The Absorption Spectrum of Cytosine Tautomers: Beyond the Static Approach

Prototropically Controlled Dynamics of Cytosine Photodecay

The effect of the existence of several prototropic tautomers of cytosine on its UV/vis spectra and the excited state decay dynamics is studied by spectral and nonadiabatic molecular dynamics (NAMD) simulations in connection with the mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. Simulated UV/vis spectra provide a strong indication that the H3N keto-amino cytosine tautomer (the least anticipated species) may be present under experimental conditions. The NAMD simulations yield a wide range of excited state decay constants for various tautomers of cytosine, ranging from ∼1.3 ps for the biologically relevant H1N keto-amino tautomer to ∼0.1 ps for the keto-imino tautomer. The slowness of the H1N decay dynamics follows from the presence of a barrier on the excited state energy surface separating the Franck-Condon structure from the major decay funnel, the conical intersection seam. It is suggested that the experimentally observed photodecay dynamics may result from a combination of the decay processes of various tautomers (H3N in particular) present simultaneously under the experimental conditions.

Charge-Tagged Nucleosides in the Gas Phase: UV-Vis Action Spectroscopy and Structures of Cytidine Cations, Dications, and Cation Radicals

Cytidine ribonucleosides were furnished at O5' with fixed-charge 6-trimethylammoniumhexan-1-aminecarbonyl tags and studied by UV-vis photodissociation action spectroscopy in the gas phase to probe isolated nucleobase chromophores in their neutral, protonated, and hydrogen-adduct radical forms. The action spectrum of the doubly charged cytidine conjugate showed bands at 310 and 270 nm that were assigned to the N3- and O2-protonated cytosine tautomers formed by electrospray, respectively. In contrast, cytidine conjugates coordinated to dibenzo-18-crown-6-ether (DBCE) in a noncovalent complex were found to strongly favor protonation at N3, forming a single-ion tautomer. This allowed us to form cytidine N3-H radicals by electron transfer dissociation of the complex and study their action spectra. Cytidine radicals showed only very weak absorption in the visible region of the spectrum for dipole-disallowed transitions to the low (A and B) excited states. The main bands were observed at 360, 300, and 250 nm that were assigned with the help of theoretical vibronic spectra obtained by time-dependent density functional theory calculations of multiple (>300) radical vibrational configurations. Collision-induced dissociations of cytidine radicals proceeded by major cleavage of the N1-C1' glycosidic bond leading to loss of cytosine and competitive loss of N3-hydrogen atom. These dissociations were characterized by calculations of transition-state structures and energies using combined Born-Oppenheimer molecular dynamics and DFT calculations. Overall, cytidine radicals were found to be kinetically and thermodynamically more stable than previously reported analogous adenosine and guanosine radicals.

Multiconfigurational Quantum Chemistry Determinations of Absorption Cross Sections (σ) in the Gas Phase and Molar Extinction Coefficients (ε) in Aqueous Solution and Air-Water Interface

Theoretical determinations of absorption cross sections (σ) in the gas phase and molar extinction coefficients (ε) in condensed phases (water solution, interfaces or surfaces, protein or nucleic acids embeddings, etc.) are of interest when rates of photochemical processes, J = ∫ ϕ(λ) σ(λ) I(λ) dλ, are needed, where ϕ(λ) and I(λ) are the quantum yield of the process and the irradiance of the light source, respectively, as functions of the wavelength λ. Efficient computational strategies based on single-reference quantum-chemistry methods have been developed enabling determinations of line shapes or, in some cases, achieving rovibrational resolution. Developments are however lacking for strongly correlated problems, with many excited states, high-order excitations, and/or near degeneracies between states of the same and different spin multiplicities. In this work, we define and compare the performance of distinct computational strategies using multiconfigurational quantum chemistry, nuclear sampling of the chromophore (by means of molecular dynamics, ab initio molecular dynamics, or Wigner sampling), and conformational and statistical sampling of the environment (by means of molecular dynamics). A new mathematical approach revisiting previous absolute orientation algorithms is also developed to improve alignments of geometries. These approaches are benchmarked through the nπ* band of acrolein not only in the gas phase and water solution but also in a gas-phase/water interface, a common situation for instance in atmospheric chemistry. Subsequently, the best strategy is used to compute the absorption band for the adduct formed upon addition of an OH radical to the C6 position of uracil and compared with the available experimental data. Overall, quantum Wigner sampling of the chromophore with molecular dynamics sampling of the environment with CASPT2 electronic-structure determinations arise as a powerful methodology to predict meaningful σ(λ) and ε(λ) band line shapes with accurate absolute intensities.

