Double Thionated Pyrimidine Nucleobases: Molecular Tools with Tunable Photoproperties.

Sulfur-substituted nucleobases are DNA and RNA base derivatives that exhibit extremely efficient photoinduced intersystem crossing (ISC) dynamics into the lowest-energy triplet state. The long-lived and reactive triplet states of sulfur-substituted nucleobases are crucial due to their wide range of potential applications in medicine, structural biology, and the development of organic light-emitting diodes (OLEDs) and other emerging technologies. However, a comprehensive understanding of non-negligible wavelength-dependent changes in the internal conversion (IC) and ISC events is still lacking. Here, we study the underlying mechanism using joint experimental gas-phase time-resolved photoelectron spectroscopy (TRPES) and theoretical quantum chemistry methods. We combine 2,4-dithiouracil (2,4-DTU) TRPES experimental data with computational analysis of the different photodecay processes, which are induced by increasing excitation energies along the entire linear absorption (LA) ultraviolet (UV) spectrum. Our results show how the double-thionated uracil (U), i.e., 2,4-DTU, appears as a versatile photoactivatable instrument. Multiple decay processes can be initiated with different ISC rates or triplet-state lifetimes that resemble the distinctive behavior of the singly substituted 2- or 4-thiouracil (2-TU or 4-TU). We obtained a clear partition of the LA spectrum based on the dominant photoinduced process. Our work clarifies the reasons behind the wavelength-dependent changes in the IC, ISC, and triplet-state lifetimes in doubly thionated U, becoming a biological system of utmost importance for wavelength-controlled applications. These mechanistic details and photoproperties are transferable to closely related molecular systems such as thionated thymines.

Engineering Azobenzene Derivatives to Control the Photoisomerization Process.

In this work, we show how the structural features of photoactive azobenzene derivatives can influence the photoexcited state behavior and the yield of the trans/cis photoisomerization process. By combining high-resolution transient absorption experiments in the vis-NIR region and quantum chemistry calculations (TDDFT and RASPT2), we address the origin of the transient signals of three poly-substituted push-pull azobenzenes with an increasing strength of the intramolecular interactions stabilizing the planar trans isomer (absence of intramolecular H-bonds, methyl, and traditional H-bond, respectively, for 4-diethyl-4'-nitroazobenzene, Disperse Blue 366, and Disperse Blue 165) and a commercial red dye showing keto-enol tautomerism involving the azo group (Sudan Red G). Our results indicate that the intramolecular H-bonds can act as a "molecular lock" stabilizing the trans isomer and increasing the energy barrier along the photoreactive CNNC torsion coordinate, thus preventing photoisomerization in the Disperse Blue dyes. In contrast, the involvement of the azo group in keto-enol tautomerism can be employed as a strategy to change the nature of the lower excited state and remove the nonproductive symmetric CNN/NNC bending pathway typical of the azo group, thus favoring the productive torsional motion. Taken together, our results can provide guidelines for the structural design of azobenzene-based photoswitches with a tunable excited state behavior.

Modus Operandi of a Pedalo-Type Molecular Switch: Insight from Dynamics and Theoretical Spectroscopy.

Molecular switches which can be triggered by light to interconvert between two or more well-defined conformation differing in their chemical or physical properties are fundamental for the development of materials with on-demand functionalities. Recently, a novel molecular switch based on a the azodicarboxamide core has been reported. It exhibits a volume-conserving conformational change upon excitation, making it a promising candidate for embedding in confined environments. In order to rationally implement and efficiently utilize the azodicarboxamide molecular switch, detailed insight into the coordinates governing the excited-state dynamics is needed. Here, we report a detailed comparative picture of the molecular motion at the atomic level in the presence and absence of explicit solvent. Our hybrid quantum mechanics/molecular mechanics (QM/MM) excited state simulations reveal that, although the energy landscape is slightly modulated by the solvation, the light-induced motion is dominated by a bending-assisted pedalo-type motion independent of the solvation. To support the predicted mechanism, we simulate time-resolved IR spectroscopy from first principles, thereby resolving fingerprints of the light-induced switching process. Our calculated time-resolved data are in good agreement with previously reported measured spectra.

Environment-Driven Coherent Population Transfer Governs the Ultrafast Photophysics of Tryptophan.

