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We combined sub-30 fs broadband transient absorption spectroscopy in the ultraviolet with state-of-the-art quantum mechanics/molecular mechanics simulations to study the ultrafast excited-state dynamics of the sulfur-substituted nucleobase 4-thiouracil. We observed a clear mismatch between the time scales for the decay of the stimulated emission from the bright pi pi* state (76 +/- 16 fs, experimentally elusive until now) and the buildup of the photoinduced absorption of the triplet state (225 +/- 30 fs). These data provide evidence that the intersystem crossing occurs via a dark state, which is intermediately populated on the sub-100 fs time scale. Nonlinear spectroscopy simulations, extrapolated from a detailed CASPT2/MM decay path topology of the solvated system together with an excited state mixed quantum-classical nonadiabatic dynamics, reproduce the experimental results and explain the experimentally observed vibrational coherences. The theoretical analysis rationalizes the observed different triplet buildup times of 4- and 2-thiouracil.

We present a new version of the simulation software COBRAMM, a program package interfacing widely known commercial and academic software for molecular modeling. It allows a problem-driven tailoring of computational chemistry simulations with effortless ground and excited-state electronic structure computations. Calculations can be executed within a pure QM or combined quantum mechanical/molecular mechanical (QM/MM) framework, bridging from the atomistic to the nanoscale. The user can perform all necessary steps to simulate ground state and photoreactions in vacuum, complex biopolymer, or solvent environments. Starting from ground-state optimization, reaction path computations, initial conditions sampling, spectroscopy simulation, and photodynamics with deactivation events, COBRAMM is designed to assist in characterization and analysis of complex molecular materials and their properties. Interpretation of recorded spectra range from steady-state to time-resolved measurements. Various tools help the user to set up the system of interest and analyze the results.

The enzyme protochlorophyllide oxidoreductase (LPOR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), a crucial step in chlorophyll biosynthesis. Molecular understanding of the photocatalytic mechanism of LPOR is essential for harnessing light energy to mediate enzymatic reactions. The absence of X-ray crystal structure has promoted the development of LPOR homology models that lack a catalytically competent active site and could not explain the variously reported spectroscopic evidence, including time-resolved optical spectroscopy data. We have refined previous structural models to account for the catalytic active site and the characteristic experimental spectral features of Pchlide binding, including the 26 cm-1 red shift of the C13(1) carbonyl stretch vibration in the mid-infrared (IR) and the 12 nm red shift of the Q x electronic band. A hierarchy of theoretical methods, including homology modeling, molecular dynamics simulations, hybrid quantum mechanics [(TD-)DFT]/molecular mechanics [AMBER] calculations, and computational vibrational and electronic spectroscopies, have been combined in an iterative protocol to reproduce experimental evidence and to predict ultrafast transient IR spectroscopic fingerprints associated with the catalytic process. The successful application to the LPOR enzyme indicates that the presented hierarchical protocol provides a general workflow to protein structure refinement.

A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows us to analyse ground state dynamics and to sample and measure different conformations attained by flexible molecular systems in solution. An explicit mixed quantum mechanics/molecular mechanics (QM/MM) approach is employed for the evaluation of the necessary electronic excited state energies and transition dipole moments. The method is applied towards a study of the highly flexible water-solvated adenine-adenine monophosphate (ApA), a system featuring two interacting adenine moieties that display various intermolecular arrangements, known to deeply affect their photochemical outcome. Molecular dynamics simulations and cluster analysis have been used to select the molecular conformations, reducing the complexity of the flexible ApA conformational space. By using our sum-over-states (SOS) approach to obtain the 2DES spectra for each of these selected conformations, we can discern spectral changes and relate them to specific nuclear arrangements: close lying π-stacked bases exhibit a splitting of their respective 1La signal traces; T-stacked bases exhibit the appearance of charge transfer states in the low-energy Vis probing window while displaying no 1La splitting, being particularly favoured when promoting amino to 5-ring interactions; unstacked and distant adenine moieties exhibit signals similar to those of the adenine monomer, as is expected for non-interacting nucleobases. 2DES maps reveal the spectral fingerprints associated with specific molecular conformations, and are thus a promising option to enable their quantitative spectroscopic detection beyond standard 1D pump-probe techniques. This is expected to aid the understanding of how nucleobase aggregation controls and modulates the photostability and photo-damage of extended DNA/RNA systems.

