Benchmark Studies on the Building Blocks of DNA. 1. Superiority of Coupled Cluster Methods in Describing the Excited States of Nucleobases in the Franck–Condon Region

Analytic Gradients for Equation-of-Motion Coupled Cluster with Single, Double, and Perturbative Triple Excitations

Understanding the process of molecular photoexcitation is crucial in various fields, including drug development, materials science, photovoltaics, and more. The electronic vertical excitation energy is a critical property, for example in determining the singlet-triplet gap of chromophores. However, a full understanding of excited-state processes requires additional explorations of the excited-state potential energy surface and electronic properties, which is greatly aided by the availability of analytic energy gradients. Owing to its robust high accuracy over a wide range of chemical problems, equation-of-motion coupled cluster with single and double excitations (EOM-CCSD) is a powerful method for predicting excited-state properties, and the implementation of analytic gradients of many EOM-CCSD variants (excitation energies, ionization potentials, electron attachment energies, etc.) along with numerous successful applications highlights the flexibility of the method. In specific cases where a higher level of accuracy is needed or in more complex electronic structures, the inclusion of triple excitations becomes essential, for example, in the EOM-CCSD* approach of Saeh and Stanton. In this work, we derive and implement for the first time the analytic gradients of EOMEE-CCSD*, which also provides a template for analytic gradients of related excited-state methods with perturbative triple excitations. The capabilities of analytic EOMEE-CCSD* gradients are illustrated by several representative examples.

Excited state properties of an A-D-A non-fullerene electron acceptor: a LC-TD-DFTB study

Understanding charge transfer processes is essential to estimate the performance of organic photovoltaic technologies. Although experimental production is on the rise, predictability strongly relies on theoretical modeling, which is limited to the size of semiconductors. As a computationally favorable approach, we benchmarked the long-range corrected (LC) time-dependent (TD) formulation of the semi-empirical density functional-based tight-binding method (DFTB) for three polycyclic aromatic hydrocarbons (PAHs) and studied the DTP-IC-4Ph molecule, a PAH-based non-fullerene electron acceptor (NFA) with an A-D-A backbone structure. After a thorough investigation into the long-range parameter (ω) tuning for naphthalene, anthracene and pyrene, the excitation energies, oscillator strengths and Natural Transition Orbitals (NTOs) were compared with the standard ωB97X-D/6-31G(d,p) level of theory and the ADC2/6-31G(d,p) multiconfigurational method. We estimated mobility-related properties of the NFA and considered 1000 thermally accessible configurations to qualitatively reproduce the experimental absorption profile and investigate the energetic disorder. Finally, we conducted a fragment-based analysis using the one-electron transition density matrix (1TDM) to determine the character of the excited states and investigate the effect of side chains on exciton formation. Our results are sensitive to the level of theory and highly dependent on the long-range parameter but suggest that the presence of alkyl chains promotes a higher average charge delocalization and allows for additional hopping mechanisms, favoring the charge transfer dynamics.

Assessment of State-Averaged Driven Similarity Renormalization Group on Vertical Excitation Energies: Optimal Flow Parameters and Applications to Nucleobases

