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.

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.

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.

Intramolecular charge transfer and dual fluorescence of 4-(dimethylamino)benzonitrile: ultrafast branching followed by a two-fold decay mechanism

In this contribution we present new experimental and theoretical results for the intramolecular charge transfer (ICT) reaction underlying the dual fluorescence of 4-(dimethylamino)benzonitrile (DMABN), which indicate that the fully twisted ICT (TICT) state is responsible for the time-resolved transient absorption spectrum while a distinct partially twisted ICT (pTICT) structure is suggested for the fluorescent ICT state.

Multiconfigurational Second-Order Perturbation Theory Restricted Active Space (RASPT2) Method for Electronic Excited States: A Benchmark Study

The recently developed second-order perturbation theory restricted active space (RASPT2) method has been benchmarked versus the well-established complete active space (CASPT2) approach. Vertical excitation energies for valence and Rydberg excited states of different groups of organic (polyenes, acenes, heterocycles, azabenzenes, nucleobases, and free base porphin) and inorganic (nickel atom and copper tetrachloride dianion) molecules have been computed at the RASPT2 and multistate (MS) RASPT2 levels using different reference spaces and compared with CASPT2, CCSD, and experimental data in order to set the accuracy of the approach, which extends the applicability of multiconfigurational perturbation theory to much larger and complex systems than previously. Relevant aspects in multiconfigurational excited state quantum chemistry such as the valence-Rydberg mixing problem in organic molecules or the double d-shell effect for first-row transition metals have also been addressed.

MOLCAS 7: the next generation

Some of the new unique features of the MOLCAS quantum chemistry package version 7 are presented in this report. In particular, the Cholesky decomposition method applied to some quantum chemical methods is described. This approach is used both in the context of a straight forward approximation of the two-electron integrals and in the generation of so-called auxiliary basis sets. The article describes how the method is implemented for most known wave functions models: self-consistent field, density functional theory, 2nd order perturbation theory, complete-active space self-consistent field multiconfigurational reference 2nd order perturbation theory, and coupled-cluster methods. The report further elaborates on the implementation of a restricted-active space self-consistent field reference function in conjunction with 2nd order perturbation theory. The average atomic natural orbital basis for relativistic calculations, covering the whole periodic table, are described and associated unique properties are demonstrated. Furthermore, the use of the arbitrary order Douglas-Kroll-Hess transformation for one-component relativistic calculations and its implementation are discussed. This section especially focuses on the implementation of the so-called picture-change-free atomic orbital property integrals. Moreover, the ElectroStatic Potential Fitted scheme, a version of a quantum mechanics/molecular mechanics hybrid method implemented in MOLCAS, is described and discussed. Finally, the report discusses the use of the MOLCAS package for advanced studies of photo chemical phenomena and the usefulness of the algorithms for constrained geometry optimization in MOLCAS in association with such studies.

The role of pyrimidine nucleobase excimers in DNA photophysics and photoreactivity

Quantum chemical studies using the accurate CASPT2//CASSCF procedure show that π-stacked interactions in biochromophores such as pyrimidine (Pyr) DNA/RNA nucleobases pairs yield excimer-like situations which behave as precursors of processes like charge transfer (CT) or photoreactivity and are the source of the emissive properties in DNA. Examples are the CT between adjacent DNA nucleobases in a strand of oligonucleotides and the photodimerization taking place in cytosine (C) pairs leading to cyclobutanecytosine (CBC) mutants. These processes take place through nonadiabatic photochemical mechanisms whose evolution is determined by the presence and accessibility of conical intersections (CIs) and other surface crossings between different electronic states.

The role of adenine excimers in the photophysics of oligonucleotides

Energies and structures of different arrangements of the stacked adenine homodimer have been computed at the ab initio CASPT2 level of theory in isolation and in an aqueous environment. Adenine dimers are shown to form excimer singlet states with different degrees of stacking and interaction. A model for a 2-fold decay dynamics of adenine oligomers can be supported in which, after initial excitation in the middle UV range, unstacked or slightly stacked pairs of nucleobases will relax by an ultrafast internal conversion to the ground state, localizing the excitation in the monomer and through the corresponding conical intersection with the ground state. On the other hand, long-lifetime intrastrand stacked excimer singlet states will be formed in different conformations, including neutral and charge transfer dimers, which originate the red-shifted emission observed in the oligonucleotide chains and that will evolve toward the same monomer decay channel after surmounting an energy barrier. By computing the transient absorption spectra for the different structures considered and their relative stability in vacuo and in water, it is concluded that in the adenine homodimers the maximum-overlap face-to-face orientations are the most stable excimer conformations observed in experiment.

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.

Determination of the electron-detachment energies of 2'-deoxyguanosine 5'-monophosphate anion: influence of the conformation

The vertical electron-detachment energies (VDEs) of the singly charged 2'-deoxyguanosine 5'-monophosphate anion (dGMP-) are determined by using the multiconfigurational second-order perturbation CASPT2 method at the MP2 ground-state equilibrium geometry of relevant conformers. The origin of the unique low-energy band in the gas phase photoelectron spectrum of dGMP-, with maximum at around 5.05 eV, is unambiguously assigned to electron detachment from the highest occupied molecular orbital of pi-character belonging to guanine fragment of a syn conformation. The presence of a short H-bond linking the 2-amino and phosphate groups, the guanine moiety acting as proton donor, is precisely responsible for the pronounced decrease of the computed VDE with respect to that obtained in other conformations. As a whole, the present research supports the nucleobase as the site with the lowest ionization potential in negatively charged (deprotonated) nucleotides at the most stable conformations as well as for B-DNA-like type arrangements, in agreement with experimental evidence.

Ab initio determination of the electron affinities of DNA and RNA nucleobases

High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic electron affinities of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. The present results aim for the accurate determination of the intrinsic electron acceptor properties of the isolated nucleic acid bases as described by their electron affinities, establishing an overall set of theoretical reference values at a level not reported before and helping to rule out less reliable theoretical and experimental data and to calibrate theoretical strategies.

Theoretical insight into the intrinsic ultrafast formation of cyclobutane pyrimidine dimers in UV-irradiated DNA: thymine versus cytosine

The higher formation yields measured in the ultrafast photoinduced formation of cyclobutane thymine dimers (T<>T) with respect to those of cytosine (C<>C) are explained, on the basis of ab initio CASPT2 results, by the existence in thymine of more reactive orientations and a less efficient photoreversibility, whereas in cytosine the funnel toward the photolesion becomes competitive with that mediating the internal conversion of the excited-cytosine monomer.

Molecular basis of DNA photodimerization: intrinsic production of cyclobutane cytosine dimers

Based on CASPT2 results, the present contribution establishes for the first time that cytosine photodimer formation (C< >C) is mediated along the triplet and singlet manifold by a singlet-triplet crossing, (T1/S0)X, and by a conical intersection, (S1/S0)CI, respectively. The former can be accessed in a barrierless way from a great variety of photochemical avenues and exhibits a covalent single bond between the ethene C6-C6' carbon atoms of each monomer. The efficiency of the stepwise triplet mechanism, however, would be modulated by the effectiveness of the intersystem crossing mechanism. The results provide the grounds for the understanding of the potential photogenotoxicity of endogenous and exogenous compounds via triplet-triplet sensitization, with a lower bound for cytosine oligonucleotides predicted to be 2.70 eV, and give support to the traditional view of the primary role of triplet excited states in the photochemistry of DNA, a well-known source of photoproducts in solution under triplet photosensitization conditions. The function played by singlet excimers (excited dimers) to explain both the red-shifted fluorescence and photoreaction is highlighted. A rationale on the pronounced wavelength dependence of the observed fluorescence is offered. Geometrical arrangements at the time of light irradiation close to, but energetically above, (S1/S0)CI are suggested as reactive orientations that become prone to produce C< >C directly, with no energy barrier. Because of the outstanding intrinsic ability of cytosine to form stable relaxed excimers, the system located near the bound relaxed excimer has to accumulate enough vibrational energy to surmount a small barrier of 0.2 eV to reach (S1/S0)CI, making the overall process to proceed at a slower relative rate as compared to other compounds such as thymine, which is not susceptible of forming so stable excimers.

Linear and nonlinear optical properties of some organoxenon derivatives

We employ a series of state-of-the-art computational techniques to study the effect of inserting one or more Xe atoms in HC2H and HC4H, on the linear and nonlinear optical (L&NLO) properties of the resulting compounds. It has been found that the inserted Xe has a great effect on the L&NLO properties of the organoxenon derivatives. We analyze the bonding in HXeC2H, and the change of the electronic structure, which is induced by inserting Xe, in order to rationalize the observed extraordinary L&NLO properties. The derivatives, which are of interest in this work, have been synthesized in a Xe matrix. Thus the effect of the local field (LF), due to the Xe environment, on the properties of HXeC2H, has also been computed. It has been found that the LF effect on some properties is significant. The calculations have been performed by employing a hierarchy of basis sets and the techniques MP2 and CCSD(T) for taking into account correlation. For the interpretation of the results we have employed the complete active space valence bond and CASSCF/CASPT2 methods.