Three-state conical intersections in nucleic acid bases

Direct Probe of Conical Intersection Photochemistry by Time-Resolved X-ray Magnetic Circular Dichroism

The direct probing of photochemical dynamics by detecting the electronic coherence generated during passage through conical intersections is an intriguing challenge. The weak coherence signal and the difficulty in preparing purely excited wave packets that exclude coherence from other sources make it experimentally challenging. We propose to use time-resolved X-ray magnetic circular dichroism to probe the wave packet dynamics around the conical intersection. The magnetic field amplifies the relative strength of the electronic coherence signal compared to populations through the magnetic field response anisotropy. More importantly, since the excited state relaxation through conical intersections involves a change of parity, the magnetic coupling matches the symmetry of the response function with the electronic coherence, making the coherence signal only sensitive to the conical intersection induced coherence and excludes the pump pulse induced coherence between the ground state and excited state. In this theoretical study, we apply this technique to the photodissociation dynamics of a pyrrole molecule and demonstrate its capability of probing electronic coherence at a conical intersection as well as population transfer. We demonstrate that a magnetic field can be effectively used to extract novel information about electron and nuclear molecular dynamics.

Coherent control from quantum commitment probabilities

We introduce a general definition of a quantum committor in order to clarify reaction mechanisms and facilitate control in processes where coherent effects are important. With a quantum committor, we generalize the notion of a transition state to quantum superpositions and quantify the effect of interference on the progress of the reaction. The formalism is applicable to any linear quantum master equation supporting metastability for which absorbing boundary conditions designating the reactant and product states can be applied. We use this formalism to determine the dependence of the quantum transition state on coherences in a polaritonic system and optimize the initialization state of a conical intersection model to control reactive outcomes, achieving yields of the desired state approaching 100%. In addition to providing a practical tool, the quantum committor provides a conceptual framework for understanding reactions in cases when classical intuitions fail.

WFOT: A Wave Function Overlap Tool between Single- and Multi-Reference Electronic Structure Methods for Spectroscopy Simulation

We report the development of a novel diagnostic tool, named wave function overlap tool (WFOT), designed to evaluate the overlap between wave functions computed at single-reference [i.e., time-dependent density functional theory or configuration interaction singles (CIS)] and multireference (i.e., CASSCF/CASPT2) electronic structure levels of theory. It relies on truncating the single- and multireference WFs to CIS-like expansions spanning the same configurational space and maximizing the molecular orbital overlap by means of a unitary transformation. To demonstrate the functionality of the tool, we calculate the transient spectrum of acetylacetone by evaluating excited state absorption signals with multireference quality on top of single-reference on-the-fly dynamics simulations. Semiautomatic spectra generation is facilitated by interfacing the tool with the COBRAMM package, which also allows one to use WFOT with several quantum chemistry codes such as Gaussian, NWChem, and OpenMolcas. Other exciting possibilities for the utilization of the code beyond the simulation of transient absorption spectroscopy are eventually discussed.

Seeking a quantum advantage with trapped-ion quantum simulations of condensed-phase chemical dynamics

Simulating the quantum dynamics of molecules in the condensed phase represents a longstanding challenge in chemistry. Trapped-ion quantum systems may serve as a platform for the analog-quantum simulation of chemical dynamics that is beyond the reach of current classical-digital simulation. To identify a 'quantum advantage' for these simulations, performance analysis of both analog-quantum simulation on noisy hardware and classical-digital algorithms is needed. In this Review, we make a comparison between a noisy analog trapped-ion simulator and a few choice classical-digital methods on simulating the dynamics of a model molecular Hamiltonian with linear vibronic coupling. We describe several simple Hamiltonians that are commonly used to model molecular systems, which can be simulated with existing or emerging trapped-ion hardware. These Hamiltonians may serve as stepping stones towards the use of trapped-ion simulators for systems beyond the reach of classical-digital methods. Finally, we identify dynamical regimes in which classical-digital simulations seem to have the weakest performance with respect to analog-quantum simulations. These regimes may provide the lowest hanging fruit to make the most of potential quantum advantages.