We present a comprehensive excited-state benchmark for the state-averaged (SA) driven similarity renormalization group (DSRG) [Li, C.; Evangelista, F. A. J. Chem. Phys. 2018, 148, 124106]. Following the QUEST database [Véril, M.; Scemama, A.; Caffarel, M.; Lipparini, F.; Boggio-Pasqua, M.; Jacquemin, D.; Loos, P.-F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2021, 11, e1517], 280 vertical transition energies of 35 medium-sized molecules are computed using the SA-DSRG derived second- and third-order perturbation theories (PT2/PT3) along with a nonperturbative approach [sq-LDSRG(2)]. Comparing to the theoretical best estimates, the optimal flow parameter is found to be 0.35 and 2.0 Eh-2 for SA-DSRG-PT2 and SA-DSRG-PT3, respectively. For SA-sq-LDSRG(2), a flow parameter of 1.5 Eh-2 provides converged equations without compromising the accuracy. We then assess the accuracy of the SA-DSRG hierarchy using these parameters. The SA-DSRG-PT2 scheme outperforms the level-shifted CASPT2 by 0.10 eV in mean absolute error (MAE), yet this accuracy is slightly inferior than that of CASPT2 with the ionization-potential-electron-affinity shift. Both SA-DSRG-PT3 and SA-sq-LDSRG(2) yield a MAE of 0.10 eV, which is comparable to that of CASPT3 (0.09 eV). Finally, we compute vertical excitation energies of several low-lying singlet states of nucleobases. The SA-sq-LDSRG(2) approach provides highly accurate results for π → π* excitations, while n → π* transitions are better described by SA-DSRG-PT3.

Ground- and Excited-State Dipole Moments and Oscillator Strengths of Full Configuration Interaction Quality

We report ground- and excited-state dipole moments and oscillator strengths (computed in different "gauges" or representations) of full configuration interaction (FCI) quality using the selected configuration interaction method known as Configuration Interaction using a Perturbative Selection made Iteratively (CIPSI). Thanks to a set encompassing 35 ground- and excited-state properties computed in 11 small molecules, the present near-FCI estimates allow us to assess the accuracy of high-order coupled-cluster (CC) calculations including up to quadruple excitations. In particular, we show that incrementing the excitation degree of the CC expansion (from CC with singles and doubles (CCSD) to CC with singles, doubles, and triples (CCSDT) or from CCSDT to CC with singles, doubles, triples, and quadruples (CCSDTQ)) reduces the average error with respect to the near-FCI reference values by approximately 1 order of magnitude.

Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT

The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.

Examining fundamental and excitation gaps at the thermodynamic limit: A combined (QTP) DFT and coupled cluster study on trans-polyacetylene and polyacene

Interest in ab initio property prediction of π-conjugated polymers for technological applications places significant demand on “cost-effective” and conceptual computational methods, particularly effective, one-particle theories. This is particularly relevant in the case of Kohn–Sham Density Functional Theory (KS-DFT) and its new competitors that arise from correlated orbital theory, the latter defining the QTP family of DFT functionals. This study presents large, ab initio equation of motion-coupled cluster calculations using the massively parallel ACESIII to target the fundamental bandgap of two prototypical organic polymers, trans-polyacetylene (tPA) and polyacene (Ac), and provides an assessment of the new quantum theory project (QTP) functionals for this problem. Further results focusing on the 1 A g (1 A g), 1 B u (1 B2 u), and 3 B u (3 B2 u) excited states of tPA (Ac) are also presented. By performing calculations on oligomers of increasing size, extrapolations to the thermodynamic limit for the fundamental and all excitation gaps, as well as estimations of the exciton binding energy, are made. Thermodynamic-limit results for a combination of “optimal” and model geometries are presented. Calculated results for excitations that are adequately described using a single-particle model illustrate the benefits of requiring a KS-DFT functional to satisfy the Bartlett ionization potential theorem.

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.

Assessment of local coupled cluster methods for excited states of BODIPY/Aza-BODIPY families

