Analytic Nuclear Gradients for Complete Active Space Linearized Pair-Density Functional Theory

Accurately modeling photochemical reactions is difficult due to the presence of conical intersections and locally avoided crossings, as well as the inherently multiconfigurational character of excited states. As such, one needs a multistate method that incorporates state interaction in order to accurately model the potential energy surface at all nuclear coordinates. The recently developed linearized pair-density functional theory (L-PDFT) is a multistate extension of multiconfiguration PDFT, and it has been shown to be a cost-effective post-MCSCF method (as compared to more traditional and expensive multireference many-body perturbation methods or multireference configuration interaction methods) that can accurately model potential energy surfaces in regions of strong nuclear-electronic coupling in addition to accurately predicting Franck-Condon vertical excitations. In this paper, we report the derivation of analytic gradients for L-PDFT and their implementation in the PySCF-forge software, and we illustrate the utility of these gradients for predicting ground- and excited-state equilibrium geometries and adiabatic excitation energies for formaldehyde, s-trans-butadiene, phenol, and cytosine.

Is 1-methylcytosine a faithful model compound for ultrafast deactivation dynamics of cytosine nucleosides in solution?

1-Methylcytosine (1mCyt) is the base for nucleoside N1-methylpseudodeoxycytidine of Hachimoji nucleic acids and a frequently used model compound for theoretical studies on excited states of cytosine nucleosides. However, there is little experimental characterization of spectra and photo-dynamic properties of 1mCyt. Herein, we report a comprehensive investigation into excited state dynamics and effects of solvents on fluorescence dynamics of 1mCyt in both water and acetonitrile. The study employed femtosecond broadband time-resolved fluorescence, transient absorption, and steady-state spectroscopy, along with density functional theory and time-dependent density functional theory calculations. The results obtained provide the first experimental evidence for identifying a dark-natured ∼5.7 ps lifetime nπ* state in the ultrafast non-radiative deactivation with 1mCyt in aqueous solution. This study also demonstrates a significant effect of the solvent on 1mCyt's fluorescence emission, which highlights the crucial role of solute-solvent hydrogen bonding in altering structures and reshaping the radiative as well as nonradiative dynamics of the 1mCyt's ππ* state in the aprotic solvent compared to the protic solvent. The solvent effect exhibited by 1mCyt is distinctive from that known for deoxycytidine, indicating the need for caution in using 1mCyt for modelling the ultrafast dynamics of Cyt nucleosides in solvents with varying properties. Overall, our study unveils a deactivation mechanism that confers a high degree of photo-stability for 1mCyt in solution, shedding light on the molecular basis for solvent-induced effects on the excited state dynamics of nucleobases and derivatives.

Non-adiabatic dynamics simulations of the S1 excited-state relaxation of diacetyl phenylenediamine

The small molecule built around the benzene ring, diacetyl phenylenediamine (DAPA), has attracted much attention due to its synthesis accessibility, large Stokes shift, etc. However, its meta structure m-DAPA does not fluoresce. In a previous investigation, it was found that such a property is due to the fact that it undergoes an energy-reasonable double proton transfer conical intersection during the deactivation of the S₁ excited-state, then returns to the ground state by a nonradiative relaxation process eventually. However, our static electronic structure calculations and non-adiabatic dynamics analysis results indicate that only one reasonable non-adiabatic deactivation channel exists: after being excited to the S₁ state, m-DAPA undergoes an ultrafast and barrierless ESIPT process and reaches the single-proton-transfer conical intersection. Subsequently, the system either returns to the keto-form S₀ state minimum with proton reversion or returns to the single-proton-transfer S₀ minimum after undergoing a slight twist of the acetyl group. The dynamics results show that the S₁ excited-state lifetime of m-DAPA is 139 fs. In other words, we propose an efficient single-proton-transfer non-adiabatic deactivation channel of m-DAPA that is different from previous work, which can provide important mechanistic information of similar fluorescent materials.

