Relative Stability of the La and Lb Excited States in Adenine and Guanine: Direct Evidence from TD-DFT Calculations of MCD Spectra

Extreme ultraviolet time-resolved photoelectron spectroscopy of adenine, adenosine and adenosine monophosphate in a liquid flat jet

Time-resolved photoelectron spectroscopy using an extreme-ultraviolet (XUV) probe pulse was used to investigate the UV photoinduced dynamics of adenine (Ade), adenosine (Ado), and adenosine-5-monophosphate (AMP) in a liquid water jet. In contrast to previous studies using UV probe pulses, the XUV pulse at 21.7 eV can photoionize all excited states of a molecule, allowing for full relaxation pathways to be addressed after excitation at 4.66 eV. This work was carried out using a gas-dynamic flat liquid jet, resulting in considerably enhanced signal compared to a cylindrical jet. All three species decay on multiple time scales that are assigned based on their decay associated spectra; the fastest decay of ∼100 fs is assigned to ππ* decay to the ground state, while a smaller component with a lifetime of ∼500 fs is attributed to the nπ* state. An additional slower channel in Ade is assigned to the 7H Ade conformer, as seen previously. This work demonstrates the capability of XUV-TRPES to disentangle non-adiabatic dynamics in an aqueous solution in a state-specific manner and represents the first identification of the nπ* state in the relaxation dynamics of adenine and its derivatives.

Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study

We study the excited state absorption (ESA) properties of the four DNA bases (thymine, cytosine, adenine, and guanine) by different single reference quantum mechanical methods, namely, equation of motion coupled cluster singles and doubles (EOM-CCSD), singles, doubles and perturbative triples (EOM-CC3), and time-dependent density functional theory (TD-DFT), with the long-range corrected CAM-B3LYP functional. Preliminary results at the Tamm-Dancoff (TDA) CAM-B3LYP level using the maximum overlap method (MOM) are reported for thymine. In the gas phase, the three methods predict similar One Photon Absorption (OPA) spectra, which are consistent with the experimental results and with the most accurate computational studies available in the literature. The ESA spectra are then computed for the ππ* states (one for pyrimidine, two for purines) associated with the lowest-energy absorption band, and for the close-lying nπ* state. The EOM-CC3, EOM-CCSD and CAM-B3LYP methods provide similar ESA spectral patterns, which are also in qualitative agreement with literature RASPT2 results. Once validated in the gas phase, TD-CAM-B3LYP has been used to compute the ESA in chloroform, including solvent effects by the polarizable continuum model (PCM). The predicted OPA and ESA spectra in chloroform are very similar to those in the gas phase, most of the bands shifting by less than 0.1 eV, with a small increase of the intensities and a moderate destabilization of the nπ* state. Finally, ESA spectra have been computed from the minima of the lowest energy ππ* state, and found in line with the available experimental transient absorption spectra of the nucleosides in solution, providing further validation of our computational approach.

Molecular Identification of the Transient Species Mediating the Deactivation Dynamics of Solvated Guanosine and Deazaguanosine

Small structural alterations of the purine/pyrimidine core have been related to important photophysical changes, such as the loss of photostability. Similarly to canonical nucleobases, solute-solvent interactions can lead to a change in the excited state lifetimes and/or to the interplay of different states in the photophysics of these modified nucleobases. To shed light on both effects, we here report a complete picture of the absorption spectra and excited state deactivation of deoxyguanosine and its closely related derivative, deoxydeazaguanosine, in water and methanol through the mapping of the excited state potential energy surfaces and molecular dynamics simulations at the TD-DFT level of theory. We show that the N by CH exchange in the imidazole ring of deoxyguanosine translates into a small red-shift of the bright states and slightly faster dynamics. In contrast, changing solvent from water to methanol implies the opposite, i.e., that the deactivation of both systems to the ground state is significantly hindered.