It was previously reported that Laplace transformed local CC2 (LCC2*) provided the best agreement (MAE = 0.145 eV) when comparing vertical excitation energies to experimental λ_max for a benchmark set of 17 BODIPY/Aza-BODIPY molecules. However, these energies did not agree with values obtained from canonical CC2. Here we report LCC2* computations of vertical excitation energies on the same benchmark set of molecules using a newly implemented treatment of the ground state. Comparison with resolution-of-identity approximate coupled cluster to second-order (RI-CC2) results demonstrate that the new LCC2* results agree quantitatively. Furthermore, these values can easily be corrected empirically to also provide excellent agreement with the experiment. We show that the local algebraic diagrammatic construction to second-order (LADC(2)) method exhibits the same differences between implementations as seen for LCC2. The source of the difference is traced to an improved treatment of the ground state in the local methods, which decreases agreement with the experiment (as attributed to a fortuitous cancellation of errors) but significantly improves agreement with RI-CC2. While the absolute vertical excitation energies now show larger deviations, there remains a strong linear correlation between the LCC2* results and the experiment. For the 17 BODIPY/Aza-BODIPY molecules vertical excitation energies are determined using DLPNO-STEOM-CCSD and shown to have excellent agreement with experimental λ_max (MAE = 0.145 eV), which is the best of all the single-reference methods. The vertical excitation energies are determined using LCC2*, empirically corrected LCC2*, and RI-CC2 for a series of eight large BODIPYs and Aza-BODIPYs.

Ultrafast Dynamics of the Two Lowest Bright Excited States of Cytosine and 1-Methylcytosine: A Quantum Dynamical Study

The nonadiabatic quantum dynamics (QD) of cytosine and 1-methylcytosine in the gas phase is simulated for 250 fs after a photoexcitation to one of the first two bright states. The nuclear wavepacket is propagated on the coupled diabatic potential energy surfaces of the lowest seven excited states, including ππ*, nπ*, and Rydberg states along all the vibrational degrees of freedom. We focus in particular on the interplay between the bright and the dark nπ* states, not considering the decay to the ground electronic state. To run these simulations, we implemented an automatic general procedure to parametrize linear vibronic coupling (LVC) models with time-dependent density functional theory (DFT) computations and interfaced it with Gaussian package. The wavepacket was propagated with the multilayer version of the multiconfigurational time dependent Hartree method. Two different density functionals, PBE0 and CAM-B3LYP, which provide a different description of the relative stability of the lowest energy dark states, were used to parametrize the LVC Hamiltonian. Part of the photoexcited population on lowest HOMO-LUMO transition (π_Hπ_L^*) decays within less than 100 fs to a nπ* state which mainly involves a promotion of an electron from the oxygen lone pair to the LUMO (n_Oπ_L^*). The population of the second ππ* state decays almost completely, in <100 fs, not only to π_Hπ_L^* and to n_Oπ_L^* states but also to another nπ_L^* state involving the nitrogen lone pair. The efficiency of the adopted protocol allowed us to check the accuracy of the predictions by repeating the QD simulations with different LVC Hamiltonians parametrized either at the ground-state minimum or at stationary structures of different relevant excited states.

Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy

The relaxation dynamics of thymine and its derivatives thymidine and thymidine monophosphate are studied using time-resolved photoelectron spectroscopy applied to a water microjet. Two absorption bands are studied; the first is a bright ππ* state which is populated using tunable-ultraviolet light in the range 4.74-5.17 eV and probed using a 6.20 eV probe pulse. By reversing the order of these pulses, a band containing multiple ππ* states is populated by the 6.20 eV pulse and the lower energy pulse serves as the probe. The lower lying ππ* state is found to decay in ∼400 fs in both thymine and thymidine independent of pump photon energy, while thymidine monophosphate decays vary from 670 to 840 fs with some pump energy dependence. The application of a computational quantum mechanical/molecular mechanical scheme at the XMS-CASPT2//CASSCF/AMBER level of theory suggests that conformational differences existing between thymidine and thymidine monophosphate in solution account for this difference. The higher lying ππ* band is found to decay in ∼600 fs in all three cases, but it is only able to be characterized when the 5.17 eV probe pulse is used. Notably, no long-lived signal from an nπ* state can be identified in either experiment on any of the three molecules.

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.