Photodynamics of azaindoles in polar media: the influence of the environment

We have studied the relaxation dynamics of a family of azaindole (AI) structural isomers, 4-, 5-, 6- and 7-AI, by steady-state and time-resolved methods (fs-transient absorption and fluorescence up-conversion), in solvents of different polarity. The measurements in aprotic solvents show distinctive fluorescence yields and excited state lifetimes among the isomers, which are tuned by the polarity of the medium. Guided by simple TD-DFT calculations and based on the behavior observed in the isolated species, it has been possible to address the influence of the environment polarity on the relaxation route. According to the obtained picture, the energy of the nπ* state, which is strongly dependent on the position of the pyridinic nitrogen, controls the rate of the internal conversion channel that accounts for the distinctive photophysical behavior of the isomers. On the other hand, preliminary measurements in protic media (methanol) show a very different photodynamical behavior, in which the anomalous measured fluorescent patterns are very likely the result of reactive channels (proton transfer) triggered by the electronic excitation.

Galván I, Rivalta I, Aquilante F, Garavelli M, Lindh R, Segarra-Martí J. Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.

Finding Excited-State Minimum Energy Crossing Points on a Budget: Non-Self-Consistent Tight-Binding Methods

The automated exploration and identification of minimum energy conical intersections (MECIs) is a valuable computational strategy for the study of photochemical processes. Due to the immense computational effort involved in calculating non-adiabatic derivative coupling vectors, simplifications have been introduced focusing instead on minimum energy crossing points (MECPs), where promising attempts were made with semiempirical quantum mechanical methods. A simplified treatment for describing crossing points between almost arbitrary diabatic states based on a non-self-consistent extended tight-binding method, GFN0-xTB, is presented. Involving only a single diagonalization of the Hamiltonian, the method can provide energies and gradients for multiple electronic states, which can be used in a derivative coupling-vector-free scheme to calculate MECPs. By comparison with high-lying MECIs of benchmark systems, it is demonstrated that the identified geometries are good starting points for further MECI refinement with ab initio methods.

Time-resolved X-ray and XUV based spectroscopic methods for nonadiabatic processes in photochemistry

The photochemistry of numerous molecular systems is influenced by conical intersections (CIs). These omnipresent nonadiabatic phenomena provide ultra-fast radiationless relaxation channels by creating degeneracies between electronic states and decide over the final photoproducts. In their presence, the Born-Oppenheimer approximation breaks down, and the timescales of the electron and nuclear dynamics become comparable. Due to the ultra-fast dynamics and the complex interplay between nuclear and electronic degrees of freedom, the direct experimental observation of nonadiabatic processes close to CIs remains challenging. In this article, we give a theoretical perspective on novel spectroscopic techniques capable of observing clear signatures of CIs. We discuss methods that are based on ultra-short laser pulses in the extreme ultraviolet and X-ray regime, as their spectral and temporal resolution allow for resolving the ultra-fast dynamics near CIs.

Nonadiabatic transition paths from quantum jump trajectories

We present a means of studying rare reactive pathways in open quantum systems using transition path theory and ensembles of quantum jump trajectories. This approach allows for the elucidation of reactive paths for dissipative, nonadiabatic dynamics when the system is embedded in a Markovian environment. We detail the dominant pathways and rates of thermally activated processes and the relaxation pathways and photoyields following vertical excitation in a minimal model of a conical intersection. We find that the geometry of the conical intersection affects the electronic character of the transition state as defined through a generalization of a committor function for a thermal barrier crossing event. Similarly, the geometry changes the mechanism of relaxation following a vertical excitation. Relaxation in models resulting from small diabatic coupling proceeds through pathways dominated by pure dephasing, while those with large diabatic coupling proceed through pathways limited by dissipation. The perspective introduced here for the nonadiabatic dynamics of open quantum systems generalizes classical notions of reactive paths to fundamentally quantum mechanical processes.

Non-radiative deactivation of excited cytosine: probing of different DFT functionals and basis sets in solvents with different polarity

The vertical excitation and emission energies of the cytosine oxo-amino form were calculated at the TD DFT level of theory with several functionals, basis sets, and solvents with different polarity (PCM). They were compared with the experimental UV absorption and fluorescence maxima, revealing that the minimal deviation of the vertical excitation energies from the of UV absorption maxima can be achieved when the hybrid functional B3LYP is applied within the calculations. Regular correlations like curves with saturation between the vertical excitation/emission energies and the dielectric constants were registered. The relaxation of the ¹ππ^* excited state through an ethylene-like conical intersection S₀/S₁ should occur through decrease of the decay rate (commented qualitatively here) with the rise of the solvent polarity.

Ultrafast Intersystem Crossing Dynamics of 6-Selenoguanine in Water

Rationalizing the photochemistry of nucleobases where an oxygen is replaced by a heavier atom is essential for applications that exploit near-unity triplet quantum yields. Herein, we report on the ultrafast excited-state deactivation mechanism of 6-selenoguanine (6SeGua) in water by combining nonadiabatic trajectory surface-hopping dynamics with an electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. We find that the predominant relaxation mechanism after irradiation starts on the bright singlet S₂ state that converts internally to the dark S₁ state, from which the population is transferred to the triplet T₂ state via intersystem crossing and finally to the lowest T₁ state. This S₂ → S₁ → T₂ → T₁ deactivation pathway is similar to that observed for the lighter 6-thioguanine (6tGua) analogue, but counterintuitively, the T₁ lifetime of the heavier 6SeGua is shorter than that of 6tGua. This fact is explained by the smaller activation barrier to reach the T₁/S₀ crossing point and the larger spin-orbit couplings of 6SeGua compared to 6tGua. From the dynamical simulations, we also calculate transient absorption spectra (TAS), which provide two time constants (τ₁ = 131 fs and τ₂ = 191 fs) that are in excellent agreement with the experimentally reported value (τ_exp = 130 ± 50 fs) (Farrel et al. J. Am. Chem. Soc. 2018, 140, 11214). Intersystem crossing itself is calculated to occur with a time scale of 452 ± 38 fs, highlighting that the TAS is the result of a complex average of signals coming from different nonradiative processes and not intersystem crossing alone.

Cavity-induced non-adiabatic dynamics and spectroscopy of molecular rovibrational polaritons studied by multi-mode quantum models

We study theoretically the quantum dynamics and spectroscopy of rovibrational polaritons formed in a model system composed of a single rovibrating diatomic molecule, which interacts with two degenerate, orthogonally polarized modes of an optical Fabry–Pérot cavity. We employ an effective rovibrational Pauli–Fierz Hamiltonian in length gauge representation and identify three-state vibro-polaritonic conical intersections (VPCIs) between singly excited vibro-polaritonic states in a two-dimensional angular coordinate branching space. The lower and upper vibrational polaritons are of mixed light–matter hybrid character, whereas the intermediate state is purely photonic in nature. The VPCIs provide effective population transfer channels between singly excited vibrational polaritons, which manifest in rich interference patterns in rotational densities. Spectroscopically, three bright singly excited states are identified when an external infrared laser field couples to both a molecular and a cavity mode. The non-trivial VPCI topology manifests as pronounced multi-peak progression in the spectral region of the upper vibrational polariton, which is traced back to the emergence of rovibro-polaritonic light–matter hybrid states. Experimentally, ubiquitous spontaneous emission from cavity modes induces a dissipative reduction of intensity and peak broadening, which mainly influences the purely photonic intermediate state peak as well as the rovibro-polaritonic progression.

Exact-Factorization-Based Surface Hopping for Multistate Dynamics

A surface-hopping algorithm recently derived from the exact factorization approach, SHXF [Ha et al. J. Phys. Chem. Lett. 2018, 9, 1097], introduces an additional term in the electronic equation of surface hopping that couples electronic states through the quantum momentum. This term not only provides a first-principles description of decoherence, but here we show it is crucial to accurately capture nonadiabatic dynamics when more than two states are occupied at any given time. Using a vibronic coupling model of the uracil cation, we show that the lack of this term in traditional surface-hopping methods, including those with decoherence corrections, leads to failure to predict the dynamics through a three-state intersection, while SHXF performs similarly to the multiconfiguration time-dependent Hartree quantum dynamics benchmark.

Adenine ultrafast photorelaxation via electron-driven proton transfer

Photorelaxation of adenine in water was reported to be ultrafast (within 180 fs) primarily due to radiationless relaxation. However, in the last two decades, several experimental and theoretical investigations on photoexcitation of adenine have revealed diverse types of decay mechanisms. Using time-dependent density functional excited-state nonadiabatic dynamics simulations we show that it is the water to adenine electron-driven proton transfer (EDPT) barrierless reaction responsible for the ultrafast component of the adenine relaxation, which, however, occurred only in the case of the 7H isomer of adenine with five water molecules. This result reveals a known reaction pathway, however not found in previous simulations, with inference for the ultrafast relaxation mechanisms of adenine reported in experiments. The 9H isomer of adenine with six water molecules relaxing in a water cluster followed the previously known structural distortion (C2) decay pathway. The observations of the adenine EDPT reaction with water provide the origin of the experimental ultrafast adenine decay component and present a possible method to tackle future computational challenges in molecular-level biological processes.

UVPD spectroscopy of differential mobility-selected prototropic isomers of protonated adenine

Two prototropic isomers of adenine are formed in an electrospray ion source and are resolved spatially in a differential mobility spectrometer before detection in a triple quadrupole mass spectrometer. Each isomer is gated in CV space before being trapped in the linear ion trap of the modified mass spectrometer, where they are irradiated by the tuneable output of an optical parametric oscillator and undergo photodissociation to form charged fragments with m/z 119, 109, and 94. The photon-normalised intensity of each fragmentation channel is measured and the action spectra for each DMS-gated tautomer are obtained. Our analysis of the action spectra, aided by calculated vibronic spectra and thermochemical data, allow us to assign the two signals in our measured ionograms to specific tautomers of protonated adenine.

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.

Photoinduced phenomena in water solution of melamine explaining the photostability of the compound

Two tautomers of melamine (triamino and imino-diamino) were studied at the BLYP/aug-cc-pVDZ theoretical level. It was found that the two tautomers are bridged with the ¹πσ^* excited-state reaction path. The high photostability of melamine in water solution was explained with the mechanism of ring deformation which occurs along the ¹ππ^* excited-state reaction path. The two mechanisms are investigated at the TD BLYP level of theory using the linear interpolation in internal coordinates approach.

How important are the residual nonadiabatic couplings for an accurate simulation of nonadiabatic quantum dynamics in a quasidiabatic representation?

Diabatization of the molecular Hamiltonian is a standard approach to remove the singularities of nonadiabatic couplings at conical intersections of adiabatic potential energy surfaces. In general, it is impossible to eliminate the nonadiabatic couplings entirely-the resulting "quasidiabatic" states are still coupled by smaller but nonvanishing residual nonadiabatic couplings, which are typically neglected. Here, we propose a general method for assessing the validity of this potentially drastic approximation by comparing quantum dynamics simulated either with or without the residual couplings. To make the numerical errors negligible to the errors due to neglecting the residual couplings, we use the highly accurate and general eighth-order composition of the implicit midpoint method. The usefulness of the proposed method is demonstrated on nonadiabatic simulations in the cubic Jahn-Teller model of nitrogen trioxide and in the induced Renner-Teller model of hydrogen cyanide. We find that, depending on the system, initial state, and employed quasidiabatization scheme, neglecting the residual couplings can result in wrong dynamics. In contrast, simulations with the exact quasidiabatic Hamiltonian, which contains the residual couplings, always yield accurate results.

Optimization of Three State Conical Intersections by Adaptive Penalty Function Algorithm in Connection with the Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory Method (MRSF-TDDFT)

A new adaptive algorithm for penalty function optimization for minimum-energy three-states conical intersections (ME3CI) is suggested. The new algorithm differs from the original penalty function algorithm by (a) removing the redundancy in the target function, (b) using an adaptive increment for the penalty function weighting factor, and (c) using tighter convergence criteria for the energy gap. The latter was introduced to guarantee convergence to a true conical intersection rather than to a narrowly avoided crossing geometry. The new algorithm was tested in the optimization of the ME3CI geometries in butadiene and malonaldehyde, where all of the previously found true ME3CI geometries were recovered. The previously found butadiene's CI_3/2/1 turned out to be a narrowly avoided crossing. For butadiene, seven new ME3CI geometries have been located. Because of the removal of the redundancy and the use of the adaptive weighting factor, the convergence rate of the new algorithm is noticeably improved as compared to that of the previously proposed penalty function algorithm. The application to malonaldehyde and butadiene demonstrates that the three-state conical intersections may be more abundant and hence more involved in the photochemistry than previously thought. The recently developed mixed-reference spin flip (MRSF)-TDDFT method yields ME3CI geometries and relative energies quantitatively consistent with the previously reported calculations at a much reduced computational cost.

Excited-State Properties and Relaxation Pathways of Selenium-Substituted Guanine Nucleobase in Aqueous Solution and DNA Duplex

The excited-state properties and relaxation mechanisms after light irradiation of 6-selenoguanine (6SeG) in water and in DNA have been investigated using a quantum mechanics/molecular mechanics (QM/MM) approach with the multistate complete active space second-order perturbation theory (MS-CASPT2) method. In both environments, the S₁ ¹(n_Seπ₅^*) and S₂ ¹(π_Seπ₅^*) states are predicted to be the spectroscopically dark and bright states, respectively. Two triplet states, T₁ ³(π_Seπ₅^*) and T₂ ³(n_Seπ₅^*), are found energetically below the S₂ state. Extending the QM region to include the 6SeG-Cyt base pair slightly stabilizes the S₂ state and destabilizes the S₁, due to hydrogen-bonding interactions, but it does not affect the order of the states. The optimized minima, conical intersections, and singlet-triplet crossings are very similar in water and in DNA, so that the same general mechanism is found. Additionally, for each excited state geometry optimization in DNA, three kind of structures ("up", "down", and "central") are optimized which differ from each other by the orientation of the C═Se group with respect to the surrounding guanine and thymine nucleobases. After irradiation to the S₂ state, 6SeG evolves to the S₂ minimum, near to a S₂/S₁ conical intersection that allows for internal conversion to the S₁ state. Linear interpolation in internal coordinates indicate that the "central" orientation is less favorable since extra energy is needed to surmount the high barrier in order to reach the S₂/S₁ conical intersection. From the S₁ state, 6SeG can further decay to the T₁ ³(π_Seπ₅^*) state via intersystem crossing, where it will be trapped due to the existence of a sizable energy barrier between the T₁ minimum and the T₁/S₀ crossing point. Although this general S₂ → T₁ mechanism takes place in both media, the presence of DNA induces a steeper S₂ potential energy surface, that it is expected to accelerate the S₂ → S₁ internal conversion.

Multiple ESIPT pathways originating from three-state conical intersections in tropolone

Internal conversion decay dynamics associated with the potential energy surfaces of three low-lying singlet excited electronic states, S₁ (ππ^*, A'), S₂ (ππ^*, A'), and S₃ (nπ^*, A″), of tropolone are investigated theoretically. Energetic and spatial aspects of conical intersections of these electronic states are explored with the aid of the linear vibronic coupling approach. Symmetry selection rules suggest that non-totally symmetric modes would act as coupling modes between S₁ and S₃ as well as between S₂ and S₃. We found that the S₁-S₂ interstate coupling via totally symmetric modes is very weak. A diabatic vibronic Hamiltonian consisting of 32 vibrational degrees of freedom is constructed to simulate the photoinduced dynamics of S₀ → S₁ and S₀ → S₂ transitions. We observe a direct nonadiabatic population transfer from S₁ to S₃, bypassing S₂, during the initial wavepacket propagation on S₁. On the other hand, the initial wavepacket evolving on S₂ would pass through the S₂-S₃ and S₁-S₃ conical intersections before reaching S₁. The presence of multiple proton transfer channels on the S₁-S₂-S₃ coupled potential energy surfaces of tropolone is analyzed. Our findings necessitate the treatment of proton tunneling dynamics of tropolone beyond the adiabatic symmetric double well potentials.

Construction of Quasi-diabatic Hamiltonians That Accurately Represent ab Initio Determined Adiabatic Electronic States Coupled by Conical Intersections for Systems on the Order of 15 Atoms. Application to Cyclopentoxide Photoelectron Detachment in the Full 39 Degrees of Freedom

We present, for systems of moderate dimension, a fitting framework to construct quasi-diabatic Hamiltonians that accurately represent ab initio adiabatic electronic structure data including the effects of conical intersections. The framework introduced here minimizes the difference between the fit prediction and the ab initio data obtained in the adiabatic representation, which is singular at a conical intersection seam. We define a general and flexible merit function to allow arbitrary representations and propose a representation to measure the fit-ab initio difference at geometries near electronic degeneracies. A fit Hamiltonian may behave poorly in insufficiently sampled regions, in which case a machine learning theory analysis of the fit representation suggests a regularization to address the deficiency. Our fitting framework including the regularization is used to construct the full 39-dimensional coupled diabatic potential energy surfaces for cyclopentoxy relevant to cyclopentoxide photoelectron detachment.

Multireference Electron Correlation Methods: Journeys along Potential Energy Surfaces

Multireference electron correlation methods describe static and dynamical electron correlation in a balanced way and, therefore, can yield accurate and predictive results even when single-reference methods or multiconfigurational self-consistent field theory fails. One of their most prominent applications in quantum chemistry is the exploration of potential energy surfaces. This includes the optimization of molecular geometries, such as equilibrium geometries and conical intersections and on-the-fly photodynamics simulations, both of which depend heavily on the ability of the method to properly explore the potential energy surface. Because such applications require nuclear gradients and derivative couplings, the availability of analytical nuclear gradients greatly enhances the scope of quantum chemical methods. This review focuses on the developments and advances made in the past two decades. A detailed account of the analytical nuclear gradient and derivative coupling theories is presented. Emphasis is given to the software infrastructure that allows one to make use of these methods. Notable applications of multireference electron correlation methods to chemistry, including geometry optimizations and on-the-fly dynamics, are summarized at the end followed by a discussion of future prospects.

Methyl substitution effects on the non-adiabatic dynamics of benzene: lifting three-state quasi-degeneracy at conical intersections

Previously, theoretical calculations on the non-adiabatic dynamics of benzene from the S₂ state have indicated that the S₂/S₁ and S₁/S₀ conical intersections (CIs) facilitate ballistic nuclear wavepacket motion from S₂ to S₀ (fast channel) and branching to S₁ (slow channel). In this paper, we present time-resolved photoelectron spectra of benzene and its methyl-derivatives (toluene and o-xylene) measured with a vacuum-UV laser, which clearly reveal both the fast and slow channels. The extremely short propagation time of the wavepacket between the two CIs of benzene indicates that the two are in close proximity to each other, while methyl substitution extends the propagation time and decreases the branching ratio into the fast channel. The results suggest that the quasi-degeneracy of the three states in benzene is lifted by the geometrical shifts of the CIs by methyl substitution.

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.

Effect of microsolvation on the non-radiative decay of the eumelanin monomer

A plethora of various low energy accessible deactivation modes of DHI were explored.

How nature covers its bases

The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.

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.

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.

Excited-state relaxation of hydrated thymine and thymidine measured by liquid-jet photoelectron spectroscopy: experiment and simulation

Time-resolved photoelectron spectroscopy is performed on thymine and thymidine in aqueous solution to study the excited-state relaxation dynamics of these molecules. We find two contributions with sub-ps lifetimes in line with recent excited-state QM/MM molecular dynamics simulations (J. Chem. Phys. 2013, 139, 214304). The temporal evolution of ionization energies for the excited ππ* state along the QM/MM molecular dynamics trajectories were calculated and are compatible with experimental results, where the two contributions correspond to the relaxation paths in the ππ* state involving different conical intersections with the ground state. Theoretical calculations also show that ionization from the nπ* state is possible at the given photon energies, but we have not found any experimental indication for signal from the nπ* state. In contrast to currently accepted relaxation mechanisms, we suggest that the nπ* state is not involved in the relaxation process of thymine in aqueous solution.

Photochemistry and photophysics at extended seams of conical intersection

The role of extended seams of conical intersection in excited-state mechanisms is reviewed. Seams are crossings of the potential energy surface in many dimensions where the decay from the excited to the ground state can occur, and the extended seam is composed of different segments lying along a reaction coordinate. Every segment is associated with a different primary photoproduct, which gives rise to competing pathways. This idea is first illustrated for fulvene and ethylene, and then it is used to explain more complex cases such as the dependence of the isomerisation of retinal chromophore isomers on the protein environment, the dependence of the efficiency of the azobenzene photochemical switch on the wavelength of irradiation and the direction of the isomerisation, and the coexistence of different mechanisms in the photo-induced Wolff rearrangement of diazonaphthoquinone. The role of extended seams in the photophysics of the DNA nucleobases and the relationship between two-state seams and three-state crossings is also discussed. As an outlook, the design of optical control strategies based on the passage of the excited molecule through the seam is considered, and it is shown how the excited-state lifetime of fulvene can be modulated by shaping the energy of the seam.

Direct probing of solvent accessibility and mobility at the binding interface of polymerase (Dpo4)-DNA complex

Water plays essential structural and dynamical roles in protein-DNA recognition through contributing to enthalpic or entropic stabilization of binding complex and by mediating intermolecular interactions and fluctuations for biological function. These interfacial water molecules are confined by the binding partners in nanospace, but in many cases they are highly mobile and exchange with outside bulk solution. Here, we report our studies of the interfacial water dynamics in the binary and ternary complexes of a polymerase (Dpo4) with DNA and an incoming nucleotide using a site-specific tryptophan probe with femtosecond resolution. By systematic comparison of the interfacial water motions and local side chain fluctuations in the apo, binary, and ternary states of Dpo4, we observed that the DNA binding interface and active site are dynamically solvent accessible and the interfacial water dynamics are similar to the surface hydration water fluctuations on picosecond time scales. Our molecular dynamics simulations also show the binding interface full of water molecules and nonspecific weak interactions. Such a fluid binding interface facilitates the polymerase sliding on DNA for fast translocation whereas the spacious and mobile hydrated active site contributes to the low fidelity of the lesion-bypass Y-family DNA polymerase.