The Ultrafast Quantum Dynamics of Photoexcited Adenine-Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling Model

In this contribution we present a quantum dynamical study of the photoexcited hydrogen bonded base pair adenine–thymine (AT) in a Watson–Crick arrangement. To that end, we parametrize Linear Vibronic Coupling (LVC) models with Time-Dependent Density Functional Theory (TD-DFT) calculations, exploiting a fragment diabatization scheme (FrD) we have developed to define diabatic states on the basis of individual chromophores in a multichromophoric system. Wavepacket propagations were run with the multilayer extension of the Multiconfiguration Time-Dependent Hartree method. We considered excitations to the three lowest bright states, a ππ* state of thymine and two ππ* states (L_a and L_b) of adenine, and we found that on the 100 fs time scale the main decay pathways involve intramonomer population transfers toward nπ* states of the same nucleobase. In AT this transfer is less effective than in the isolated nucleobases, because hydrogen bonding destabilizes the nπ* states. The population transfer to the A → T charge transfer state is negligible, making the ultrafast (femtosecond) decay through the proton coupled electron transfer mechanism unlikely, in line with experimental results in apolar solvents. The excitation energy transfer is also very small. We carefully compare the predictions of LVC Hamiltonians obtained with different sets of diabatic states, defined so to match either local states of the two separated monomers or the base pair adiabatic states in the Franck–Condon region. To that end we also extend the flexibility of the FrD-LVC approach, introducing a new strategy to define fragments diabatic states that account for the effect of the rest of the multichromohoric system through a Molecular Mechanics potential.

Ultrafast Dynamics of the Isolated Adenosine-5'-triphosphate Dianion Probed by Time-Resolved Photoelectron Imaging

The excited state dynamics of the doubly deprotonated dianion of adenosine-5'-triphosphate, [ATP-H₂]^2-, has been spectroscopically explored by time-resolved photoelectron spectroscopy following excitation at 4.66 eV. Time-resolved photoelectron spectra show that two competing processes occur for the initially populated ¹ππ* state. The first is rapid electron emission by tunneling through a repulsive Coulomb barrier as the ¹ππ* state is a resonance. The second is nuclear motion on the ¹ππ* state surface leading to an intermediate that no longer tunnels and subsequently decays by internal conversion to the ground electronic state. The spectral signatures of the features are similar to those observed for other adenine-derivatives, suggesting that this nucleobase is quite insensitive to the nearby negative charges localized on the phosphates, except of course for the appearance of the additional electron tunneling channel, which is open in the dianion.

Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2-3 bright states and all the close by dark states, for a total of 6-9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.

Magnetic Circular Dichroism of Naphthalene Derivatives: A Coupled Cluster Singles and Approximate Doubles and Time-Dependent Density Functional Theory Study

The UV-vis absorption and magnetic circular dichroism spectra of naphthalene and some of its derivatives have been simulated at the Coupled Cluster Singles and Approximate Doubles (CC2) level of theory, and at the Time-Dependent Density Functional Theory (TD-DFT) level using the B3LYP and CAM-B3LYP functionals. DFT and CC2 predict in general opposite energetic ordering of the L_b and L_a transitions (in gas phase), as previously observed in adenine. The CC2 simulations of UV and MCD spectra show the best agreement with the experimental data. Analysis of the Cartesian components of the electric dipole transition strengths and the magnetic dipole transition moment between the excited states have been considered in the interpretation of the electronic transitions and the Faraday B term inversion among the naphthalene derivatives.

Site-Specific Photo-oxidation of the Isolated Adenosine-5'-triphosphate Dianion Determined by Photoelectron Imaging

Photoelectron imaging of the isolated adenosine-5'-triphosphate dianion excited to the ¹ππ* states reveals that electron emission is predominantly parallel to the polarization axis of the light and arises from subpicosecond electron tunneling through the repulsive Coulomb barrier (RCB). The computed RCB shows that the most probable electron emission site is on the amino group of adenine. This is consistent with the photoelectron imaging: excitation to the ¹ππ* states leads to an aligned ensemble distributed predominantly parallel to the long axis of adenine; the subsequent electron tunneling site is along this axis; and the negatively charged phosphate groups guide the outgoing electron mostly along this axis at long range. Imaging of electron tunneling from polyanions combined with computational chemistry may offer a general route for probing the intrinsic photo-oxidation site and dynamics as well as the overall structure of complex isolated species.

Dyson orbitals within the fc-CVS-EOM-CCSD framework: theory and application to X-ray photoelectron spectroscopy of ground and excited states

Ionization energies and Dyson orbitals within frozen-core core–valence separated equation-of-motion coupled cluster singles and doubles (fc-CVS-EOM-CCSD) enable efficient and reliable calculations of standard XPS and of UV-pump/XPS probe spectra.

First-principles characterization of the singlet excited state manifold in DNA/RNA nucleobases

TD-DFT characterization of the high-energy singlet excited state manifold of the canonical DNA/RNA nucleobasesin vacuumis assessed against RASPT2 reference computations for reliable simulations of linear and non-linear electronic spectra.