A theoretical study of 5,6,7,8-tetrahydro-6-hydroxymethylpterin: insight into intrinsic photoreceptor properties of 6-substituted tetrahydropterins

Tetrahydropterins are essential biological cofactors, which play a crucial role in DNA and RNA syntheses, NO synthesis, hydroxylation of aromatic amino acids, etc. In the last few years, it has been shown that 6-substituted "unconjugated" tetrahydropterins can also play a photoreceptor chromophoric role in plants and cyanobacteria. However, the nature of the initial light signal transduction act in which H4pterins participate is unknown. Our quantum chemical calculations have shown the possibility of the fast internal conversion of excited states of H4pterins. The potential energy surface scan along the 1ππ* state shows no energy barrier leading to 1ππ*/S0 conical intersection, this explains the absence of fluorescence for H4pterins. Other trajectories of the internal conversion relate to the stretching vibrations of the N-H bonds of the pyrimidine ring for the Rydberg state. The presence of several trajectories of nonradiative quenching of the photoexcited singlet states provides the photostability of the molecule. It was demonstrated for the first time that the nature of the excited states of H4pterins is similar to the nature of the excited states of guanine.

How intermolecular interactions influence electronic absorption spectra: insights from the molecular packing of uracil in condensed phases

Intermolecular interactions in terms of molecular packing are crucial for the investigation of the absorption spectra of uracil in different environments.

Assessment of Functionals for TDDFT Calculations of One- and Two-Photon Absorption Properties of Neutral and Anionic Fluorescent Proteins Chromophores

Performance of DFT functionals with different percentages of exact Hartree-Fock exchange energy (EX) is assessed for recovery of the CC2 reference one- (OPA) and two-photon absorption (TPA) spectra of fluorescent proteins chromophores in vacuo. The investigated DFT functionals, together with their EX contributions are BLYP (0%), B3LYP (20%), B1LYP (25%), BHandHLYP (50%), and CAM-B3LYP (19% at short range and 65% at long range). Our test set consists of anionic and neutral chromophores as naturally occurring in the fluorescent proteins. For the first time, we compare TDDFT and CC2 methods for higher excited states than the S₁ state, exhibiting relatively large TPA intensity. Our TDDFT results for neutral chromophores reveal an increase in excitation energies as well as TPA and OPA intensities errors, compared to CC2-derived results, as the DFT functional contains less exact exchange. The long-range-corrected CAM-B3LYP functional performs the best, closely followed by BHandHLYP, while BLYP usually significantly underestimates all investigated spectral properties, hence being the worst in reproducing the reference CC2 results. The hybrid B3LYP and B1LYP functionals can be roughly placed in between. We propose that TDDFT may underestimate the TPA intensities for neutral chromophores of fluorescent proteins due to underestimated oscillator strengths between some excited states. In the case of anionic chromophores, we find that B3LYP and B1LYP functionals overcome others in terms of reproducing CC2 excitation energies. On the other hand, however, TPA intensity is usually significantly underestimated, and in this respect, CAM-B3LYP functional seems to be again superior. In contrast to the case of neutral chromophores, it seems that a large magnitude of excited-state dipole moments or changes in dipole moments upon excitation may be the driving force behind high TPA transition moments.

Mixed Quantum/Classical Method for Nonadiabatic Quantum Dynamics in Explicit Solvent Models: The ππ*/nπ* Decay of Thymine in Water as a Test Case

We present a novel mixed quantum classical dynamical method to include solvent effects on internal conversion (IC) processes. All the solute degrees of freedom are represented by a wavepacket moving according to nonadiabatic quantum dynamics, while the motion of an explicit solvent model is described by an ensemble of classical trajectories. The mutual coupling of the solute and solvent dynamics is included within a mean-field framework and the quantum and classical equations of motions are solved simultaneously. As a test case we apply our method to the ultrafast ππ* → nπ* decay of thymine in water. Solvent dynamical response modifies IC yield already on the 50 fs time scale. This effect is due to water librational motions that stabilize the most populated state. Pure static disorder, that is, the existence of different solvent configurations when photoexcitation takes place, also has a remarkable impact on the dynamics.