Excited-State Deactivation Mechanism of 3,5-bis(2-hydroxyphenyl)-1H-1,2,4-triazole: Electronic Structure Calculations and Nonadiabatic Dynamics Simulations

3,5-bis(2-Hydroxyphenyl)-1H-1,2,4-triazole (bis-HPTA) has attracted wide attention due to the important application in the detection of microorganisms and insecticidal activity. However, the mechanisms of excited-state intramolecular proton transfer (ESIPT) process and decay pathways are still a matter of debate. In this work, we have comprehensively investigated the photodynamics of bis-HPTA by executing combined electronic structure calculations and nonadiabatic surface-hopping dynamics simulations. Based on the computed electronic structure and dynamics information, we propose two nonadiabatic deactivation channels that efficiently populate the ground state from the Franck-Condon region. In the first one, after being excited to the bright S₁ state, bis-HPTA molecule undergoes an ultrafast and barrierless ESIPT-1 process. Then, the system encounters with an energetically accessible S₁/S₀ conical intersection (CI), which funnels the system to the ground state speedily. Afterward, the keto species either arrives at the keto product or return to its enol species via a ground-state proton transfer in the S₀ state. In the other excited-state decay channel, the S₁ system hops to the ground state through a different CI, which involves the ESIPT-2 process. In our dynamics simulations, about 79.6% of the trajectories decay to the S₀ state via the first CI, while the remaining ones employ the second conical intersection. The results of dynamics simulations also demonstrated that the lifetime of the S₁ state is estimated as 315 fs. The present work will give elaborating mechanistic information of similar compounds in various environments.

Assessing the Performances of CASPT2 and NEVPT2 for Vertical Excitation Energies

Methods able to simultaneously account for both static and dynamic electron correlations have often been employed, not only to model photochemical events but also to provide reference values for vertical transition energies, hence allowing benchmarking of lower-order models. In this category, both the complete-active-space second-order perturbation theory (CASPT2) and the N-electron valence state second-order perturbation theory (NEVPT2) are certainly popular, the latter presenting the advantage of not requiring the application of the empirical ionization-potential-electron-affinity (IPEA) and level shifts. However, the actual accuracy of these multiconfigurational approaches is not settled yet. In this context, to assess the performances of these approaches, the present work relies on highly accurate (±0.03 eV) aug-cc-pVTZ vertical transition energies for 284 excited states of diverse character (174 singlet, 110 triplet, 206 valence, 78 Rydberg, 78 n → π*, 119 π → π*, and 9 double excitations) determined in 35 small- to medium-sized organic molecules containing from three to six non-hydrogen atoms. The CASPT2 calculations are performed with and without IPEA shift and compared to the partially contracted (PC) and strongly contracted (SC) variants of NEVPT2. We find that both CASPT2 with IPEA shift and PC-NEVPT2 provide fairly reliable vertical transition energy estimates, with slight overestimations and mean absolute errors of 0.11 and 0.13 eV, respectively. These values are found to be rather uniform for the various subgroups of transitions. The present work completes our previous benchmarks focused on single-reference wave function methods ( J. Chem. Theory Comput. 2018, 14, 4360; J. Chem. Theory Comput. 2020, 16, 1711), hence allowing for a fair comparison between various families of electronic structure methods. In particular, we show that ADC(2), CCSD, and CASPT2 deliver similar accuracies for excited states with a dominant single-excitation character.

Electronic Structure Methods for the Description of Nonadiabatic Effects and Conical Intersections

Nonadiabatic effects are ubiquitous in photophysics and photochemistry, and therefore, many theoretical developments have been made to properly describe them. Conical intersections are central in nonadiabatic processes, as they promote efficient and ultrafast nonadiabatic transitions between electronic states. A proper theoretical description requires developments in electronic structure and specifically in methods that describe conical intersections between states and nonadiabatic coupling terms. This review focuses on the electronic structure aspects of nonadiabatic processes. We discuss the requirements of electronic structure methods to describe conical intersections and nonadiabatic couplings, how the most common excited state methods perform in describing these effects, and what the recent developments are in expanding the methodology and implementing nonadiabatic couplings.

Theoretical insights on the excited-state-deactivation mechanisms of protonated thymine and cytosine

Ab initio and surface-hopping nonadiabatic dynamics simulation methods were employed to investigate relaxation mechanisms in protonated thymine (TH⁺) and cytosine (CH⁺). A few conical intersections were located between ¹ππ* and S₀ states for each system with the CASSCF (8,8) theoretical model and relevant contributions to the deactivation mechanism of titled systems were addressed by the determination of potential energy profiles at the CASPT2 (12,10) theoretical level. It was revealed that the relaxation of the ¹ππ* state of the most stable conformer of both systems to the ground state is mostly governed by the accessible S₁/S₀ conical intersection resulting from the barrier-free out-of-plane deformation. Interestingly, it was exhibited that the ring puckering coordinate driven from the C₆ position of the heterocycle ring in TH⁺ and CH⁺ plays the most prominent role in the deactivation mechanism of considered systems. Our ab initio results are also supported by excited-state nonadiabatic dynamics simulations based on ADC(2), describing the ultrashort S₁ lifetime of TH⁺/CH⁺ by analyzing trajectories leading excited systems to the ground. It was confirmed that the excited-state population mostly relaxes to the ground via the ring puckering coordinate from the C₆ moiety. Overall, the theoretical results of this study shed light on the deactivation mechanism of protonated DNA bases.