Benzophenone (BP) despite its relatively simple molecular structure is a paradigmatic sensitizer, featuring both photocatalytic and photobiological effects due to its rather complex photophysical properties. In this contribution we report an original theoretical approach to model realistic, ultra-fast spectroscopy data, which requires describing intra- and intermolecular energy and structural relaxation. In particular we explicitly simulate time-resolved pump-probe spectra using a combination of state-of-the art hybrid quantum mechanics/molecular mechanics dynamics to treat relaxation and vibrational effects. The comparison with experimental transient absorption data demonstrates the efficiency and accuracy of our approach. Furthermore the explicit inclusion of the solvent, water for simulation and methanol for experiment, allows us, despite the inherent different behavior of the two, to underline the role played by the H-bonding relaxation in the first hundreds of femtoseconds after optical excitation. Finally we predict for the first time the two-dimensional electronic spectrum (2DES) of BP taking into account the vibrational effects and hence modelling partially symmetric and asymmetric ultrafast broadening.

We show that the speed of the chromophore photoisomerization of animal rhodopsins is not a relevant control knob for their light sensitivity. This result is at odds with the momentum-driven tunnelling rationale (i.e., assuming a one-dimensional Landau-Zener model for the decay: Zener, C. Non-Adiabatic Crossing of Energy Levels. Proc. R. Soc. London, Ser. A 1932, 137 (833), 696-702) holding that a faster nuclear motion through the conical intersection translates into a higher quantum yield and, thus, light sensitivity. Instead, a model based on the phase-matching of specific excited state vibrational modes should be considered. Using extensive semiclassical hybrid quantum mechanics/molecular mechanics trajectory computations to simulate the photoisomerization of three animal rhodopsin models (visual rhodopsin, squid rhodopsin and human melanopsin), we also demonstrate that phase-matching between three different modes (the reactive carbon and hydrogen twisting coordinates and the bond length alternation mode) is required to achieve high quantum yields. In fact, such "phase-matching" mechanism explains the computational results and provides a tool for the prediction of the photoisomerization outcome in retinal proteins.

On the example of 2-, 4- and 2,4-thiouracil we demonstrate the performance of the RASPT2/RASSCF protocol in reproducing the spectral positions and line shapes of linear absorption spectra that have been recorded in water and documented in this work. Through a QM/MM scheme coupled to a room-temperature Wigner sampling we simulate condensed phase spectra, permitting to compare our results against experiments. We discuss the sensitivity of the simulations to: a) the active space size by pushing the limits beyond the full-valence active spaces; b) the consideration of “dark” nπ∗-states in the state averaging; c) the flavor of RASPT2 technique; d) the basis set. The benchmarking demonstrates that full-π valence active spaces tend to red-shift the absorption band. Increasing the active space rectifies the problem and we obtain near-quantitative agreement between our experiments and calculations. We, furthermore, demonstrate that the choice of RASPT2 flavor has to be made through rigorous benchmarking.

We introduce the basic concepts of two-dimensional electronic spectroscopy (2DES) and a general theoretical framework adopted to calculate, from first principles, the nonlinear response of multi-chromophoric systems in realistic environments. Specifically, we focus on UV-active chromophores representing the building blocks of biological systems, from proteins to nucleic acids, describing our progress in developing computational tools and protocols for accurate simulation of their 2DUV spectra. The roadmap for accurate 2DUV spectroscopy simulations is illustrated starting with benchmarking of the excited-state manifold of the chromophoric units in a vacuum, which can be used for building exciton Hamiltonians for large-scale applications or as a reference for first-principles simulations with reduced computational cost, enabling treatment of minimal (still realistic) multi-chromophoric model systems. By adopting a static approximation that neglects dynamic processes such as spectral diffusion and population transfer, we show how 2DUV is able to characterize the ground-state conformational space of dinucleosides and small peptides comprising dimeric chromophoric units (in their native environment) by tracking inter-chromophoric electronic couplings. Recovering the excited-state coherent vibrational dynamics and population transfers, we observe a remarkable agreement between the predicted 2DUV spectra of the pyrene molecule and the experimental results. These results further led to theoretical studies of the excited-state dynamics in a solvated dinucleoside system, showing that spectroscopic fingerprints of long-lived excited-state minima along the complex photoinduced decay pathways of DNA/RNA model systems can be simulated at a reasonable computational cost. Our results exemplify the impact of accurate simulation of 2DES spectra in revealing complex physicochemical properties of fundamental biological systems and should trigger further theoretical developments as well as new experiments.