The Bethe–Salpeter equation in chemistry: relations with TD-DFT, applications and challenges

We review the Bethe–Salpeter formalism and analyze its performances for the calculation of the excited state properties of molecular systems.

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.

Mechanism Underlying the Nucleobase-Distinguishing Ability of Benzopyridopyrimidine (BPP)

Benzopyridopyrimidine (BPP) is a fluorescent nucleobase analogue capable of forming base pairs with adenine (A) and guanine (G) at different sites. When incorporated into oligodeoxynucleotides, it is capable of differentiating between the two purine nucleobases by virtue of the fact that its fluorescence is largely quenched when it is base-paired to guanine, whereas base-pairing to adenine causes only a slight reduction of the fluorescence quantum yield. In the present article, the photophysics of BPP is investigated through computer simulations. BPP is found to be a good charge acceptor, as demonstrated by its positive and appreciably large electron affinity. The selective quenching process is attributed to charge transfer (CT) from the purine nucleobase, which is predicted to be efficient in the BPP-G base pair, but essentially inoperative in the BPP-A base pair. The CT process owes its high selectivity to a combination of two factors: the ionization potential of guanine is lower than that of adenine, and less obviously, the site occupied by guanine enables a greater stabilization of the CT state through electrostatic interactions than the one occupied by adenine. The case of BPP illustrates that molecular recognition via hydrogen bonding can enhance the selectivity of photoinduced CT processes.

Ultrafast Nuclear Dynamics of Photoexcited Guanosine-5'-Monophosphate in Three Singlet States

We report measurement of resonance Raman (RR) spectra of guanosine-5'-monophosphate (GMP), a DNA nucleotide at excitation wavelengths throughout its ππ* absorption band (B_b) in the 210-230 nm range. From these data, we constructed wavelength-dependent Raman intensity excitation profiles (REPs) for all observed modes. These profiles and the absorption spectrum were then modeled using self-consistent simulations based on the time-dependent wave packet propagation formalism. We inferred the initial structural dynamics of GMP immediately after photoexcitation in terms of dimensionless displacements. The simulations also provide linewidth-broadening parameters that in turn report on the time scale of dynamics. We compared deduced structural changes in the purine ring upon photoabsorption into the B_b state with those deduced for the two lowest lying ππ* (L_a and L_b at 280 and 248 nm, respectively) excited states of GMP. We find that excitation to the L_b state lengthens C₆-N₁ and C₂═N₃ bonds, which lie along the formation coordinate of various oxidative adducts but B_b excitation does not. We also find that photoabsorption by the B_b state weakens the C₈-N₉ bond and thus might assist imidazole ring opening via cleavage of the same bond. Electronic excitation to different ππ* states of the guanine chromophore results in contrasting structural changes; although absorption by the L_a and L_b states induces expansion of pyrimidine and contraction of imidazole rings, excitation results in overall shrinkage of both the rings. Computed absolute changes in internal coordinates imply that photoexcitation to any of the three singlet states of GMP does not lead directly to the formation of a cation radical of guanine.

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.

Nonadiabatic dynamics simulation of keto isocytosine: a comparison of dynamical performance of different electronic-structure methods

Different reaction channels are obtained in the nonadiabatic dynamics simulations of isocytosine at CASSCF and ADC(2) levels.

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.

The Importance of Short- and Long-Range Exchange on Various Excited State Properties of DNA Monomers, Stacked Complexes, and Watson-Crick Pairs

We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of nonempirically tuned range-separated functionals, for predicting a diverse set of electronic excitations in DNA nucleobase monomers and dimers. This large and extensive set of excitations comprises a total of 50 different transitions (for each tested DFT functional) that includes several n → π and π → π* valence excitations, long-range charge-transfer excitations, and extended Rydberg transitions (complete with benchmark calculations from high-level EOM-CCSD(T) methods). The presence of localized valence excitations as well as extreme long-range charge-transfer excitations in these systems poses a serious challenge for TD-DFT methods that allows us to assess the importance of both short- and long-range exchange contributions for simultaneously predicting all of these various transitions. In particular, we find that functionals that do not have both short- and full long-range exchange components are unable to predict the different types of nucleobase excitations with the same accuracy. Most importantly, the current study highlights the importance of both short-range exchange and a nonempirically tuned contribution of long-range exchange for accurately predicting the diverse excitations in these challenging nucleobase systems.