UV absorption spectra of DNA bases in the 350-190 nm range: assignment and state specific analysis of solvation effects

The theoretical assignment of electronic spectra of polyatomic molecules is a challenging problem that requires the specification of the character of a large number of electronic states. We propose a procedure for automatically determining the character of electronic transitions and apply it to the study of UV spectra of DNA bases in the gas phase and in the aqueous environment. The procedure is based on the computation of electronic wave function overlaps and accounts for an extensive sampling of nuclear geometries. Novelties of this work are the theoretical assignment of the electronic spectra of DNA bases up to 190 nm and a state specific analysis of solvation effects. By accounting for different effects contributing to the total solvent shift we obtained a good agreement between the computed and experimental spectra. Effects of vibrational averaging, temperature and solvent-induced structural changes shift excitation energies to lower values. Solvent-solute electrostatic interactions are state specific and strongly destabilize nRyd states, and to lesser extent nπ* and πRyd states. Altogether, this results in the stabilization of ππ* states and destabilization of nπ*, πRyd and nRyd states in solution.

Novel Molecular-Dynamics-Based Protocols for Phase Space Sampling in Complex Systems

The adequate exploration of the phase space of a chromophore is a fundamental necessity for the simulation of their optical and photophysical properties, taking into account the effects of vibrational motion and, most importantly, the coupling with a (non-homogeneous) molecular environment. A representative set of conformational snapshots around the Franck-Condon region is also required to perform non-adiabatic molecular dynamics, for instance in the framework of surface hopping. Indeed, in the latter case one needs to prepare a set of initial conditions providing a meaningful and complete statistical base for the subsequent trajectory propagation. In this contribution, we propose two new protocols for molecular dynamics-based phase space sampling, called "local temperature adjustment" and "individual QM/MM-based relaxation." These protocols are intended for situations in which the popular Wigner distribution sampling procedure is not applicable-as it is the case when anharmonic or nonlinear vibrations are present-and where regular molecular dynamics sampling might suffer from an inaccurate distribution of internal energy or from inaccurate force fields. The new protocols are applied to the case of phase space sampling of [Re(CO)3(Im)(Phen)]+ (im, imidazole; phen, phenanthroline) in aqueous solution, showing the advantages and limitations of regular Wigner and molecular dynamics sampling as well as the strengths of the new protocols.

Spin States and Other Ligand-Field States of Aqua Complexes Revisited with Multireference ab Initio Calculations Including Solvation Effects

High-level multireference (CASPT2, NEVPT2) calculations are reported for transition metal aqua complexes with electronic configurations from (3d)¹ to (3d)⁸. We focus on the experimentally evidenced excitation energies to their various ligand-field states, including different spin states. By employing models accounting for both explicit and implicit solvation, we find that solvation effect may contribute up to 0.5 eV to the excitation energies depending on the charge of ion and character of the electronic transition. We further demonstrate that with an adequate choice of the active space and the energetics extrapolated to the complete basis set limit, the presently computed excitation energies are in a good agreement with the experimental data. This allows us to conclusively resolve significant discrepancies reported in earlier theory works [e.g., J. Phys. Chem. C 2014 , 118 , 29196 - 29208 ]. For the benchmark set of 19 spin-forbidden and 24 spin-allowed transitions (for which experimental data are unambiguous), we find the mean absolute error of 0.15 or 0.13 eV and the maximum error of 0.56 or 0.42 eV for CASPT2 or NEVPT2 calculations, respectively. For the particularly challenging sextet-quartet gap for [Fe(H₂O)₆]³⁺, we support our interpretation by additional calculations with multireference configuration interaction (MRCI) and coupled cluster theory up to the CCSDT(Q) level. By underlining a rather subtle interplay between the solvation and correlation effects, the findings of this Article are relevant not only for modeling and interpretation of optical spectra of transition metal complexes but also in further benchmarking of theoretical methods for the challenging problem of spin-state energetics.

Phenylazopyridine as Switch in Photochemical Reactions. A Detailed Computational Description of the Mechanism of Its Photoisomerization

Azo compounds are organic photochromic systems that have the possibility of switching between cis and trans isomers under irradiation. The different photochemical properties of these isomers make azo compounds into good light-triggered switches, and their significantly different geometries make them very interesting as components in molecular engines or mechanical switches. For instance, azo ligands are used in coordination complexes to trigger photoresponsive properties. The light-induced trans-to-cis isomerization of phenylazopyridine (PAPy) plays a fundamental role in the room-temperature switchable spin crossover of Ni-porphyrin derivatives. In this work, we present a computational study developed at the SA-CASSCF/CASPT2 level (State Averaged Complete Active Space Self Consistent Field/CAS second order Perturbation Theory) to elucidate the mechanism, up to now unknown, of the cis-trans photoisomerization of 3-PAPy. We have analyzed the possible reaction pathways along its lowest excited states, generated by excitation of one or two electrons from the lone pairs of the N atoms of the azo group (n_azoπ*² and n_azo²π*² states), from a π delocalized molecular orbital (ππ* state), or from the lone pair of the N atom of the pyridine moiety (n_pyπ* state). Our results show that the mechanism proceeds mainly along the rotation coordinate in both the n_azoπ* and ππ* excited states, although the n_azo²π*² state can also be populated temporarily, while the n_pyπ* does not intervene in the reaction. For rotationally constrained systems, accessible paths to reach the cis minimum along planar geometries have also been located, again on the n_azoπ* and ππ* potential energy surfaces, while the n_azo²π*² and n_pyπ* states are not involved in the reaction. The relative energies of the different paths differ from those found for azobenzene in a previous work, so our results predict some differences between the reactivities of both compounds.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

Electronic excitation energies in dimers between radical ions presenting long, multicenter bonding

The formation of long, multicenter dimers between radical ions is usually monitored through UV-vis spectroscopy given the characteristic low-energy absorption band that they exhibit, not observed for the parent monomers. In this work, the performance of CASPT2, RASPT2, and TD-DFT methods for obtaining excitation energies of the long, multicenter bonded π-[TCNE]2(2-) and π-[TTF]2(2+) dimers has been addressed (TCNE = tetracyanoethylene; TTF = tetrathiafulvalene). The impact of the active space on the vertical electronic transitions computed at the RASPT2 and CASPT2 levels has been tested against experimentally observed absorption bands. Analogous tests have been carried out for a wide variety of density functionals within the TD-DFT formalism. Our calculations show that whereas CASPT2 predicts very accurate excitation energies for the π-[TCNE]2(2-), the mean absolute error for π-[TTF]2(2+) is higher for CASPT2 than for TD-DFT calculations, whenever pure density functionals or low % HF exchange hybrid functionals are used. Hybrid functionals with high % HF exchange (and thus RSH functionals) conduct to large errors on the excitation energies in both dimers. Furthermore, vertical electronic transitions are also obtained for 100 configurations extracted from a 45 ps molecular dynamics (CPMD) simulation aimed at providing an accurate description of the thermal fluctuation effects of a π-[TCNE]2(2-) dimer in dichloromethane. These thermal effects explain the shape of the experimental UV-vis spectrum, where the lowest HOMO → LUMO absorption presents a broad band and the following HOMO-1 → LUMO absorption exhibits a narrower band.

Modification of the optical spectrum of Cytosine by the formation of an ordered monolayer of molecules at a au(110)/electrolyte interface

An analysis of the reflection anisotropy spectrum (RAS) of an ordered monolayer of cytosine adsorbed at a Au(110)/electrolyte interface is found to contain optical contributions from both the substrate and the cytosine. The spectrum of cytosine in an aqueous environment is significantly broadened by the interaction between the molecule and the Au(110). Successful simulations of the Au(110)/cytosine interface consisting of two additional molecular transitions, which sit in the middle of previously observed molecular absorption bands, are produced by an empirical Lorentzian transition model that is consistent with previous theoretical and experimental studies. While this analysis alone cannot determine the number of π→π* dipole transitions, it confirms that the only cytosine transitions that contribute to the optical response of the Au(110)/cytosine interface are located in the plane of the molecule, which is vertical to the gold surface with the long axis along the [1$\bar 1$0] direction.

Dynamical effects on the magnetic properties of dithiazolyl bistable materials

The magnetic properties of molecule-based magnets are commonly rationalized by considering only a single nuclear configuration of the system under study (usually an X-ray crystal structure). Here, by means of a computational study, we compare the results obtained using such a static approach with those obtained by explicitly accounting for thermal fluctuations, and uncover the serious limitations of the static perspective when dealing with magnetic crystals whose radicals undergo wide-amplitude motions. As a proof of concept, these limitations are illustrated for the magnetically bistable 1,3,5-trithia-2,4,6-triazapentalenyl (TTTA) material. For its high-temperature phase at 300 K, we show that nuclear dynamics induce large fluctuations in the magnetic exchange interactions (JAB) between spins (up to 1000% of the average value). These deviations result in a ∼20% difference between the 300 K magnetic susceptibility computed by explicitly considering the nuclear dynamics and that computed using the X-ray structure, the former being in better agreement with the experimental data. The unveiled strong coupling between JAB interactions and intermolecular vibrations reveals that considering JAB as a constant value at a given temperature (as always done in molecular magnetism) leads to a flawed description of the magnetism of TTTA. Instead, the physically relevant concept in this case is the statistical distribution of JAB values. The discovery that a single X-ray structure is not adequate enough to interpret the magnetic properties of TTTA is also expected to be decisive in other organic magnets with dominant exchange interactions propagating through labile π-π networks.

ABSORPTION SPECTRA OF NUCLEIC ACID BASES IN WATER ENVIRONMENT: INSIGHTS INTO FROM COMBINED QM/MM AND CLUSTER-CONTINUUM MODEL CALCULATIONS

Electronic spectra of uracil, thymine, adenine, guanine, and cytosine in the gas phase and aqueous solution have been studied by extensive time-dependent density functional calculations. Calculations show that the Quantum mechanics/molecular mechanics (QM/MM) geometry optimization based on the molecular dynamics (MD) equilibrated configuration can locate an optimal solvated cluster for the base solvation, and the combined QM/MM and cluster-continuum computational protocol is capable of handling the solvent effect on the excited states of nucleic acid bases and providing realistic absorption spectra in water environment with relatively low computational costs. Generally, the vertical excitation energies in aqueous solution by PCM/TD-X3LYP calculations show excellent agreement with the experimental observations and the maximum deviation is less than 0.2 eV. The present results reveal that the hydrogen bond network around the excited-state base and its dipole moment change may remarkably modify the absorption spectra of nucleic acid bases in aqueous solution.