both electronic structure computations and ab initio molecular dynamics simulations are carried out. The results obtained show small shifts relative to a single water molecule on the vertical excitation energies of the dimer due to the hydrogen bond placed between the water donor (W(D)) and the water acceptor (W(A)). A red-shift and a blue-shift are predicted for the W(D) and W(A), respectively, supporting previous theoretical and experimental results. The photoinduced chemistry of the water dimer is described as a process occurring between two single water molecules in which the effect of the hydrogen bond plays a minor role. Thus, the photoinduced decay routes correspond to two photodissociation processes, one for each water molecule. The proposed mechanism for the decay channels of the lowest-lying excited states of the system is established as the photochemical production of a hydrogen-bonded H(2)O...HO species plus a hydrogen H atom.

On the N1-H and N3-H Bond Dissociation in Uracil by Low Energy Electrons: A CASSCF/CASPT2 Study.

The dissociative electron-attachment (DEA) phenomena at the N1-H and N3-H bonds observed experimentally at low energies (<3 eV) in uracil are studied with the CASSCF/CASPT2 methodology. Two valence-bound π(-) and two dissociative σ(-) states of the uracil anionic species, together with the ground state of the neutral molecule, are proven to contribute to the shapes appearing in the experimental DEA cross sections. Conical intersections (CI) between the π(-) and σ(-) are established as the structures which activate the DEA processes. The N1-H and N3-H DEA mechanisms in uracil are described, and experimental observations are interpreted on the basis of two factors: (1) the relative energy of the (U-H)(-) + H fragments obtained after DEA with respect to the ground-state equilibrium structure (S0) of the neutral molecule (threshold for DEA) and (2) the relative energy of the CIs also with respect to S0 (band maxima). The π1(-) state is found to be mainly responsible for the N1-H bond breaking, whereas the π2(-) state is proved to be involved in the cleavage of the N3-H bond.

A distance-dependent parameterization of the extended Hubbard model for conjugated and aromatic hydrocarbons derived from stretched ethene.

The Hubbard model, which is widely used in physics but is mostly unfamiliar to chemists, provides an attractive yet simple model for chemistry beyond the self consistent field molecular orbital approximation. The Hubbard model adds an effective electron-electron repulsion when two electrons occupy the same atomic orbital to the familiar Hückel Hamiltonian. Thus it breaks the degeneracy between excited singlet and triplet states and allows an explicit treatment of electron correlation. We show how to evaluate the parameters of the model from high-level ab initio calculations on two-atom fragments and then to transfer the parameters to large molecules and polymers where accurate ab initio calculations are difficult or impossible. The recently developed MS-RASPT2 method is used to generate accurate potential energy curves for ethene as a function of carbon-carbon bond length, which are used to parameterize the model for conjugated hydrocarbons. Test applications to several conjugated/aromatic molecules show that even though the model is very simple, it is capable of reasonably accurate predictions for bond lengths, and predicts molecular excitation energies in reasonable agreement with those from the MS-RASPT2 method.

Essential on the Photophysics and Photochemistry of the Indole Chromophore by Using a Totally Unconstrained Theoretical Approach.

Indole is a chromophore present in many different molecules of biological interest, such as the essential amino acid tryptophan and the neurotransmitter serotonin. On the basis of CASPT2//CASSCF quantum chemical calculations, the photophysical properties of the system after UV irradiation have been studied through the exploration of the potential energy hypersurfaces of the singlet and triplet low-lying valence excited states. In contrast to previous studies, the present work has been carried out without imposing any restriction to the geometry of the molecule (C1 symmetry) and by performing minimum energy path calculations, which is the only instrument able to provide the lowest-energy evolution of the system. Relevant findings to the photophysics of bare indole have been obtained, which compete with the currently accepted mechanism for the energy decay in the molecule. The results show the presence of a conical intersection (CI) between the initially populated (1)(La ππ*) and the (1)(Lb ππ*) state, easily accessible through a barrierless pathway from the Franck-Condon region. At this CI region, part of the population is switched from the bright (1)(La ππ*) state to the (1)(Lb ππ*) state, and the system evolves toward a minimum structure from which the expected fluorescence takes place. The reported low values of the fluorescence quantum yield are explained by means of a new nonradiative mechanism specific for the (1)(Lb ππ*) state, in which the presence of an ethene-like CI between the (Lb ππ*) and ground states is the main feature.

Singlet-Triplet States Interaction Regions in DNA/RNA Nucleobase Hypersurfaces.