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.

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.

Analytic gradients for state-averaged multiconfiguration pair-density functional theory

Analytic gradients are important for efficient calculations of stationary points on potential energy surfaces, for interpreting spectroscopic observations, and for efficient direct dynamics simulations. For excited electronic states, as are involved in UV-Vis spectroscopy and photochemistry, analytic gradients are readily available and often affordable for calculations using a state-averaged complete active space self-consistent-field (SA-CASSCF) wave function. However, in most cases, a post-SA-CASSCF step is necessary for quantitative accuracy, and such calculations are often too expensive if carried out by perturbation theory or configuration interaction. In this work, we present the analytic gradients for multiconfiguration pair-density functional theory based on SA-CASSCF wave functions, which is a more affordable alternative. A test set of molecules has been studied with this method, and the stationary geometries and energetics are compared to values in the literature as obtained by other methods. Excited-state geometries computed with state-averaged pair-density functional theory have similar accuracy to those from complete active space perturbation theory at the second-order.

Locating Cytosine Conical Intersections by Laser Experiments and Ab Initio Calculations

The decay mechanism of S₀ → S₁ excited cytosine (Cyt) and the effect of substitution are studied combining jet-cooled spectroscopy (nanosecond resonant two-photon ionization (R2PI) and picosecond lifetime measurements) with CASPT2//CASSCF computations for eight derivatives. For Cyt and five derivatives substituted at N1, C5, and C6, rapid internal conversion sets in at 250-1200 cm^-1 above the 0₀⁰ bands. The break-off in the spectra correlates with the calculated barriers toward the "C5-C6 twist" conical intersection, which unambiguously establishes the decay mechanism at low S₁ state vibrational energies. The barriers increase with substituents that stabilize the charge shifts at C4, C5, and C6 following (¹ππ*) excitation. The R2PI spectra of the clamped derivatives 5,6-trimethyleneCyt (TMCyt) and 1-methyl-TMCyt (1M-TMCyt), which decay along an N3 out-of-plane coordinate, extend up to +3500 and +4500 cm^-1.

Excited-state vibrations, lifetimes, and nonradiative dynamics of jet-cooled 1-ethylcytosine

The S₁ excited-state lifetime of jet-cooled 1-ethylcytosine (1ECyt) is ∼1 ns, one of the longest lifetimes for cytosine derivatives to date. Here, we analyze its S₀ → S₁ vibronic spectrum using two-color resonant two-photon ionization and UV/UV holeburning spectroscopy. Compared to cytosine and 1-methylcytosine, the S₀ → S₁ spectrum of 1ECyt shows a progression in the out-of-plane "butterfly" mode ν₁ ^', identified by spin-component scaled-second-order coupled-cluster method ab initio calculations. We also report time-resolved S₁ state nonradiative dynamics at ∼20 ps resolution by the pump/delayed ionization technique. The S₁ lifetime increases with the number of ν₁ ^' quanta from τ = 930 ps at v₁ ^'=0 to 1030 ps at v₁ ^'=2, decreasing to 14 ps at 710 cm^-1 vibrational energy. We measured the rate constants for S₁ ⇝ S₀ internal conversion and S₁ ⇝ T₁ intersystem crossing (ISC): At the v' = 0 level, k_IC is 8 × 10⁸ s^-1 or three times smaller than 1-methylcytosine. The ISC rate constant from v' = 0 to the T₁(³ππ^*) state is k_ISC = 2.4 × 10⁸ s^-1, 10 times smaller than the ISC rate constants of cytosine, but similar to that of 1-methylcytosine. Based on the calculated S₁(¹ππ^*) state radiative lifetime τ_rad = 12 ns, the fluorescence quantum yield of 1ECyt is Φ_fl ∼ 7% and the intersystem crossing yield is Φ_ISC ∼ 20%. We measured the adiabatic ionization energy of 1-ethylcytosine via excitation of the S₁ state as 8.353 ± 0.008 eV, which is 0.38 eV lower than that of amino-keto cytosine. Measurement of the ionization energy of the long-lived T₁(ππ^*) state formed via ISC reveals that it lies 3.2-3.4 eV above the S₀ ground state.

Photochemical mechanism of 1,5-benzodiazepin-2-one: electronic structure calculations and nonadiabatic surface-hopping dynamics simulations

Due to the significant applications in bioimaging, sensing, optoelectronics etc., photoluminescent materials have attracted more and more attention in recent years. 1,5-Benzodiazepin-2-one and its derivatives have been used as fluorogenic probes for the detection of biothiols. However, their photochemical and photophysical properties have remained ambiguous until now. In this work, we have adopted combined static electronic structure calculations and nonadiabatic surface-hopping dynamics simulations to study the photochemical mechanism of 1,5-benzodiazepin-2-one. Firstly, we optimized minima and conical intersections in S0 and S1 states; then, we proposed three nonadiabatic decay pathways that efficiently populate the ground state from the Franck-Condon region based on computed electronic structure information and dynamics simulations. In the first pathway, upon photoexcitation to the S1 state, the system proceeds with an ultrafast excited-state intramolecular proton transfer (ESIPT) process. Then, the molecule tends to rotate around the C-C bond until it encounters keto conical intersections, from which the system can easily decay to the ground state. The other two pathways involve the enol channels in which the S1 system hops to the ground state via two enol S1/S0 conical intersections, respectively. These three energetically allowed S1 excited-state deactivation pathways are responsible for the decrease of fluorescence quantum yield. The present work will provide detailed mechanistic information of similar systems.

Constraint structure optimization to a specific minimum using ionization energy

A structure optimization method with ionization energy constraint is developed to explore structures with specific ionization energy. The Levine-Coe-Martínez penalty function (J Phys Chem B 2008, 112, 405) was adopted, and the penalty function includes a predefined core-ionization energy and inner-shell ionization energy. For an S_N 2 reaction, isomerization of a platinum complex, a proton transfer reaction, and carbon monoxide adsorption on a palladium cluster, the present method was tested, and the targeted energy minima were obtained as designated by the input ionization energy. The shape of the objective function, the parameters in the penalty function, and structural changes during the optimization process were discussed. An automated parameter setting and possible problems are discussed for future direction. © 2018 Wiley Periodicals, Inc.

Ultrafast Excited-State Dynamics of Hydrogen-Bonded Cytosine Microsolvated Clusters with Protic and Aprotic Polar Solvents

Microsolvation effects on the ultrafast excited-state deactivation dynamics of cytosine (Cy) were studied in hydrogen-bonded Cy clusters with protic and aprotic solvents using mass-resolved femtosecond pump-probe ionization spectroscopy. Two protic solvents, water (H₂O) and methanol (MeOH), and one aprotic solvent, tetrahydrofuran (THF), were investigated, and transients of Cy·(H₂O)_1-6, Cy·(MeOH)_1-3, and Cy·THF microsolvated clusters produced in supersonic expansions were measured. With the aid of electronic structure calculations, we assigned the observed dynamics to the low-energy isomers of various Cy clusters and discussed the microsolvation effect on the excited-state deactivation dynamics. With the protic solvents only the microsolvated clusters of Cy keto tautomer were observed. The observed decay time constants of Cy·(H₂O) _n are 0.5 ps for n = 1 and ∼0.2-0.25 ps for n = 2-6. For Cy·(MeOH) _n clusters, the decay time constant for n = 1 cluster is similar to that of the Cy monohydrate, but for n = 2 and 3 the decays are about a factor of 2 slower than the corresponding microhydrates. With the aprotic solvent, THF, hydrogen-bonded complexes of both keto and enol tautomers are present in the beam. The keto-Cy·THF shows a decay similar to that of the keto-Cy monomer, whereas the enol-Cy·THF exhibits a 2-fold slower decay than the enol-Cy monomer, suggesting an increase in the barrier to excited-state deactivation upon binding of one THF molecule to the enol form of Cy.

Ab initio surface hopping excited-state molecular dynamics approach on the basis of spin-orbit coupled states: An application to the A-band photodissociation of CH3 I

Ab initio molecular dynamics approach has been extended to multi-state dynamics on the basis of the spin-orbit coupled electronic states that are obtained through diagonalization of the spin-orbit coupling matrix with the multi-state second-order multireference perturbation theory energies in diagonal elements and the spin-orbit coupling terms at the state-averaged complete active space self-consistent field level in off-diagonal elements. Nonadiabatic transitions over the spin-orbit coupled states were taken into account explicitly by a surface hopping scheme with utilizing the nonadiabatic coupling terms calculated by numerical differentiation of the spin-orbit coupled wavefunctions and analytical nonadiabatic coupling terms. The present method was applied to the A-band photodissociation of methyl iodide, CH₃ I + hv → CH₃ + I (² P_3/2 )/I* (² P_1/2 ), for which a pioneering theoretical work was reported by Amatatsu, Yabushita, and Morokuma. The present results reproduced well the experimental branching ratio and energy distributions in the dissociative products. © 2018 Wiley Periodicals, Inc.

Planarizing cytosine: The S1 state structure, vibrations, and nonradiative dynamics of jet-cooled 5,6-trimethylenecytosine

We measure the S₀ → S₁ spectrum and time-resolved S₁ state nonradiative dynamics of the "clamped" cytosine derivative 5,6-trimethylenecytosine (TMCyt) in a supersonic jet, using two-color resonant two-photon ionization (R2PI), UV/UV holeburning, and ns time-resolved pump/delayed ionization. The experiments are complemented with spin-component scaled second-order approximate coupled cluster (SCS-CC2), time-dependent density functional theory, and multi-state second-order perturbation-theory (MS-CASPT2) ab initio calculations. While the R2PI spectrum of cytosine breaks off ∼500 cm^-1 above its 0₀⁰ band, that of TMCyt extends up to +4400 cm^-1 higher, with over a hundred resolved vibronic bands. Thus, clamping the cytosine C⁵-C⁶ bond allows us to explore the S₁ state vibrations and S₀ → S₁ geometry changes in detail. The TMCyt S₁ state out-of-plane vibrations ν₁^', ν₃^', and ν₅^' lie below 420 cm^-1, and the in-plane ν₁₁^', ν₁₂^', and ν₂₃^' vibrational fundamentals appear at 450, 470, and 944 cm^-1. S₀  →  S₁ vibronic simulations based on SCS-CC2 calculations agree well with experiment if the calculated ν₁^', ν₃^', and ν₅^' frequencies are reduced by a factor of 2-3. MS-CASPT2 calculations predict that the ethylene-type S₁ ⇝ S₀ conical intersection (CI) increases from +366 cm^-1 in cytosine to >6000 cm^-1 in TMCyt, explaining the long lifetime and extended S₀ → S₁ spectrum. The lowest-energy S₁ ⇝ S₀ CI of TMCyt is the "amino out-of-plane" (OP_X) intersection, calculated at +4190 cm^-1. The experimental S₁ ⇝ S₀ internal conversion rate constant at the S₁(v^'=0) level is k_IC=0.98-2.2⋅10⁸ s^-1, which is ∼10 times smaller than in 1-methylcytosine and cytosine. The S₁(v^'=0) level relaxes into the T₁(³ππ*) state by intersystem crossing with k_ISC=0.41-1.6⋅10⁸ s^-1. The T₁ state energy is measured to lie 24 580±560 cm^-1 above the S₀ state. The S₁(v^'=0) lifetime is τ=2.9 ns, resulting in an estimated fluorescence quantum yield of Φ_fl=24%. Intense two-color R2PI spectra of the TMCyt amino-enol tautomers appear above 36 000 cm^-1. A sharp S₁ ionization threshold is observed for amino-keto TMCyt, yielding an adiabatic ionization energy of 8.114±0.002 eV.

Sub-50 fs excited state dynamics of 6-chloroguanine upon deep ultraviolet excitation

The photophysical properties of natural nucleobases and their respective nucleotides are ascribed to the sub-picosecond lifetime of their first singlet states in the UV-B region (260-350 nm). Electronic transitions of the ππ* type, which are stronger than those in the UV-B region, lie at the red edge of the UV-C range (100-260 nm) in all isolated nucleobases. The lowest energetic excited states in the UV-B region of nucleobases have been investigated using a plethora of experimental and theoretical methods in gas and solution phases. The sub-picosecond lifetime of these molecules is not a general attribute of all nucleobases but specific to the five primary nucleobases and a few xanthine and methylated derivatives. To determine the overall UV photostability, we aim to understand the effect of more energetic photons lying in the UV-C region on nucleobases. To determine the UV-C initiated photophysics of a nucleobase system, we chose a halogen substituted purine, 6-chloroguanine (6-ClG), that we had investigated previously using resonance Raman spectroscopy. We have performed quantitative measurements of the resonance Raman cross-section across the Bb absorption band (210-230 nm) and constructed the Raman excitation profiles. We modeled the excitation profiles using Lee and Heller's time-dependent theory of resonance Raman intensities to extract the initial excited state dynamics of 6-ClG within 30-50 fs after photoexcitation. We found that imidazole and pyrimidine rings of 6-ClG undergo expansion and contraction, respectively, following photoexcitation to the Bb state. The amount of distortions of the excited state structure from that of the ground state structure is reflected by the total internal reorganization energy that is determined at 112 cm(-1). The contribution of the inertial component of the solvent response towards the total reorganization energy was obtained at 1220 cm(-1). In addition, our simulation also yields an instantaneous response of the first solvation shell within an ultrafast timescale of less than 30 fs following photoexcitation.

Resolving Ultrafast Photoinduced Deactivations in Water-Solvated Pyrimidine Nucleosides

For the first time, ultrafast deactivations of photoexcited water-solvated pyrimidine nucleosides are mapped employing hybrid QM(CASPT2)/MM(AMBER) optimizations that account for explicit solvation, sugar effects, and dynamically correlated potential energy surfaces. Low-energy S₁/S₀ ring-puckering and ring-opening conical intersections (CIs) are suggested to drive the ballistic coherent subpicosecond (<200 fs) decays observed in each pyrimidine, the energetics controlling this processes correlating with the lifetimes observed. A second bright ¹π₂π* state, promoting excited-state population branching and leading toward a third CI with the ground state, is proposed to be involved in the slower ultrafast decay component observed in Thd/Cyd. The transient spectroscopic signals of the competitive deactivation channels are computed for the first time. A general unified scheme for ultrafast deactivations, spanning the sub- to few-picosecond time domain, is eventually delivered, with computed data that matches the experiments and elucidates the intrinsic photoprotection mechanism in solvated pyrimidine nucleosides.

The IPEA dilemma in CASPT2

Multi-configurational second order perturbation theory (CASPT2) has become a very popular method for describing excited-state properties since its development in 1990. To account for systematic errors found in the calculation of dissociation energies, an empirical correction applied to the zeroth-order Hamiltonian, called the IPEA shift, was introduced in 2004. The errors were attributed to an unbalanced description of open-shell versus closed-shell electronic states and is believed to also lead to an underestimation of excitation energies. Here we show that the use of the IPEA shift is not justified and the IPEA should not be used to calculate excited states, at least for organic chromophores. This conclusion is the result of three extensive analyses. Firstly, we survey the literature for excitation energies of organic molecules that have been calculated with the unmodified CASPT2 method. We find that the excitation energies of 356 reference values are negligibly underestimated by 0.02 eV. This value is an order of magnitude smaller than the expected error based on the calculation of dissociation energies. Secondly, we perform benchmark full configuration interaction calculations on 137 states of 13 di- and triatomic molecules and compare the results with CASPT2. Also in this case, the excited states are underestimated by only 0.05 eV. Finally, we perform CASPT2 calculations with different IPEA shift values on 309 excited states of 28 organic small and medium-sized organic chromophores. We demonstrate that the size of the IPEA correction scales with the amount of dynamical correlation energy (and thus with the size of the system), and gets immoderate already for the molecules considered here, leading to an overestimation of the excitation energies. It is also found that the IPEA correction strongly depends on the size of the basis set. The dependency on both the size of the system and of the basis set, contradicts the idea of a universal IPEA shift which is able to compensate for systematic CASPT2 errors in the calculation of excited states.

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 origin of efficient triplet state population in sulfur-substituted nucleobases

Elucidating the photophysical mechanisms in sulfur-substituted nucleobases (thiobases) is essential for designing prospective drugs for photo- and chemotherapeutic applications. Although it has long been established that the phototherapeutic activity of thiobases is intimately linked to efficient intersystem crossing into reactive triplet states, the molecular factors underlying this efficiency are poorly understood. Herein we combine femtosecond transient absorption experiments with quantum chemistry and nonadiabatic dynamics simulations to investigate 2-thiocytosine as a necessary step to unravel the electronic and structural elements that lead to ultrafast and near-unity triplet-state population in thiobases in general. We show that different parts of the potential energy surfaces are stabilized to different extents via thionation, quenching the intrinsic photostability of canonical DNA and RNA nucleobases. These findings satisfactorily explain why thiobases exhibit the fastest intersystem crossing lifetimes measured to date among bio-organic molecules and have near-unity triplet yields, whereas the triplet yields of canonical nucleobases are nearly zero.

Intersystem Crossing Pathways in the Noncanonical Nucleobase 2-Thiouracil: A Time-Dependent Picture

The deactivation mechanism after ultraviolet irradiation of 2-thiouracil has been investigated using nonadiabatic dynamics simulations at the MS-CASPT2 level of theory. It is found that after excitation the S2 quickly relaxes to S1, and from there intersystem crossing takes place to both T2 and T1 with a time constant of 400 fs and a triplet yield above 80%, in very good agreement with recent femtosecond experiments in solution. Both indirect S1 → T2 → T1 and direct S1 → T1 pathways contribute to intersystem crossing, with the former being predominant. The results contribute to the understanding of how some noncanonical nucleobases respond to harmful ultraviolet light, which could be relevant for prospective photochemotherapeutic applications.

Intersystem crossing rates of S1 state keto-amino cytosine at low excess energy

The amino-keto tautomer of supersonic jet-cooled cytosine undergoes intersystem crossing (ISC) from the v = 0 and low-lying vibronic levels of its S1((1)ππ(∗)) state. We investigate these ISC rates experimentally and theoretically as a function of S1 state vibrational excess energy Eexc. The S1 vibronic levels are pumped with a ∼5 ns UV laser, the S1 and triplet state ion signals are separated by prompt or delayed ionization with a second UV laser pulse. After correcting the raw ISC yields for the relative S1 and T1 ionization cross sections, we obtain energy dependent ISC quantum yields QISC (corr)=1%-5%. These are combined with previously measured vibronic state-specific decay rates, giving ISC rates kISC = 0.4-1.5 ⋅ 10(9) s(-1), the corresponding S1⇝S0 internal conversion (IC) rates are 30-100 times larger. Theoretical ISC rates are computed using SCS-CC2 methods, which predict rapid ISC from the S1; v = 0 state with kISC = 3 ⋅ 10(9) s(-1) to the T1((3)ππ(∗)) triplet state. The surprisingly high rate of this El Sayed-forbidden transition is caused by a substantial admixture of (1)nOπ(∗) character into the S1((1)ππ(∗)) wave function at its non-planar minimum geometry. The combination of experiment and theory implies that (1) below Eexc = 550 cm(-1) in the S1 state, S1⇝S0 internal conversion dominates the nonradiative decay with kIC ≥ 2 ⋅ 10(10) s(-1), (2) the calculated S1⇝T1 ((1)ππ(∗)⇝(3)ππ(∗)) ISC rate is in good agreement with experiment, (3) being El-Sayed forbidden, the S1⇝T1 ISC is moderately fast (kISC = 3 ⋅ 10(9) s(-1)), and not ultrafast, as claimed by other calculations, and (4) at Eexc ∼ 550 cm(-1) the IC rate increases by ∼50 times, probably by accessing the lowest conical intersection (the C5-twist CI) and thereby effectively switching off the ISC decay channels.

Remarkable effects of solvent and substitution on the photo-dynamics of cytosine: a femtosecond broadband time-resolved fluorescence and transient absorption study

Cytosine (Cyt) among all the nucleic acid bases features the most complex and least understood nonradiative deactivation, a process that is crucially important for its photostability. Herein, the excited state dynamics of Cyt and a series of its N1- and C5-derivatives, including the full set of Cyt nucleosides and nucleotides in DNA and RNA and the nucleosides of 5-methyl cytosine, 5-methylcytidine and 2'-deoxy-5-methylcytidine, have been investigated in water and in methanol employing femtosecond broadband time-resolved fluorescence coupled with fs transient absorption spectroscopy. The results reveal remarkable state-specific effects of the substitution and solvent in tuning distinctively the timescales and pathways of the nonradiative decays. For Cyt and the N1-derivatives, the nonradiative deactivations occur in a common two-state process through three channels, two from the light-absorbing ππ* state with respectively the sub-picosecond (∼0.2 ps) and the picosecond (∼1.5 ps) time constant, and the third is due to an optically dark nπ* state with the lifetime ranging from several to hundreds of picoseconds depending on solvents and substitutions. Compared to Cyt, the presence of the ribose or deoxyribose moiety at the N1 position of N1-derivatives facilitates the formation of the nπ* at the sub-picosecond timescale and at the same time increases its lifetime by ∼4-6 times in both water and methanol. In sharp contrast, the existence of the methyl group at the C5 position of the C5-derivatives eliminates completely the sub-picosecond ππ* channel and the channel due to the nπ*, but on the other hand slows down the decay of the ππ* state which after relaxation exhibits a single time constant of ∼4.1 to ∼7.6 ps depending on solvents. Varying the solvent from water to methanol accelerates only slightly the decay of the ππ* state in all the compounds; while for Cyt and its N1-derivatives, this change of solvent also retards strongly the nπ* channel, prolongs its lifetime from such as ∼7.7 ps in water to ∼52 ps in methanol for Cyt and from ∼30 ps in water to ∼186 ps in methanol for deoxycytidine. The spectral signatures we obtained for the ππ* and the nπ* states allow unambiguous evidence for clarifying uncertainties in the excited states of Cyt and the derivatives. The results provide a unifying experimental characterization at an improved level of detail about the photophysics of Cyt and its analogues under biologically relevant conditions and may help in understanding the photostability as well as photo-damages of the bases and related DNAs.

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 DFT and multi-configurational perturbation theory study on O2 binding to a model heme compound via the spin-change barrier

Potential energy surface of the O₂ binding to a model heme compound via minimum energy intersystem crossing point (MEISCP) was investigated with DFT and MS-CASPT2. The porphyrin's symmetric shrinking vibration mode contributes to reach the MESICP from the T₁ minimum.

Energy dissipative photoprotective mechanism of carotenoid spheroidene from the photoreaction center of purple bacteria Rhodobacter sphaeroides

Carotenoid spheroidene (SPO) functions for photoprotection in the photosynthetic reaction centers (RCs) and effectively dissipates its triplet excitation energy. Sensitized cis-to-trans isomerization was proposed as a possible mechanism for a singlet-triplet energy crossing for the 15,15'-cis-SPO; however, it has been questioned recently. To understand the dissipative photoprotective mechanism of this important SPO and to overcome the existing controversies on this issue, we carried out a theoretical investigation using density functional theory on the possible triplet energy relaxation mechanism through the cis-to-trans isomerization. Together with the earlier experimental observations, the possible mechanism was discussed for the triplet energy relaxation of the 15,15'-cis-SPO. The result shows that complete cis-to-trans isomerization is not necessary. Twisting the C15-C15' bond leads to singlet-triplet energy crossing at ϕ(14,15,15',14') = 77° with an energy 32.5 kJ mol(-1) (7.7 kcal mol(-1)) higher than that of the T1 15,15'-cis minimum. Further exploration of the minimum-energy intersystem crossing (MEISC) point shows that triplet relaxation could occur at a less distorted structure (ϕ = 58.4°) with the energy height of 26.5 KJ mol(-1) (6.3 kcal mol(-1)). Another important reaction coordinate to reach the MEISC point is the bond-length alternation. The model truncation effect, solvent effect, and spin-orbit coupling were also investigated. The singlet-triplet crossing was also investigated for the 13,14-cis stereoisomer and locked-13,14-cis-SPO. We also discussed the origin of the natural selection of the cis over trans isomer in the RC.

Solvent effects on the ultrafast nonradiative deactivation mechanisms of thymine in aqueous solution: excited-state QM/MM molecular dynamics simulations

On-the-fly excited-state quantum mechanics/molecular mechanics molecular dynamics (QM/MM-MD) simulations of thymine in aqueous solution are performed to investigate the role of solvent water molecules on the nonradiative deactivation process. The complete active space second-order perturbation theory (CASPT2) method is employed for a thymine molecule as the QM part in order to provide a reliable description of the excited-state potential energies. It is found that, in addition to the previously reported deactivation pathway involving the twisting of the C-C double bond in the pyrimidine ring, another efficient deactivation pathway leading to conical intersections that accompanies the out-of-plane displacement of the carbonyl group is observed in aqueous solution. Decay through this pathway is not observed in the gas phase simulations, and our analysis indicates that the hydrogen bonds with solvent water molecules play a key role in stabilizing the potential energies of thymine in this additional decay pathway.

Time-resolved photoelectron imaging of the isolated deprotonated nucleotides

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

Photoinduced processes in nucleic acids

Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.

Excited-state tautomerization of gas-phase cytosine

In order to investigate experimentally observed phototautomerization of gas-phase cytosine, several excited-state tautomerization mechanisms were characterized at the EOM-CCSD and TDDFT levels. All pathways that took place exclusively on the S1 surface were found to have significant barriers that were much higher than the barriers involved in radiationless decay of cytosine tautomers through conical intersections back to the ground state; tautomerization in this fashion cannot compete with radiationless relaxation. However, an alternative possibility is that the conical intersections that facilitate radiationless decay could also facilitate tautomerization. Barrierless pathways indicate that it is energetically possible that bifurcation at the conical intersections can lead to a subset of the population reaching different tautomers. This could be an explanation for the observed tautomerization of keto cytosine after exposure to low-energy UV light.