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.

Role of Explicit Solvation in the Simulation of Resonance Raman Spectra within Short-Time Dynamics Approximation

In short-time dynamics approximation, relative resonance Raman (RR) intensity of a vibrational mode primarily depends on the magnitude of square of the excited-state gradient along the corresponding normal coordinate, ground-state normal mode eigenvector, and harmonic vibrational wavenumbers. In this study, through simulation of RR spectra of guanosine-5'-monophosphate (GMP) in two ππ* singlet excited states, we analyze how the explicitly hydrogen-bonded local solvation structure of the chromophore dictates intensities of the RR active modes in an unprecedented manner. We show that the accuracy of the structural model of solvated chromophore plays a decisive role in determining an optimal theoretical method for prediction of the Franck-Condon region of the ππ* excited states. 9-Methylguanine (9-meG) in complex with six water molecules (9-meG·6H₂O) is found out to be the most accurate one for describing GMP in two different bright electronic states. We find that explicit hydrogen-bonded water molecules strongly influence computed RR intensities of GMP by modulating both the ground-state normal mode vectors and the excited-state energy gradients. We find that simultaneous inclusion of six explicit waters to describe the solute-solvent interaction near all hydration sites is essential for reliable prediction of the features of RR spectra in L_b and B_b electronic states of GMP.

Electron-Hole Correlation as Unambiguous and Universal Classification for the Nature of Low-Lying ππ* States of Nitrogen Heterocycles

The ¹L_a and ¹L_b classification of electronically excited states of cata-condensed hydrocarbons proposed by Platt in 1949 ( Platt , J. R. J. Chem. Phys. 1949 , 17 , 484 ) is challenged by investigating a series of N-heteronaphthalenes and comparison of their low-lying ππ* excited states to those of naphthalene. The breakdown of Platt's classification scheme for N-heterocycles is highlighted, and a reliable and versatile alternative using exciton analyses is presented. The strength of electron-hole correlation turns out to be the most reliable distinguishing feature, and thus, an alternative nomenclature of ¹L_w (weakly correlated) and ¹L_s (strongly correlated) is proposed. Furthermore, fundamental guidelines for their property modulation through N-atom substitution patterns are discussed.

New and Efficient Equation-of-Motion Coupled-Cluster Framework for Core-Excited and Core-Ionized States

We present a fully analytical implementation of the core-valence separation (CVS) scheme for the equation-of-motion (EOM) coupled-cluster singles and doubles (CCSD) method for calculations of core-level states. Inspired by the CVS idea as originally formulated by Cederbaum, Domcke, and Schirmer, pure valence excitations are excluded from the EOM target space and the frozen-core approximation is imposed on the reference-state amplitudes and multipliers. This yields an efficient, robust, practical, and numerically balanced EOM-CCSD framework for calculations of excitation and ionization energies as well as state and transition properties (e.g., spectral intensities, natural transition, and Dyson orbitals) from both the ground and excited states. The errors in absolute excitation/ionization energies relative to the experimental reference data are on the order of 0.2-3.0 eV, depending on the K-edge considered and on the basis set used, and the shifts are systematic for each edge. Compared to a previously proposed CVS scheme where CVS was applied as a posteriori projection only during the solution of the EOM eigenvalue equations, the new scheme is computationally cheaper. It also achieves better cancellation of errors, yielding similar spectral profiles but with absolute core excitation and ionization energies that are systematically closer to the corresponding experimental data. Among the presented results are calculations of transient-state X-ray absorption spectra, relevant for interpretation of UV-pump/X-ray probe experiments.

Time-resolved photoelectron spectroscopy of adenosine and adenosine monophosphate photodeactivation dynamics in water microjets

The excited state relaxation dynamics of adenosine and adenosine monophosphate were studied at multiple excitation energies using femtosecond time-resolved photoelectron spectroscopy in a liquid water microjet. At pump energies of 4.69-4.97 eV, the lowest ππ^* excited state, S₁, was accessed and its decay dynamics were probed via ionization at 6.20 eV. By reversing the role of the pump and probe lasers, a higher-lying ππ^* state was excited at 6.20 eV and its time-evolving photoelectron spectrum was monitored at probe energies of 4.69-4.97 eV. The S₁ ππ^* excited state was found to decay with a lifetime ranging from ∼210 to 250 fs in adenosine and ∼220 to 250 fs in adenosine monophosphate. This lifetime drops with increasing pump photon energy. Signal from the higher-lying ππ^* excited state decayed on a time scale of ∼320 fs and was measureable only in adenosine monophosphate.

Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates

A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows characterising ground state conformations of flexible nucleobase aggregates that play a crucial role in nucleic acid photochemistry.

Linear photoabsorption spectra and vertical excitation energies of microsolvated DNA nucleobases in aqueous solution

Employing density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations in combination with the semiclassical nuclear ensemble method, we have simulated the photoabsorption spectra of the four canonical DNA nucleobases in aqueous solution. In order to model the effects of solvation, for each nucleobase, a number of solvating water molecules were explicitly included in the simulations, and additionally, the bulk solvent was represented by a continuous polarizable medium. We find that the effect of the solvation shell in general is significant, and its inclusion improves the realism of the spectral simulations. The involvement of lone electron pairs in the hydrogen bonding with the solvating water molecules has the effect of systematically increasing the energies of vertical excitation into the [Formula: see text]-type states. Apart from a systematic blue shift of around [Formula: see text][Formula: see text]eV observed in the absorption peaks, the calculated photoabsorption spectra reproduce the measured ones with good accuracy. The photoabsorption spectra are dominated by excited states with [Formula: see text] and partial [Formula: see text] character. No low-energy charge transfer states are observed with the use of the CAM-B3LYP and M06-2X functionals.

Optical absorption and magnetic circular dichroism spectra of thiouracils: a quantum mechanical study in solution

The excited electronic states of thiouracils, the analogues of uracil where the carbonyl oxygens are substituted by sulphur atoms, have been investigated by computing the magnetic circular dichroism (MCD) and one-photon absorption (OPA) spectra at the TD-DFT level of theory.

Ultrafast structural dynamics of photoexcited adenine

Ultraviolet Resonance Raman (UVRR) spectroscopy derives distinct electronic properties of adenine in the L_a (260 nm) and B_b (210 nm) excited states.

A fast but accurate excitonic simulation of the electronic circular dichroism of nucleic acids: how can it be achieved?

We present and discuss a simple and fast computational approach to the calculation of electronic circular dichroism spectra of nucleic acids. It is based on a exciton model in which the couplings are obtained in terms of the full transition-charge distributions, as resulting from TDDFT methods applied on the individual nucleobases. We validated the method on two systems, a DNA G-quadruplex and a RNA β-hairpin whose solution structures have been accurately determined by means of NMR. We have shown that the different characteristics of composition and structure of the two systems can lead to quite important differences in the dependence of the accuracy of the simulation on the excitonic parameters. The accurate reproduction of the CD spectra together with their interpretation in terms of the excitonic composition suggest that this method may lend itself as a general computational tool to both predict the spectra of hypothetic structures and define clear relationships between structural and ECD properties.

Low-Lying ππ* States of Heteroaromatic Molecules: A Challenge for Excited State Methods

The description of low-lying ππ* states of linear acenes by standard electronic structure methods is known to be challenging. Here, we broaden the framework of this problem by considering a set of fused heteroaromatic rings and demonstrate that standard electronic structure methods do not provide a balanced description of the two (typically) lowest singlet state (L_a and L_b) excitations. While the L_b state is highly sensitive to correlation effects, L_a suffers from the same drawbacks as charge transfer excitations. We show that the comparison between CIS/CIS(D) can serve as a diagnostic for detecting the two problematic excited states. Standard TD-DFT and even its spin-flip variant lead to inaccurate excitation energies and interstate gaps, with only a double hybrid functional performing somewhat better. The complication inherent to a balanced description of these states is so important that even CC2 and ADC(2) do not necessarily match the ADC(3) reference.

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.

A complex-polarization-propagator protocol for magneto-chiral axial dichroism and birefringence dispersion

A schematic representation of magneto-chiral effects.