Multiconfigurational Second-Order Perturbation Theory with Frozen Natural Orbitals Extended to the Treatment of Photochemical Problems

A new flavor of the frozen natural orbital complete active space second-order perturbation theory method (FNO-CASPT2, Aquilante et al., J. Chem. Phys. 131, 034113) is proposed herein. In this new implementation, the virtual space in Cholesky decomposition-based CASPT2 computations (CD-CASPT2) is truncated by excluding those orbitals that contribute the least toward preserving a predefined value of the trace of an approximate density matrix, as that represents a measure of the amount of dynamic correlation retained in the model. In this way, the amount of correlation included is practically constant at all nuclear arrangements, thus allowing for the computation of smooth electronic states surfaces and energy gradients-essential requirements for theoretical studies in photochemistry. The method has been benchmarked for a series of relevant biochromophores for which large speed-ups have been recorded while retaining the accuracy achieved in the corresponding CD-CASPT2 calculations. Both vertical excitation energies and gradient calculations have been carried out to establish general guidelines as to how much correlation needs to be retained in the calculation for the results to be consistent with the CD-CASPT2 findings. Our results feature errors within a tenth of an eV for the most difficult cases and have been validated to be used for gradient computations where an up to 3-fold speed-up is observed depending on the size of the system and the basis set employed.

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.

Excitation Spectra of Nucleobases with Multiconfigurational Density Functional Theory

Range-separated hybrid methods between wave function theory and density functional theory (DFT) can provide high-accuracy results, while correcting some of the inherent flaws of both the underlying wave function theory and DFT. We here assess the accuracy for excitation energies of the nucleobases thymine, uracil, cytosine, and adenine, using a hybrid between complete active space self-consistent field (CASSCF) and DFT methods. The method is based on range separation, thereby avoiding all double-counting of electron correlation and is denoted long-range CASSCF short-range DFT (CAS-srDFT). Using a linear response extension of CAS-srDFT, we compare the first 7-8 excited states of the nucleobases with perturbative multireference approaches as well as coupled cluster based methods. Our results show that the CAS-srDFT method can provide accurate excitation energies in good correspondence with the computationally more expensive methods.

Quantum chemical MP2 results on some hydrates of cytosine: binding sites, energies and the first hydration shell

A detailed quantum chemical investigation was undertaken to obtain the structure and energetics of cytosine hydrates Cyt·nH2O, with n = 1 to 7. The MP2(fc)/aug-cc-pVDZ level was used as the standard, with some DFT (B3LYP) and coupled cluster calculations, as well as calculations with the aug-cc-pVTZ basis set added for comparison. In a systematic search for microhydrated forms of cytosine, we have found that several structures have not yet been reported in the literature. The energies of different isomers, as well as binding energies are compared. When predicting the stability of a complex, we suggest using a scheme where the water molecules are extracted from a finite model of bulk water. Finally, based on energetic data, we suggest a rational definition of the first hydration shell; with this definition, it contains just six water molecules.