Opsins are a broad class of photoactive proteins, found in all classes of living beings from bacteria to higher animals, which work either as light-driven ion pumps or as visual pigments. The photoactive function in opsins is triggered by the ultrafast isomerization of the retinal chromophore around a specific carbon double bond, leading to a highly distorted, spectrally red-shifted photoproduct. Understanding, by either experimental or computational methods, the time course of this photoisomerization process is of utmost importance, both for its biological significance and because opsin proteins are the blueprint for molecular photoswitches. This paper focuses on the ultrafast 11-cis to all-trans isomerization in visual rhodopsins, and has a twofold goal: (i) to review the most recent experimental and computational efforts aimed at exposing the very early phases of photoconversion; and (ii) discuss future advanced experiments and calculations that will allow an even deeper understanding of the process. We present high time resolution pump-probe data, enabling us to follow the wavepacket motion through the conical intersection connecting excited and ground states, as well as femtosecond stimulated Raman scattering data allowing us to track the subsequent structural evolution until the first stable all-trans photoproduct is reached. We conclude by introducing computational results for two-dimensional electronic spectroscopy, which has the potential to provide even greater detail on the evolution of the electronic structure of retinal during the photoisomerization process.

Kunal Dhoke, Martin Zanni, Upendra Harbola, Ravi Kumar Venkatraman, Elangannan Arunan, King-Chuen Lin, Artur Nenov, Jonathan Skelton, R J Dwayne Miller, Jonathan D. Hirst, Vincenzo Aquilanti, John R. Helliwell, Srihari Keshavamurthy, Sai Ramesh, Mike Ashfold, Anuradha Pallipurath, Priyadarshi Roy Chowdhury, Sanghamitra Mukhopadhyay, Jemmis E D, Himani Medhi, Debabrata Goswami, Prasenjit Halder, Wolfgang Junge, Mahesh Hariharan, Santosh Kumar Singh, Siva Umapathy, Adithya Lakshmannam, Martin Meedom Nielsen, Sankarampadi Aravamudhan, Volker Deckert, Kenneth Ghiggino, Keisuke Tominaga and Alison Edwards

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.

© 2015 the Owner Societies. We outline a computational approach for nonlinear electronic spectra, which accounts for the electronic energy fluctuations due to nuclear degrees of freedom and explicitly incorporates the fluctuations of higher excited states, induced by the dynamics in the photoactive state(s). This approach is based on mixed quantum-classical dynamics simulations. Tedious averaging over multiple trajectories is avoided by employing the linearly displaced Brownian harmonic oscillator to model the correlation functions. The present strategy couples accurate computations of the high-lying excited state manifold with dynamics simulations. The application is made to the two-dimensional electronic spectra of pyrene, a polycyclic aromatic hydrocarbon characterized by an ultrafast (few tens of femtoseconds) decay from the bright S2state to the dark S1state. The spectra for waiting times t2= 0 and t2= 1 ps demonstrate the ability of this approach to model electronic state fluctuations and realistic lineshapes. Comparison with experimental spectra [Krebs et al., New Journal of Physics, 2013, 15, 085016] shows excellent agreement and allows us to unambiguously assign the excited state absorption features.

Martin Zanni, E. D. Jemmis, Sankarampadi Aravamudhan, Elangannan Arunan, Neil Hunt, Sanghamitra Mukhopadhyay, Helena J. Shepherd, Srihari Keshavamurthy, Arend G. Dijkstra, Mike Ashfold, Himangshu Prabal Goswami, Artur Nenov, Himani Medhi, Kenneth Ghiggino, Kiran Moirangthem, R. J. Dwayne Miller, Debabrata Goswami, Siva Umapathy, John R. Helliwell, Jonathan D. Hirst, Stephen Meech, Shaul Mukamel, Biman Bagchi and Marylise Buron-Le Cointe

International audience; The T–T photodimerization paths leading to the formation of cyclobutane pyrimidine dimer (CPD) and 6–4 pyrimidine pyrimidone (64-PP), the two main DNA photolesions, have been resolved for a T–T step in a DNA duplex by two complementary state-of-the-art quantum mechanical approaches: QM(CASPT2//CASSCF)/MM and TD-DFT/PCM. Based on the analysis of several different representative structures, we define a new-ensemble of cooperating geometrical and electronic factors (besides the distance between the reacting bonds) ruling T–T photodimerization in DNA. CPD is formed by a barrierless path on an exciton state delocalized over the two bases. Large interbase stacking and shift values, together with a small pseudorotation phase angle for T at the 3′-end, favor this reaction. The oxetane intermediate, leading to a 64-PP adduct, is formed on a singlet T→T charge-transfer state and is favored by a large interbase angle and slide values. A small energy barrier (

International audience; The study concerns the relaxation of electronic excited states of the DNA nucleoside deoxycytidine (dCyd) and its methylatedanalogue 5-methyldeoxycytidine (5mdCyd), known to be involved in the formation of UV-induced lesions of the genetic code. Due to the existence of four closely lying and potentially coupled excited states, the deactivation pathways in these systems are particularly complex and have not been assessed so far. Here, we provide a complete mechanistic picture of theexcited state relaxation of dCyd/5mdCyd in three solvents water, acetonitrile, and tetrahydrofuran by combining femtosecond fluorescence experiments, addressing the effect of solvent proticity on the relaxation dynamics of dCyd and 5mdCyd for the first time, and two complementary quantum mechanical approaches (CASPT2/MM and PCM/TD-CAM-B3LYP). The lowest energy ππ* state is responsible for the sub-picosecond lifetime observed for dCyd in all the solvents. In addition, computed excited state absorption and transient IR spectra allow one, for the first time, to assign the tens of picoseconds time constant, reported previously, to a dark state (nOπ*) involving the carbonyl lone pair. A second low-lying dark state, involving the nitrogen lone pair (nNπ*), does significantly participate in the excited state dynamics. The 267 nm excitation of dCyd leads to a non-negligible population of the second bright ππ* state, which affects the dynamics, acting mainly as a “doorway” state for the nOπ* state. The solvent plays a key role governing the interplay between the different excited states; unexpectedly, water favors population of the dark states. In the case of 5mdCyd, an energy barrier present on the main nonradiative decay route explains the 6-fold lengthening of the excited state lifetime compared to that of dCyd, observed for all the examined solvents. Moreover, C5-methylation destabilizes both nOπ* and nNπ* dark states, thus preventing them from being populated.

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 (

The electronic transitions of indole, the aromatic UV chromophore of the amino acid tryptophan, are characterized by using state-of-the-art multiconfigurational methods in gas-phase and aqueous solution, revealing the electronic spectrum up to 10 eV. Bidimensional near-ultraviolet (2D-NUV) electronic spectra of indole are simulated using the sum-over-states approach, based on ab initio calculations, accounting for different experimental set-ups, including rephasing (KI = -k(1) + k(2) +k(3)), quasi-absorptive (PP) and double quantum coherence (KIII = k(1) + k(2) - k(3)) signals, and both one-color (2D-NUV) and two-colors (2D-NUV/Vis) regimes. In order to obtain accurate energies of high lying excited states and reliable 2DES spectra, extravalence virtual orbitals have been included using the restricted active space technique. The 2D-NUV spectrum of indole shows off-diagonal signals due to the correlation of the GS -> L-b and GS La transitions, an indole "fingerprint" in the NUV region that differentiate it from other aromatic chromophores in proteins. Further indole-specific transitions are resolved in the whole Vis-NUV range. A background-free region bellow the ionization potential, which shows no absorption signals in the monomer, can be used to resolve charge transfer states in coupled chromophore aggregates with a two-color 2D-NUV/Vis experimental set-up. Fundamental information for design of the 2DES experiments of indole is provided, including possible experimental pulse configurations that improve spectral resolution, revealing anharmonicities and selecting transitions. The proposed 2DES experiments could provide unprecedented level of detail for tracking indole electronic transitions in proteins, laying the groundwork for the use of nonlinear ultrafast optical spectroscopy for the study of protein structure and dynamics in solution. C) 2014 Elsevier B.V. All rights reserved.

International audience; Retinal chromophores are the photoactive molecular units of visual and archaeal rhodopsins, an important class of light-activated biological photoreceptors. Extensive computational studies aimed to reveal the intrinsic photophysical and photochemical behavior of retinals in vacuo and the environmental effects that tune their properties in proteins and in solution are reviewed. Multiconfigurational and multireference perturbative ab initio methods have been used to study retinal models with increasing size, from minimal to unreduced models. The hybrid quantum mechanics/molecular mechanics (QM/MM) approach has been employed for modeling retinals in solution and in proteins. QM/MM studies of the retinal photoisomerization in rhodopsin, a prototype opsin protein responsible for the peripheral vision, have provided fundamental understanding of the electrostatic effects regulating the spectral tuning in proteins and have elucidated the photoisomerization mechanism with atomistic details, consistently with ultrafast optical spectroscopy experiments with sub-20 fs resolution. Different photochemical behaviors are observed for retinals in proteins and in solution. A molecular mechanism involving the interplay between ionic and covalent states during photoisomerization has been hypothesized but it remains uncertain and direct experimental evidences are lacking. Here, we propose transient bidimensional electronic spectroscopy as a conceivable tool for obtaining key information on the retinal photoisomerization in different environments. Combination of computational techniques and ultimate ultrafast spectroscopy experiments could provide fundamental insights on retinals photochemistry and basic understanding for the design of biomimetic photochromic devices.

Accurate ab initio modeling of spectroscopic signals in nonlinear electronic spectra, such as bidimensional (2D) spectra, requires the computation of the electronic transitions induced by the incoming pump/probe pulses, resulting in a challenging calculation of many electronic excited states. A protocol is thus required to evaluate the variations of spectral properties, like transition energies and dipole moments, with the computational level, and to estimate the sensitivity of the spectra to these variations. Such a protocol is presented here within the framework of complete and restricted active space self-consistent field (CASSCF/RASSCF) theory and its second-order perturbation theory extensions (CASPT2/RASPT2). The electronic excited-state manifolds of pyrimidine nucleobases (thymine, uracil, and cytosine) are carefully characterized in vacuo employing high-level RAS(0,0|10,8|2,12)//SS-RASPT2 calculations. The results provide a reference data set that can be used for optimizing computational efforts and costs, as required for studying computationally more demanding multichromophoric systems (e.g., di- and oligonucleotides). The spectroscopic signatures of the 2D electronic spectrum of a perfectly stacked uracil–cytosine dimer model are characterized, and experimental setups are proposed that can resolve non-covalent interchromophoric interactions in canonical pyrimidine nucleobase-stacked dimers.

The Siberian hamster ultraviolet (SHUV) visual pigment has an unprotonated Schiff-base (SB) retinyl chromophore in the dark state, which becomes protonated after photoexcitation during the early stages of the photobleaching cycle. While the photochemical relaxation processes of the SHUV remain poorly understood, they are expected to show significant differences when compared to those of the protonated SB (PSB) chromophore in visual rhodopsin. Here, we report a study of the photophysical properties of the SHUV unprotonated SB (SHUV-USB), based on multiconfigurational and multireference perturbative methods within a hybrid quantum mechanics/molecular mechanics scheme. Comparisons of multireference and time-dependent density functional theory results indicate that both methodologies predict an ionic excited state (S1), similar to the PSB of rhodopsin, although its minimum has even bond-lengths in the central region of the retinyl polyene chain. The analysis of excited-state manifolds at the Franck–Condon region and S1 minimum configuration indicates that the skeletal relaxation initiated in the S1 surface is likely to involve S1/S2 surface crossing. These results provide valuable insights for future studies of the SHUV-USB photoisomerization mechanism.

A combination of experimental and theoretical techniques is used to study the photoinduced ring-opening/closure of a trifluoromethyl-indolylfulgide. Time-resolved UV/vis pump and IR probe measurements are performed in the subpicosecond to 50 ps time range. Probing in the mid-IR between 1200 and 1900 cm(-1) provides mode-specific dynamics and reveals photochemical reaction dynamics as well as the presence of a noncyclizable conformer. Ring-opening occurs with about 3 ps. Experiments on the open isomer confirm that the ring-closure occurs on the subpicosecond time scale. They also show a 10 ps transient that can be assigned to internal conversion of a noncyclizable conformer. Quantum chemical calculations with multireference methods are used to explore the complex potential energy landscape in the excited electronic state showing paths for ring-opening and closure reactions as well as for competing side-reactions. The calculations reveal that photoexcitation induces a charge transfer from the indole to the anhydride. The same charge transfer drives the system toward a low-energy conical intersection seam spreading from the closed to the open ring side and is responsible for the ultrafast relaxation to the ground state. The ultrafast photoreactivity comes at the expense of selectivity.

Sub-20-fs transient absorption spectroscopy and simulations show that CNN-bendings dominate the sub-ps dynamics of ππ*-excited trans-azobenzene, thereby driving the system to the ground state through a non-productive decay channel in violation of the Kasha rule.

The photoinduced ring-opening reaction of cyclohexadiene (CHD) is a textbook example for electrocyclic reactions. In this paper we report the complete "minimum energy path" of the low-lying region of the conical intersection space reaching from the closed to the open ring side. The general role of conical intersections (CoIns) is to provide the locus for ultrafast transfer between electronic states, in the present case, to the closed or open form in the ground state after photoexcitation. The seam was calculated with use of an analytic approach in which the intersection space in the vicinity of a CoIn is described to second order. The topography of the seam was investigated, revealing minimum energy and transition state structures. In addition the energy profile of the seam was rationalized with valence bond (VB) theory. The geometrical changes along the seam have been related to the motions along the excited state minimum energy path (S(1)-IRC-MEP) in a conceptual model highlighting the quasiparallel orientation of seam and IRC-MEP. Our model shows that even though the van der Lugt and Oosterhoff concept predicts the formation of an avoided crossing along the S(1)-IRC-MEP, it provides an incomplete description of the decay process to the ground state. The latter requires, in addition, vibrational motions orthogonal to the MEP, directed toward the CoIn seam.

Time-resolved two-dimensional (2D) electronic spectra (ES) tracking the evolution of the excited state manifolds of the retinal chromophore have been simulated along the photoisomerization pathway in bovine rhodopsin, using a state-of-the-art hybrid QM/MM approach based on multiconfigurational methods. Simulations of broadband 2D spectra provide a useful picture of the overall detectable 2D signals from the near-infrared (NIR) to the near-ultraviolet (UV). Evolution of the stimulated emission (SE) and excited state absorption (ESA) 2D signals indicates that the S1→ SN(with N ≥ 2) ESAs feature a substantial blue-shift only after bond inversion and partial rotation along the cis → trans isomerization angle, while the SE rapidly red-shifts during the photoinduced skeletal relaxation of the polyene chain. Different combinations of pulse frequencies are proposed in order to follow the evolution of specific ESA signals. These include a two-color 2DVis/NIR setup especially suited for tracking the evolution of the S1→ S2transitions that can be used to discriminate between different photochemical mechanisms of retinal photoisomerization as a function of the environment. The reported results are consistent with the available time-resolved pump-probe experimental data, and may be used for the design of more elaborate transient 2D electronic spectroscopy techniques. © 2014 American Chemical Society.

International audience; The ability of nonlinear electronic spectroscopy to track folding/unfolding processes of proteins in solution by monitoring aromatic interactions is investigated by first-principles simulations of two-dimensional (2D) electronic spectra of a model peptide. A dominant reaction pathway approach is employed to determine the unfolding pathway of a tetrapeptide, which connects the initial folded configuration with stacked aromatic side chains and the final unfolded state with distant noninteracting aromatic residues. The π-stacking and excitonic coupling effects are included through ab initio simulations based on multiconfigurational methods within a hybrid quantum mechanics/molecular mechanics scheme. It is shown that linear absorption spectroscopy in the ultraviolet (UV) region is unable to resolve the unstacking dynamics characterized by the three-step process: T-shaped[RIGHTWARDS ARROW]twisted offset stacking[RIGHTWARDS ARROW]unstacking. Conversely, pump–probe spectroscopy can be used to resolve aromatic interactions by probing in the visible region, the excited-state absorptions (ESAs) that involve charge-transfer states. 2D UV spectroscopy offers the highest sensitivity to the unfolding process, by providing the disentanglement of ESA signals belonging to different aromatic chromophores and high correlation between the conformational dynamics and the quartic splitting.

Two-dimensional (2D) optical spectroscopy techniques based on ultrashort laser pulses have been recently extended to the optical domain in the ultraviolet (UV) spectral region. UV-active aromatic side chains can thus be used as local highly specific markers for tracking dynamics and structural rearrangements of proteins. Here we demonstrate that 2D electronic spectra of a model proteic system, a tetrapeptide with two aromatic side chains, contain enough structural information to distinguish between two different configurations with distant and vicinal side chains. For accurate simulations of the 2DUV spectra in solution, we combine a quantum mechanics/molecular mechanics approach based on wave function methods, accounting for interchromophores coupling and environmental effects, with nonlinear response theory. The proposed methodology reveals effects, such as charge transfer between vicinal aromatic residues that remain concealed in conventional exciton Hamiltonian approaches. Possible experimental setups are discussed, including multicolor experiments and signal manipulation techniques for limiting undesired background contributions and enhancing 2DUV signatures of specific electronic couplings. © 2014 American Chemical Society.

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization. QC 20210506

A theoretical investigation based on DFT, TD-DFT, and CASSCF/CASPT2 methods has been carried out to elucidate the photophysics of two anilino-substituted pentacyano- and tetracyanobuta-1,3-dienes (PCBD and TCBD, respectively). These molecules exhibit exceptional electron-accepting properties, but their effective use in multicomponent systems for photoinduced electron transfer is limited because they undergo ultrafast (∼1 ps) radiationless deactivation. We show that the lowest-energy excited states of these molecules have a twisted intramolecular charge-transfer character and deactivate to the ground state through energetically accessible conical intersections (CIs). The topology of the lowest-energy CI, analyzed with a linear interpolation of the two branching-space vectors (g and h), indicates it is a sloped CI, ultimately responsible for the ultrafast deactivation of this class of compounds.

First-principles simulations of two-dimensional electronic spectroscopy in the ultraviolet region (2DUV) require computationally demanding multiconfigurational approaches that can resolve doubly excited and charge transfer states, the spectroscopic fingerprints of coupled UV-active chromophores. Here, we propose an efficient approach to reduce the computational cost of accurate simulations of 2DUV spectra of benzene, phenol, and their dimer (i.e., the minimal models for studying electronic coupling of UV-chromophores in proteins). We first establish the multiconfigurational recipe with the highest accuracy by comparison with experimental data, providing reference gas-phase transition energies and dipole moments that can be used to construct exciton Hamiltonians involving high-lying excited states. We show that by reducing the active spaces and the number of configuration state functions within restricted active space schemes, the computational cost can be significantly decreased without loss of accuracy in predicting 2DUV spectra. The proposed recipe has been successfully tested on a realistic model proteic system in water. Accounting for line broadening due to thermal and solvent-induced fluctuations allows for direct comparison with experiments.

© 2015 AIP Publishing LLC. 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/Latransitions with the pump pulse pair and probing in the Vis to near ultraviolet spectral window.

E. D. Jemmis, Sankarampadi Aravamudhan, Elangannan Arunan, Abhishek Shahi, Neil Hunt, Christoph Schnedermann, John R. Helliwell, Mike Ashfold, Himangshu Prabal Goswami, Artur Nenov, Volker Deckert, Priyadarshi Roy Chowdhury, Kenneth Ghiggino, R. J. Dwayne Miller, Debabrata Goswami, Wolfgang Junge, Judith Howard, Keisuke Tominaga, Tim Brandt van Driel, Martin Zanni, Siva Umapathy, Martin Meedom Nielsen, R. Pal and Shaul Mukamel

The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ(*) La and Lb states, whereas the energy of the oxygen lone-pair nπ(*) state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ(*) state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region.

Ultrafast excited-state dynamics in indigo-based photochromic compounds was studied with the transient absorption spectroscopy and ab initio calculations. We demonstrated an approach of adjusting excited state relaxation routes and photoisomerization rates for applications where fast photoswitching is needed.

Deactivation routes of bright ππ* (La) and excimer charge transfer (CT) states have been mapped for two stacked quantum mechanical (CASPT2//CASSCF) adenines inside a solvated DNA double strand decamer (poly(dA)·poly(dT)) described at the molecular mechanics level. Calculations show that one carbon (C2) puckering is a common relaxation coordinate for both the La and CT paths. By mapping the lowest crossing regions between La and CT states, together with the paths connecting the two states, we conclude that at least one CT state can be easily accessible. The lowest-lying conical intersections between ground state (GS) and CT states have been fully characterized in a realistic DNA environment for the first time. We show that the path to reach this crossing region from the CT minima involves high barriers that are not consistent with experimental data lifetimes. Instead, the multiexponential decay recorded in DNA, including the longest (ca. 100 picoseconds) lifetime component detected in oligomeric single- and double-stranded systems, is compatible with both intra-monomer relaxation processes along the La deactivation path (involving small barriers) and the population of the excimer (CT) state that behaves as a trap. In the latter case, deactivation is feasible only going back to the La state by following its preferred decay coordinate.

Hemithioindigo (HTI) photoswitches have a tremendous potential for biological and supramolecular applications due to their absorptions in the visible-light region in conjunction with ultrafast photoisomerization and high thermal bistability. Rational tailoring of the photophysical properties for a specific application is the key to exploit the full potential of HTIs as photoswitching tools. Herein we use time-resolved absorption spectroscopy and Hammett analysis to discover an unexpected principal limit to the photoisomerization rate for donor-substituted HTIs. By using stationary absorption and fluorescence measurements in combination with theoretical investigations, we offer a detailed mechanistic explanation for the observed rate limit. An alternative way of approaching and possibly even exceeding the maximum rate by multiple donor substitution is demonstrated, which give access to the fastest HTI photoswitch reported to date. An unexpected principal limit to the photoisomerization rate for donor-substituted hemithioindigos (HTIs; see figure) has been discovered; this provides a quantitative estimate for the highest possible photoisomerization rate. A mechanistic explanation for the observed limit is offered together with an alternative way of approaching the maximum rate by multiple donor substitution. This approach gave access to the fastest HTI photoswitch reported to date.

The photoinduced electrocyclic ring-opening of a fluorinated indolylfulgide is investigated by stationary and ultrafast spectroscopy in the UV/vis spectral range. Photoreactions, initiated by optical excitation into the S(1) (570 nm) and S(N) (340 nm) absorption band of the closed isomer, lead to considerable differences in reaction dynamics and quantum yields. Transient absorption studies point to different reaction pathways depending on the specific excitation wavelength: excitation into the S(1) state leads to the known reaction behavior with a picosecond decay to the ground state and a small quantum yield of 7% for the photoproduct. The S(N) state shows an unexpected long lifetime of 0.5 ps. The photoreaction starting from the S(N) state leads to a large extent directly to the product ground state and back to the educt ground state. This results in an increased reaction quantum yield of 28%. In contradiction to Kasha's rule, the S(1) state is only populated with an efficiency of 38%. The observed behavior strongly differs from the expected picture with fast relaxation into the S(1) state and a subsequent ring-opening reaction starting from the lowest excited electronic state. Quantum chemical calculations confirm and complement the experimental findings allowing a sound molecular interpretation to be obtained.

The knowledge of conical intersection seams is important to predict and explain the outcome of ultrafast reactions in photochemistry and photobiology. They define the energetic low-lying reachable regions that allow for the ultrafast non-radiative transitions. In complex molecules it is not straightforward to locate them. We present a systematic approach to predict conical intersection seams in multifunctionalized polyenes and their sensitivity to substituent effects. Included are seams that facilitate the photoreaction of interest as well as seams that open competing loss channels. The method is based on the extended two-electron two-orbital method [A. Nenov and R. de Vivie-Riedle, J. Chem. Phys. 135, 034304 (2011)]. It allows to extract the low-lying regions for non-radiative transitions, which are then divided into small linear segments. Rules of thumb are introduced to find the support points for these segments, which are then used in a linear interpolation scheme for a first estimation of the intersection seams. Quantum chemical optimization of the linear interpolated structures yields the final energetic position. We demonstrate our method for the example of the electrocyclic isomerization of trifluoromethyl-pyrrolylfulgide.

The knowledge of the intersection space topography of electronic states is essential for deciphering and predicting photoinduced reactions. Michl and Bonacić-Koutecký developed a two-electron two-orbital model that allowed first systematic studies of the chemical origin of conical intersections in strongly polar systems. We generalize this approach to arbitrary functionalized and unfunctionalized polyene systems. For the extended model, a set of mathematical conditions for the formation of conical intersections are derived. These conditions are translated into geometrical motions and electronic effects, which help to explain and predict the structure and energetics of conical intersections. A three-step strategy for the conceptual search of conical intersections is outlined. Its universal validity is demonstrated using the textbook example cyclohexadiene and its functionalized derivative trifluoromethyl-indolylfulgide, a chromophore studied for possible application as a molecular switch.

We have used state-of-the-art ab initio restricted active RASPT2 computations using a 16 orbitals, 18 electrons active space to produce an extended three-dimensional map of the potential energy surfaces (PESs) of the ground and first nπ∗ excited states of azobenzene along CNNC torsion and the two CNN bending angles, which are the most relevant coordinates for the trans-cis photoisomerization process. Through comparison with fully unconstrained optimizations performed at the same level of theory, we show that the three selected coordinates suffice to correctly describe the photoisomerization mechanism and the S1-S0 crossing seam. We also provide a map of the nonadiabatic coupling between the two states in the region where they get closer in energy. Eventually, we show that treating the two CNN bending angles as independent coordinates is fundamental to break the symmetry and couple the two electronic states. The accuracy of the S0 and S1 PESs and couplings was validated with semiclassical dynamics simulations in the reduced space of the scanned coordinates, showing results in good agreement with published full-coordinate dynamics.

Computational spectroscopy is becoming a mandatory tool for the interpretation of the complex, and often congested, spectral maps delivered by modern non-linear multi-pulse techniques. The fields of Electronic Structure Methods, Non- Adiabatic Molecular Dynamics, and Theoretical Spectroscopy represent the three pillars of the virtual ultrafast optical spectrometer, able to deliver transient spectra in silico from first principles. A successful simulation strategy requires a synergistic approach that balances between the three fields, each one having its very own challenges and bottlenecks. The aim of this Perspective is to demonstrate that, despite these challenges, an impressive agreement between theory and experiment is achievable now regarding the modeling of ultrafast photoinduced processes in complex molecular architectures. Beyond that, some key recent developments in the three fields are presented that we believe will have major impacts on spectroscopic simulations in the very near future. Potential directions of development, pending challenges, and rising opportunities are illustrated.

Azobenzene (AB) is a diazene derivative where both hydrogens are replaced by phenyl groups. Under irradiation with UV light, it undergoes ultrafast trans→cis isomerization; the inverse cis→trans isomerization can be driven by light or occurs thermally in dark. AB photochromic properties enable its application as a light triggered switch in numerous molecular devices and functional materials [1]. Here we use femtosecond pump-probe and two-dimensional electronic spectroscopy in the UV range (2DUV) with sub-20-fs time resolution, combined with ab initio quantum mechanics simulations, to study the initial dynamics of trans-AB isomerization with unprecedented mechanistic detail.