Modeling the high-energy electronic state manifold of adenine: Calibration for nonlinear electronic spectroscopy

Pump-probe electronic spectroscopy using femtosecond laser pulses has evolved into a standard tool for tracking ultrafast excited state dynamics. Its two-dimensional (2D) counterpart is becoming an increasingly available and promising technique for resolving many of the limitations of pump-probe caused by spectral congestion. The ability to simulate pump-probe and 2D spectra from ab initio computations would allow one to link mechanistic observables like molecular motions and the making/breaking of chemical bonds to experimental observables like excited state lifetimes and quantum yields. From a theoretical standpoint, the characterization of the electronic transitions in the visible (Vis)/ultraviolet (UV), which are excited via the interaction of a molecular system with the incoming pump/probe pulses, translates into the determination of a computationally challenging number of excited states (going over 100) even for small/medium sized systems. A protocol is therefore required to evaluate the fluctuations of spectral properties like transition energies and dipole moments as a function of the computational parameters and to estimate the effect of these fluctuations on the transient spectral appearance. In the present contribution such a protocol is presented within the framework of complete and restricted active space self-consistent field theory and its second-order perturbation theory extensions. The electronic excited states of adenine have been carefully characterized through a previously presented computational recipe [Nenov et al., Comput. Theor. Chem. 1040-1041, 295-303 (2014)]. A wise reduction of the level of theory has then been performed in order to obtain a computationally less demanding approach that is still able to reproduce the characteristic features of the reference data. Foreseeing the potentiality of 2D electronic spectroscopy to track polynucleotide ground and excited state dynamics, and in particular its expected ability to provide conformational dependent fingerprints in dimeric systems, the performances of the selected reduced level of calculations have been tested in the construction of 2D electronic spectra for the in vacuo adenine monomer and the unstacked adenine homodimer, thereby exciting the Lb/La transitions with the pump pulse pair and probing in the Vis to near ultraviolet spectral window.

Ultrafast Excited-State Deactivation of 8-Hydroxy-2'-deoxyguanosine Studied by Femtosecond Fluorescence Spectroscopy and Quantum-Chemical Calculations

The fluorescence properties of the 8-hydroxy-2'-deoxyguanosine (8-oxo-dG) in aqueous solution at pH 6.5 are studied by steady-state spectroscopy and femtosecond fluorescence up-conversion and compared with those of 2'-deoxyguanine (dG) and 2'-deoxyguanine monophosphate (dGMP). The steady-state fluorescence spectrum of 8-oxo-dG is composed of a broad band that peaks at 356 nm and extends over the entire visible spectral region, and its fluorescence quantum yield is twice that of dG/dGMP. After excitation at 267 nm, the initial fluorescence anisotropy at all wavelengths is lower than 0.1, giving evidence of an ultrafast internal conversion (<100 fs) between the two lowest excited ππ* states (Lb and La). The fluorescence decays of 8-oxo-dG are biexponential with an average lifetime of 0.7 ± 0.1 ps, which is about two times longer than that of dGMP. In contrast with dGMP, only a moderate dynamical shift (∼1400 vs 10,000 cm(-1)) of the fluorescence spectra of 8-oxo-dG is observed on the time scale of a few picoseconds without modification of the spectral shape. PCM/TD-DFT calculations, employing either the PBE0 or the M052X functionals, provide absorption spectra in good agreement with the experimental one and show that the deactivation path is similar to that proposed for dGMP, with a fast motion toward an energy plateau, where the purine ring keeps an almost planar geometry, followed by decay to S0, via out-of-the plane motion of amino substituent.

Computational methodology study of the optical and thermochemical properties of a molecular photoswitch

We assess how the utilization of different DFT functionals for obtaining the equilibrium geometries and vibrational frequencies affect the description of the thermochemistry and subsequent calculation of the optical properties of a dihydroazulene-vinylheptafulvene photoswitch. The assessment covers nine popular DFT functionals (BLYP, B3LYP, CAM-B3LYP, M06-L, M06, M06-2X, PBE, PBE0, and ωB97X-D) in conjugation with five different Pople style basis sets (6-31+G(d), 6-31++G(d,p), 6-311+G(d), 6-311++G(d,p), and 6-311++G(3df,3pd)). It is identified that only CAM-B3LYP, M06-2X, and PBE0 are able to quantitatively describe the correct trends in the thermochemical properties. The subsequent calculation of the optical properties using the CAM-B3LYP functional shows that there is little difference in whether the CAM-B3LYP, M06-2X, or PBE0 functionals have been used to calculate the equilibrium geometries. Utilizing the identified functionals, we investigate how the number of electron withdrawing cyano substituents influence the thermochemistry and optical properties of the molecular photoswitch.

Time-resolved photoelectron imaging of the isolated deprotonated nucleotides

Time-resolved photoelectron spectroscopy of deprotonated nucleotides provides new insights into their relaxation dynamics.