Using DNA origami nanostructures to determine absolute cross sections for UV photon-induced DNA strand breakage

We have characterized ultraviolet (UV) photon-induced DNA strand break processes by determination of absolute cross sections for photoabsorption and for sequence-specific DNA single strand breakage induced by photons in an energy range from 6.50 to 8.94 eV. These represent the lowest-energy photons able to induce DNA strand breaks. Oligonucleotide targets are immobilized on a UV transparent substrate in controlled quantities through attachment to DNA origami templates. Photon-induced dissociation of single DNA strands is visualized and quantified using atomic force microscopy. The obtained quantum yields for strand breakage vary between 0.06 and 0.5, indicating highly efficient DNA strand breakage by UV photons, which is clearly dependent on the photon energy. Above the ionization threshold strand breakage becomes clearly the dominant form of DNA radiation damage, which is then also dependent on the nucleotide sequence.

Assessment of Approximate Coupled-Cluster and Algebraic-Diagrammatic-Construction Methods for Ground- and Excited-State Reaction Paths and the Conical-Intersection Seam of a Retinal-Chromophore Model

As a minimal model of the chromophore of rhodopsin proteins, the penta-2,4-dieniminium cation (PSB3) poses a challenging test system for the assessment of electronic-structure methods for the exploration of ground- and excited-state potential-energy surfaces, the topography of conical intersections, and the dimensionality (topology) of the branching space. Herein, we report on the performance of the approximate linear-response coupled-cluster method of second order (CC2) and the algebraic-diagrammatic-construction scheme of the polarization propagator of second and third orders (ADC(2) and ADC(3)). For the ADC(2) method, we considered both the strict and extended variants (ADC(2)-s and ADC(2)-x). For both CC2 and ADC methods, we also tested the spin-component-scaled (SCS) and spin-opposite-scaled (SOS) variants. We have explored several ground- and excited-state reaction paths, a circular path centered around the S1/S0 surface crossing, and a 2D scan of the potential-energy surfaces along the branching space. We find that the CC2 and ADC methods yield a different dimensionality of the intersection space. While the ADC methods yield a linear intersection topology, we find a conical intersection topology for the CC2 method. We present computational evidence showing that the linear-response CC2 method yields a surface crossing between the reference state and the first response state featuring characteristics that are expected for a true conical intersection. Finally, we test the performance of these methods for the approximate geometry optimization of the S1/S0 minimum-energy conical intersection and compare the geometries with available data from multireference methods. The present study provides new insight into the performance of linear-response CC2 and polarization-propagator ADC methods for molecular electronic spectroscopy and applications in computational photochemistry.

Computational modeling of photoexcitation in DNA single and double strands

The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.

Influence of base stacking geometry on the nature of excited states in G-quadruplexes: a time-dependent DFT study

G-quadruplexes are four-stranded structures of nucleic acids that are formed from the association of guanine nucleobases into cyclical arrangements known as tetrads. G-quadruplexes are involved in a host of biological processes and are of interest in nanomaterial applications. However, not much is known about their electronic properties. In this paper, we analyze electronic excited states of G-quadruplexes using a combination of time-dependent DFT calculations and molecular dynamics simulations. We systematically consider experimentally observed arrangements of stacked guanine tetrads. The effects of structural features on exciton delocalization and photoinduced charge separation are explored using a quantitative analysis of the transition electron density. It is shown that collective coherent excitations shared between two guanine nucleobases dominate in the absorption spectrum of stacked G-tetrads. These excitations may also include a significant contribution of charge transfer states. Large variation in exciton localization is also observed between different structures with a general propensity toward localization between two bases. We reveal large differences in how charge separation occurs within different nucleobase arrangements, with some geometries favoring separation within a single tetrad and others favoring separation between tetrads. We also investigate the effects of the coordinating K(+) ion located in the central cavity of G-quadruplexes on the relative excited state properties of such systems. Our results demonstrate how the nature of excited states in G-quadruplexes depends on the nucleobase stacking geometry resulting from the mutual arrangement of guanine tetrads.

Photochemistry of methyl hypobromite (CH3OBr): excited states and photoabsorption spectrum

From photoabsorption to photodissociation, from MRCI to TDDFT; a comprehensive benchmark on the photochemistry of methyl hypobromite (CH₃OBr) is provided.

Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory

It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles.