Electronic excitation and structural relaxation of the adenine dinucleotide in gas phase and solution

Revisiting the benzene excimer using [2,2] paracyclophane model system: Experiment and theory

We report high-level calculations of the excited states of [2,2]-paracyclophane (PCP), which was recently investigated experimentally by ultrafast pump-probe experiments on oriented single crystals [Haggag et al., ChemPhotoChem 6 e202200181 (2022)]. PCP, in which the orientation of the two benzene rings and their range of motion are constrained, serves as a model for studying benzene excimer formation. The character of the excimer state and the state responsible for the brightest transition are similar to those of the benzene dimer. The constrained structure of PCP allows one to focus on the most important degree of freedom, the inter-ring distance. The calculations explain the main features of the transient absorption spectral evolution. This brightest transition of the excimer is polarized along the inter-fragment axis. The absorption of the light polarized in the plane of the rings reveals the presence of other absorbing states of Rydberg character, with much weaker intensities. We also report new transient absorption data obtained by a broadband 8 fs pump, which time-resolve strong modulations of the excimer absorption. The combination of theory and experiment provides a detailed picture of the evolution of the electronic structure of the PCP excimer in the course of a single molecular vibration.

Multistate Energy Decomposition Analysis of Molecular Excited States

A multistate energy decomposition analysis (MS-EDA) method is described to dissect the energy components in molecular complexes in excited states. In MS-EDA, the total binding energy of an excimer or an exciplex is partitioned into a ground-state term, called local interaction energy, and excited-state contributions that include exciton excitation energy, superexchange stabilization, and orbital and configuration-state delocalization. An important feature of MS-EDA is that key intermediate states associated with different energy terms can be variationally optimized, providing quantitative insights into widely used physical concepts such as exciton delocalization and superexchange charge-transfer effects in excited states. By introducing structure-weighted adiabatic excitation energy as the minimum photoexcitation energy needed to produce an excited-state complex, the binding energy of an exciplex and excimer can be defined. On the basis of the nature of intermolecular forces through MS-EDA analysis, it was found that molecular complexes in the excited states can be classified into three main categories, including (1) encounter excited-state complex, (2) charge-transfer exciplex, and (3) intimate excimer or exciplex. The illustrative examples in this Perspective highlight the interplay of local excitation polarization, exciton resonance, and superexchange effects in molecular excited states. It is hoped that MS-EDA can be a useful tool for understanding photochemical and photobiological processes.

Exciton decay mechanism in DNA single strands: back-electron transfer and ultrafast base motions

The photochemistry of DNA systems is characterized by the ultraviolet (UV) absorption of π-stacked nucleobases, resulting in exciton states delocalized over several bases. As their relaxation sensitively depends on local stacking conformations, disentangling the ensuing electronic and structural dynamics has remained an experimental challenge, despite their fundamental role in protecting the genome from potentially harmful UV radiation. Here we use transient absorption and transient absorption anisotropy spectroscopy with broadband femtosecond deep-UV pulses (250–360 nm) to resolve the exciton dynamics of UV-excited adenosine single strands under physiological conditions. Due to the exceptional deep-UV bandwidth and polarization sensitivity of our experimental approach, we simultaneously resolve the population dynamics, charge-transfer (CT) character and conformational changes encoded in the UV transition dipoles of the π-stacked nucleotides. Whilst UV excitation forms fully charge-separated CT excitons in less than 0.3 ps, we find that most decay back to the ground state via a back-electron transfer. Based on the anisotropy measurements, we propose that this mechanism is accompanied by a structural relaxation of the photoexcited base-stack, involving an inter-base rotation of the nucleotides. Our results finally complete the exciton relaxation mechanism for adenosine single strands and offer a direct view into the coupling of electronic and structural dynamics in aggregated photochemical systems.

Despite its key role in DNA photochemistry, the decay mechanism of excitons in stacked bases has remained difficult to resolve. Ultrafast polarization spectroscopy now reveals a back-electron transfer and ultrafast base motions in adenosine strands.

Excimer Intermediates en Route to Long-Lived Charge-Transfer States in Single-Stranded Adenine DNA as Revealed by Nonadiabatic Dynamics

The ultrafast time evolution of a single-stranded adenine DNA is studied using a hybrid multiscale quantum mechanics/molecular mechanics (QM/MM) scheme coupled to nonadiabatic surface hopping dynamics. As a model, we use (dA)₂₀ where a stacked adenine tetramer is treated quantum chemically. The dynamical simulations combined with on-the-fly quantitative wave function analysis evidence the nature of the long-lived electronically excited states formed upon absorption of UV light. After a rapid decrease of the initially excited excitons, relaxation to monomer-like states and excimers occurs within 100 fs. The former monomeric states then relax into additional excimer states en route to forming stabilized charge-transfer states on a longer timescale of hundreds of femtoseconds. The different electronic-state characters is reflected on the spatial separation between the adenines: excimers and charge-transfer states show a much smaller spatial separation than the monomer-like states and the initially formed excitons.

Excitation energy transport in DNA modelled by multi-chromophoric field-induced surface hopping

Revealing the extended excited state lifetime due to excitation energy transport in DNA by multi-chromophoric field-induced surface-hopping (McFISH).

Analysis of charge transfer transitions in stacked π-electron donor-acceptor complexes

Charge-transfer (CT) interactions have recently attracted enhanced interest in creating ordered ferroelectric networks of electron donors (D) and acceptors (A) and in providing the basis of functional photonic devices. In the present work, the CT character of three distinct donor-acceptor (D-A) complex interactions (pyromellitic diimide (PDI)/1,5-diaminonaphthalene (DAN), para-chloranil (pClA)/tetramethyl-para-phenylenediamine (TMPD) and tetracyanobenzene (TCNB)/1,2-di(4-pyridyl)ethylene (Bpe)) has been investigated in their ground and excited states using high-level quantum chemical methods (second-order algebraic diagrammatic construction (ADC(2)) and time-dependent density functional theory (TD-DFT) using a long-range corrected functional (ωB97xD)). The calculations show that the lowest electronic excitation has pronounced CT character in all the three dimers investigated. On the contrary, the ground states possess only smaller amounts of CT degree except for the pClA/TMPD complex, which has a strong amount of CT of 0.4 e. Optimization of the S1 state and calculation of the resulting vertical fluorescence transitions led to the interesting finding of a zero-energy gap for pClA/TMPD. The next smallest energy gap is computed for PDI/DAN (1 eV) followed by TCNB/Bpe (2.6 eV). The analysis of the electronic charge distribution of the D-A complex in the excited state shows a significant variation even though practically a full electron charge has been transferred from D to A.

Sequential electron transfer governs the UV-induced self-repair of DNA photolesions

Cyclobutane pyrimidine dimers (CpDs) are among the most common DNA lesions occurring due to the interaction with ultraviolet light. While photolyases have been well known as external factors repairing CpDs, the intrinsic self-repairing capabilities of the GAT 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 T DNA sequence were discovered only recently and are still largely obscure. Here, we elucidate the mechanistic details of this self-repair process by means of MD simulations and QM/MM computations involving the algebraic diagrammatic construction to the second order [ADC(2)] method. We show that local UV-excitation of guanine may be followed by up to three subsequent electron transfers, which may eventually enable efficient CpD ring opening when the negative charge resides on the T 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 T dimer. Consequently, the molecular mechanism of GAT 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 T self-repair can be envisaged as sequential electron transfer (SET) occurring downhill along the slope of the S₁ potential energy surface. Even though the general features of the SET mechanism are retained in both of the studied stacked conformers, our optimizations of different S₁/S₀ state crossings revealed minor differences which could influence their self-repair efficiencies. We expect that such assessment of the availability and efficiency of the SET process in other DNA oligomers could hint towards other sequences exhibiting similar photochemical properties. Such explorations will be particularly fascinating in the context of the origins of biomolecules on Earth, owing to the lack of external repairing factors in the Archean age.

Electronic delocalization, charge transfer and hypochromism in the UV absorption spectrum of polyadenine unravelled by multiscale computations and quantitative wavefunction analysis

The characterization of the electronically excited states of DNA strands populated upon solar UV light absorption is essential to unveil light-induced DNA damage and repair processes. We report a comprehensive analysis of the electronic properties of the UV spectrum of single-stranded polyadenine based on theoretical calculations that include excitations over eight nucleobases of the DNA strand and environmental effects by a multiscale quantum mechanics/molecular mechanics scheme, conformational sampling by molecular dynamics, and a meaningful interpretation of the electronic structure by quantitative wavefunction analysis. We show that electronic excitations are extended mainly over two nucleobases with additional important contributions of monomer-like excitations and excitons delocalized over three monomers. Half of the spectral intensity derives from locally excited and Frenkel exciton states, while states with partial charge-transfer character account for the other half and pure charge-transfer states represent only a minor contribution. The hypochromism observed when going from the isolated monomer to the strand occurs independently from delocalization and charge transfer and is instead explained by long-range environmental perturbations of the monomer states.

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.

Challenges in Simulating Light-Induced Processes in DNA

In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.

Photophysical deactivation pathways in adenine oligonucleotides

In this work we study deactivation processes in adenine oligomers after absorption of UV radiation using Quantum Mechanics combined with Molecular Mechanics (QM/MM). Correlated electronic structure methods appropriate for describing the excited states are used to describe a π-stacked dimer of adenine bases incorporated into (dA)20(dT)20. The results of these calculations reveal three different types of excited state minima which play a role in deactivation processes. Within this set of minima there are minima where the excited state is localized on one adenine (monomer-like) as well as minima where the excited state is delocalized on two adenines, forming different types of excimers and bonded excimers of varying but inter-related character. The proximity of their energies reveals that the minima can decay into one another along a flat potential energy surface dependent on the interbase separation. Additionally, analysis of the emissive energies and other physical properties, including theoretical anisotropy calculations, and comparison with fluorescence experiments, provides evidence that excimers play an important role in long-lived signals in adenine oligonucleotides while the subpicosecond decay is attributed to monomer-like minima. The necessity for a close approach of the nucleobases reveals that the deactivation mechanism is tied to macro-molecular motion.

An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications

Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tully's surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).

Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate

The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D-UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine (1) La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine (1) Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter-base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long-lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the (1) Lb , S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D-UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm(-1) in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D-UV spectroscopy to disentangle the photophysics of multichromophoric systems.

Excimers and Exciplexes in Photoinitiated Processes of Oligonucleotides

A lot has been learned about the physical and chemical transformations that originate from the absorption of light by DNA, and computational chemistry has played a critical role in revealing the mechanisms of how these transformations occur. Nucleic acids consist of chromophores interacting via π stacking and hydrogen bonding. The fate of these systems after they absorb light is determined by the interplay and competition between pathways involving one chromophore or interacting chromophores. This Perspective highlights the role of π stacking in photophysical and photochemical processes in oligonucleotides and reveals the importance of excimers and exciplexes. Special types of excimers/exciplexes, characterized as bonded excimers/exciplexes, are also found to be important.

High-Energy Long-Lived Mixed Frenkel-Charge-Transfer Excitons: From Double Stranded (AT)n to Natural DNA

The electronic excited states populated upon absorption of UV photons by DNA are extensively studied in relation to the UV-induced damage to the genetic code. Here, we report a new unexpected relaxation pathway in adenine-thymine double-stranded structures (AT)n . Fluorescence measurements on (AT)n hairpins (six and ten base pairs) and duplexes (20 and 2000 base pairs) reveal the existence of an emission band peaking at approximately 320 nm and decaying on the nanosecond time scale. Time-dependent (TD)-DFT calculations, performed for two base pairs and exploring various relaxation pathways, allow the assignment of this emission band to excited states resulting from mixing between Frenkel excitons and adenine-to-thymine charge-transfer states. Emission from such high-energy long-lived mixed (HELM) states is in agreement with their fluorescence anisotropy (0.03), which is lower than that expected for π-π* states (≥0.1). An increase in the size of the system quenches π-π* fluorescence while enhancing HELM fluorescence. The latter process varies linearly with the hypochromism of the absorption spectra, both depending on the coupling between π-π* and charge-transfer states. Subsequently, we identify the common features between the HELM states of (AT)n structures with those reported previously for alternating (GC)n : high emission energy, low fluorescence anisotropy, nanosecond lifetimes, and sensitivity to conformational disorder. These features are also detected for calf thymus DNA in which HELM states could evolve toward reactive π-π* states, giving rise to delayed fluorescence.

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.

Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires

Photochemically created πσ* states were classified among the most prominent factors determining the ultrafast radiationless deactivation and photostability of many biomolecular building blocks. In the past two decades, the gas phase photochemistry of πσ* excitations was extensively investigated and was attributed to N–H and O–H bond fission processes. However, complete understanding of the complex photorelaxation pathways of πσ* states in the aqueous environment was very challenging, owing to the direct participation of solvent molecules in the excited-state deactivation. Here, we present non-adiabatic molecular dynamics simulations and potential energy surface calculations of the photoexcited imidazole–(H₂O)₅ cluster using the algebraic diagrammatic construction method to the second-order [ADC(2)]. We show that electron driven proton transfer (EDPT) along a wire of at least two water molecules may lead to the formation of a πσ*/S₀ state crossing, similarly to what we suggested for 2-aminooxazole. We expand on our previous findings by direct comparison of the imidazole–(H₂O)₅ cluster to non-adiabatic molecular dynamics simulations of imidazole in the gas phase, which reveal that the presence of water molecules extends the overall excited-state lifetime of the chromophore. To embed the results in a biological context, we provide calculations of potential energy surface cuts for the analogous photorelaxation mechanism present in adenine, which contains an imidazole ring in its structure.

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.

Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations

The SOS//QM/MM [Rivalta et al., Int. J. Quant. Chem., 2014, 114, 85] method consists of an arsenal of computational tools allowing accurate simulation of one-dimensional (1D) and bi-dimensional (2D) electronic spectra of monomeric and dimeric systems with unprecedented details and accuracy. Prominent features like doubly excited local and excimer states, accessible in multi-photon processes, as well as charge-transfer states arise naturally through the fully quantum-mechanical description of the aggregates. In this contribution the SOS//QM/MM approach is extended to simulate time-resolved 2D spectra that can be used to characterize ultrafast excited state relaxation dynamics with atomistic details. We demonstrate how critical structures on the excited state potential energy surface, obtained through state-of-the-art quantum chemical computations, can be used as snapshots of the excited state relaxation dynamics to generate spectral fingerprints for different de-excitation channels. The approach is based on high-level multi-configurational wavefunction methods combined with non-linear response theory and incorporates the effects of the solvent/environment through hybrid quantum mechanics/molecular mechanics (QM/MM) techniques. Specifically, the protocol makes use of the second-order Perturbation Theory (CASPT2) on top of Complete Active Space Self Consistent Field (CASSCF) strategy to compute the high-lying excited states that can be accessed in different 2D experimental setups. As an example, the photophysics of the stacked adenine-adenine dimer in a double-stranded DNA is modeled through 2D near-ultraviolet (NUV) spectroscopy.

The influence of phosphorothioate on charge migration in single and double stranded DNA: a theoretical approach

In this study the influence of the phosphorothioate internucleotide bond on the electronic properties of single and double-stranded short nucleotides has been investigated at the M06-2X/6-31+G** level of theory in the gaseous phase. Due to the chirality of the phosphorus atom in a phosphorothioate (PT) internucleotide diester bond, the adiabatic/vertical mode of electron affinity/ionization potential, spin density and molecular orbital distribution, as well as structural analysis were taken under consideration for the single stranded (ss) R(P) and S(P) diastereomers of d[G(PS)G] and for double stranded (ds) d[G(PS)G]*d[C(PO)C], in comparison with the corresponding parent phosphate compounds. Moreover, the excitation states, HOMO and LUMO energies were calculated using a TD-DFT methodology at the M06-2X/6-31+G**//M06-2X/6-31++G** level of theory in the aqueous phase. The obtained results show that the PT plays a significant role in the case of ss-oligonucleotides, and to a much smaller extent in ds-oligomers.

Stabilization of Mixed Frenkel-Charge Transfer Excitons Extended Across Both Strands of Guanine-Cytosine DNA Duplexes

The photoreactive pathways that may lead to DNA damage depend crucially upon the nature of the excited electronic states. The study of alternating guanine-cytosine duplexes by fluorescence spectroscopy and quantum mechanical calculations identifies a novel type of excited states that can be populated following UVB excitation. These states, denoted High-energy Emitting Long-lived Mixed (HELM) states, extend across both strands and arise from mixing between cytosine Frenkel excitons and guanine-to-cytosine charge transfer states. They emit at energies higher than ππ* states localized on single bases, survive for several nanoseconds, are sensitive to the ionic strength of the solution, and are strongly affected by the structural transition from the B form to the Z form. Their impact on the formation of lesions of the genetic code needs to be assessed.

New tools for the systematic analysis and visualization of electronic excitations. II. Applications

The excited states of a diverse set of molecules are examined using a collection of newly implemented analysis methods. These examples expose the particular power of three of these tools: (i) natural difference orbitals (the eigenvectors of the difference density matrix) for the description of orbital relaxation effects, (ii) analysis of the one-electron transition density matrix in terms of an electron-hole picture to identify charge resonance and excitonic correlation effects, and (iii) state-averaged natural transition orbitals for a compact simultaneous representation of several states. Furthermore, the utility of a wide array of additional analysis methods is highlighted. Five molecules with diverse excited state characteristics are chosen for these tasks: pyridine as a prototypical small heteroaromatic molecule, a model system of six neon atoms to study charge resonance effects, hexatriene in its neutral and radical cation forms to exemplify the cases of double excitations and spin-polarization, respectively, and a model iridium complex as a representative metal organic compound. Using these examples a number of phenomena, which are at first sight unexpected, are highlighted and their physical significance is discussed. Moreover, the generality of the conclusions of this paper is verified by a comparison of single- and multireference ab initio methods.

New tools for the systematic analysis and visualization of electronic excitations. I. Formalism

A variety of density matrix based methods for the analysis and visualization of electronic excitations are discussed and their implementation within the framework of the algebraic diagrammatic construction of the polarization propagator is reported. Their mathematical expressions are given and an extensive phenomenological discussion is provided to aid the interpretation of the results. Starting from several standard procedures, e.g., population analysis, natural orbital decomposition, and density plotting, we proceed to more advanced concepts of natural transition orbitals and attachment/detachment densities. In addition, special focus is laid on information coded in the transition density matrix and its phenomenological analysis in terms of an electron-hole picture. Taking advantage of both the orbital and real space representations of the density matrices, the physical information in these analysis methods is outlined, and similarities and differences between the approaches are highlighted. Moreover, new analysis tools for excited states are introduced including state averaged natural transition orbitals, which give a compact description of a number of states simultaneously, and natural difference orbitals (defined as the eigenvectors of the difference density matrix), which reveal details about orbital relaxation effects.

Atomic and molecular analysis highlights the biophysics of unprotonated and protonated retinal in UV and scotopic vision

Unprotonated (UR) and protonated (PR) retinal have marked atomic and molecular differences in cis and trans configurations. In conclusion, UR and PR uphold UV and light vision through their different biophysical properties.

Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back

L_a and excimer state population exchange, along the common puckering decay coordinate, explains the longest DNA lifetime component.

Photodynamic behavior of electronic coupling in a N-methylformamide dimer

The role of the bridging water molecules has been studied during the excited state photodynamics of a N-methylformamide dimer in complex with water molecules employing the complete active space self-consistent field (CASSCF) and CAS perturbation theory (CASPT2) methods.

Why water makes 2-aminopurine fluorescent?

Depending on where it binds, a water molecule may change the excited-state lifetime of 2-aminopurine by a factor of 100. We explain why?

Role of excitonic coupling and charge-transfer states in the absorption and CD spectra of adenine-based oligonucleotides investigated through QM/MM simulations

In this work, we study the photophysical properties of an adenine-based oligonucleotide using an ensemble of about 200 configurations obtained from molecular dynamics simulations. Specifically, a QM/MM approach is used to obtain the excited-state energies and properties of (dA)20(dT)20 with a dimer of π-stacked adenine bases included in the quantum region. The absorption and circular dichroism spectra are computed and analyzed using the algebraic diagrammatic construction through second order level of theory method (ADC(2)) combined with classical mechanics. We find that the experimentally observed red-shifted shoulder in the absorption spectrum is due to excitonic interactions, while charge-transfer states are present within the absorption band at the higher-energy end of the spectrum. More importantly, low-energy states with charge-transfer mixing exist, which could lead to excimers and bonded excimers. These observations suggest that mixing between charge-transfer and excitonic states plays an important role in the photophysics of oligonucleotides. They also highlight the importance of taking into account the conformational flexibility of the oligonucleotide when investigating photophysical properties.

Base stacking in adenosine dimers revealed by femtosecond transient absorption spectroscopy

Excitons formed in DNA by UV absorption decay via poorly understood pathways that can culminate in mutagenic photoproducts. In order to gain insight into how base stacking influences UV excited states in DNA, five dinucleosides composed of adenosine or 2'-deoxyadenosine units joined by flexible linkers were studied by femtosecond transient absorption spectroscopy. In aqueous solution, transient absorption signals recorded at pump and probe wavelengths of 267 and 250 nm, respectively, show that UV absorption produces excimer states in all dimers that decay orders of magnitude more slowly than excitations in a single adenine nucleotide. Adding methanol as a cosolvent disrupts π-π stacking of the adenine moieties and causes the excimer states in all five dinucleosides to vanish for a methanol concentration of 80% by volume. These observations confirm that base stacking is an essential requirement for the slow decay channel seen in these and other DNA model compounds. This channel appears to be insensitive to the precise stacking conformation at the instant of photon absorption as long as the bases are cofacially stacked. Notably, circular dichroism (CD) spectra of several of the dinucleosides are weak and monomer-like and lack the exciton coupling that has been emphasized in the past as an indicator of base-stacked structure. For these dimers, the coupled transition dipole moments of the two adenines are proposed to adopt left- and right-handed arrangements upon stacking with roughly equal probability. Although the mechanism behind slow nonradiative decay in DNA is still uncertain, these results show that the signature of these states in transient absorption experiments can be a more reliable diagnostic of base stacking than the occurrence of exciton-coupled CD signals. These observations also draw attention to the important role the backbone plays in producing structures with axial (helical) chirality.

Surface Hopping Dynamics with Correlated Single-Reference Methods: 9H-Adenine as a Case Study

Surface hopping dynamics methods using the coupled cluster to approximated second order (CC2), the algebraic diagrammatic construction scheme to second order (ADC(2)), and the time-dependent density functional theory (TDDFT) were developed and implemented into the program system Newton-X. These procedures are especially well-suited to simulate nonadiabatic processes involving various excited states of the same multiplicity and the dynamics in the first excited state toward an energetic minimum or up to the region where a crossing with the ground state is found. 9H-adenine in the gas phase was selected as the test case. The results showed that dynamics with ADC(2) is very stable, whereas CC2 dynamics fails within 100 fs, because of numerical instabilities present in the case of quasi-degenerate excited states. ADC(2) dynamics correctly predicts the ultrafast character of the deactivation process. It predicts that C2-puckered conical intersections should be the preferential pathway for internal conversion for low-energy excitation. C6-puckered conical intersection also contributes appreciably to internal conversion, becoming as important as C2-puckered for high-energy excitations. In any case, H-elimination plays only a minor role. TDDFT based on a long-range corrected functional fails to predict the ultrafast deactivation. In the comparison with several other methods previously used for dynamics simulations of adenine, ADC(2) has the best performance, providing the most consistent results so far.

Intermolecular interactions and charge transfer transitions in aromatic hydrocarbon–tetracyanoethylene complexes

ADC(2) calculations accurately describe charge transfer transitions in complexes of the tetracyanoethylene electron acceptor and three distinct aromatic donors.