The present study provides new insight into the intrinsic mechanisms for the population of the triplet manifold in DNA nucleobases by determining, at the multiconfigurational CASSCF/CASPT2 level, the singlet-triplet states crossing regions and the main decay paths for their lowest singlet and triplet states after near-UV irradiation. The studied singlet-triplet interacting regions are accessible along the minimum energy path of the initially populated singlet bright (1)ππ* state. In particular, all five natural DNA/RNA nucleobases have, at the end of the main minimum energy path and near a conical intersection of the ground and (1)ππ* states, a low-energy, easily accessible, singlet-triplet crossing region directly connecting the lowest singlet and triplet ππ* excited states. Adenine, thymine, and uracil display additional higher-energy crossing regions related to the presence of low-lying singlet and a triplet nπ* state. These funnels are absent in guanine and cytosine, which have the bright (1)ππ* state lower in energy and less accessible nπ* states. Knowledge of the location and accessibility of these regions, in which the singlet-triplet interaction is related to large spin-orbit coupling elements, may help to understand experimental evidence such as the wavelength dependence measured for the triplet formation quantum yield in nucleobases and the prevalence of adenine and thymine components in the phosphorescence spectra of DNA.

Photophysics of 1-aminonaphthalene: a theoretical and time-resolved experimental study.

The photophysics of 1-aminonaphthalene (1-napthylamine, AMN) has been investigated on the basis of a constructive experimental-theoretical interplay derived from time-resolved measurements and high-level quantum-chemical ab initio CASPT2//CASSCF calculations. Transient ionization signals at femtosecond resolution were collected for AMN cold isolated molecules following excitation from the vibrationless ground level to a number of vibrational states (within the pump resolution) in the lowest accessible excited state and further multiphoton ionization probing at 500, 800, and 1300 nm. Theory predicts two pipi* states, (1)L(b) and (1)L(a), as the lowest singlet electronic excitations, with adiabatic transitions from S(0) at 3.50 and 3.69 eV, respectively. Since the associated oscillator strength for the lowest transition is exceedingly small, the (1)L(b) state is not expected to become populated significantly and the (1)L(a) state appears as the main protagonist of the AMN photophysics. Though calculations foresee a surface crossing between (1)L(a) and the lower (1)L(b) states, no dynamical signature of it is observed in the time-dependent measurements. In the relaxation of (1)L(a), the radiant emission competes with the intersystem crossing and internal conversion channels. The rates of these mechanisms have been determined at different excitation energies. The internal conversion is mediated by a (1)L(a)/S(0) conical intersection located 0.7 eV above the (1)L(a) minimum. The relaxation of a higher-lying singlet excited state, observed above 40 000 cm(-1) (4.96 eV) and calculated at 5.18 eV, has been also explored.

Deciphering intrinsic deactivation/isomerization routes in a phytochrome chromophore model.

High level ab initio correlated (CASPT2) computations have been used to elucidate the details of the photoinduced molecular motion and decay mechanisms of a realistic phytochrome chromophore model in vacuo and to explore the reasons underneath its photophysical/photochemical properties. Competitive deactivation routes emerge that unveil the primary photochemical event and the intrinsic photoisomerization ability of this system. The emerged in vacuo based static (i.e., nondynamical) reactivity model accounts for the formation of different excited state intermediates and suggests a qualitative rationale for the short (picosecond) excited state lifetime and ultrafast decay of the emission, its small quantum yield, and the multiexponential decay observed in both solvent and phytochromes. It is thus tentatively suggested that this is a more general deactivation scheme for photoexcited phytochrome chromophores that is independent of the surrounding environment. Spectroscopic properties have also been simulated in both isolated conditions and the protein that satisfactorily match experimental data. For this purpose, preliminary hybrid QM/MM computations at the correlated (CASPT2) level have been used in the protein and are reported here for the first time.

Electrostatic control of the photoisomerization efficiency and optical properties in visual pigments: on the role of counterion quenching.

Hybrid QM(CASPT2//CASSCF/6-31G*)/MM(Amber) computations have been used to map the photoisomerization path of the retinal chromophore in Rhodopsin and explore the reasons behind the photoactivity efficiency and spectral control in the visual pigments. It is shown that while the electrostatic environment plays a central role in properly tuning the optical properties of the chromophore, it is also critical in biasing the ultrafast photochemical event: it controls the slope of the photoisomerization channel as well as the accessibility of the S(1)/S(0) crossing space triggering the ultrafast decay. The roles of the E113 counterion, the E181 residue, and the other amino acids of the protein pocket are explicitly analyzed: it appears that counterion quenching by the protein environment plays a key role in setting up the chromophore's optical properties and its photochemical efficiency. A unified scenario is presented that discloses the relationship between spectroscopic and mechanistic properties in rhodopsins and allows us to draw a solid mechanism for spectral tuning in color vision pigments: a tunable counterion shielding appears as the elective mechanism for L<-->M spectral modulation, while a retinal conformational control must dictate S absorption. Finally, it is suggested that this model may contribute to shed new light into mutations-related vision deficiencies that opens innovative perspectives for experimental biomolecular investigations in this field.