By combining UV transient absorption spectroscopy with sub-30-fs temporal resolution and CASPT2/MM calculations, we present a complete description of the primary photoinduced processes in solvated tryptophan. Our results shed new light on the role of the solvent in the relaxation dynamics of tryptophan. We unveil two consecutive coherent population transfer events involving the lowest two singlet excited states: a sub-50-fs nonadiabatic La → Lb transfer through a conical intersection and a subsequent 220 fs reverse Lb → La transfer due to solvent-assisted adiabatic stabilization of the La state. Vibrational fingerprints in the transient absorption spectra provide compelling evidence of a vibronic coherence established between the two excited states from the earliest times after photoexcitation and lasting until the back-transfer to La is complete. The demonstration of response to the environment as a driver of coherent population dynamics among the excited states of tryptophan closes the long debate on its solvent-assisted relaxation mechanisms and extends its application as a local probe of protein dynamics to the ultrafast time scales.

Modelling quenching mechanisms of disordered molecular systems in the presence of molecular aggregates.

Exciton density dynamics recorded in time-resolved spectroscopic measurements is a useful tool to recover information on energy transfer (ET) processes that can occur at different timescales, up to the ultrafast regime. Macroscopic models of exciton density decays, involving both direct Förster-like ET and diffusion mechanisms for exciton-exciton annihilation, are largely used to fit time-resolved experimental data but generally neglect contributions from molecular aggregates that can work as quenching species. In this work, we introduce a macroscopic model that includes contributions from molecular aggregate quenchers in a disordered molecular system. As an exemplifying case, we considered a homogenous distribution of rhodamine B dyes embedded in organic nanoparticles to set the initial parameters of the proposed model. The influence of such model parameters is systematically analysed, showing that the presence of molecular aggregate quenchers can be monitored by evaluating the exciton density long time decays. We showed that the proposed model can be applied to molecular systems with ultrafast decays, and we anticipated that it could be used in future studies for global fitting of experimental data with potential support from first-principles simulations.

Coherent vibrational modes promote the ultrafast internal conversion and intersystem crossing in thiobases.

Thionated nucleobases are obtained by replacing oxygen with sulphur atoms in the canonical nucleobases. They absorb light efficiently in the near-ultraviolet, populating singlet states which undergo intersystem crossing to the triplet manifold on an ultrashort time scale with a high quantum yield. Nonetheless there are still important open questions about the primary mechanisms responsible for this ultrafast transition. Here we track both the electronic and the vibrational ultrafast excited-state dynamics towards the triplet state for solvated 4-thiothymidine (4TT) and 4-thiouracil (4TU) with sub-30 fs broadband transient absorption spectroscopy in the ultraviolet. A global and target analysis allows us to simultaneously resolve the contributions of the different electronically and vibrationally excited states to the whole data set. Our experimental results, combined with state-of-the-art quantum mechanics/molecular mechanics simulations and Damped Oscillation Associated Spectra (DOAS) and target analysis, support that the relaxation to the triplet state is mediated by conical intersections promoted by vibrational coherences through the population of an intermediate singlet state. In addition, the analysis of the coherent vibrational dynamics reveals that, despite sharing the same relaxation mechanism and similar chemical structures, 4TT and 4TU exhibit rather different geometrical deformations, characterized by the conservation of planarity in 4TU and its partial rupture in 4TT.

Ultrafast Spectroscopy of Photoactive Molecular Systems from First Principles: Where We Stand Today and Where We Are Going.

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.

A Unified Experimental/Theoretical Description of the Ultrafast Photophysics of Single and Double Thionated Uracils.

Photoinduced processes in thiouracil derivatives have lately attracted considerable attention due to their suitability for innovative biological and pharmacological applications. Here, sub-20 fs broadband transient absorption spectroscopy in the near-UV are combined with CASPT2/MM decay path calculations to unravel the excited-state decay channels of water solvated 2-thio and 2,4-dithiouracil. These molecules feature linear absorption spectra with overlapping ππ* bands, leading to parallel decay routes which we systematically track for the first time. The results reveal that different processes lead to the triplet states population, both directly from the ππ* absorbing state and via the intermediate nπ* dark state. Moreover, the 2,4-dithiouracil decay pathways is shown to be strongly correlated either to those of 2- or 4-thiouracil, depending on the sulfur atom on which the electronic transition localizes.

Spectral Tuning and Photoisomerization Efficiency in Push-Pull Azobenzenes: Designing Principles.

This work demonstrates how push-pull substitution can induce spectral tuning toward the visible range and improve the photoisomerization efficiency of azobenzene-based photoswitches, making them good candidates for technological and biological applications. The red-shifted bright ππ* state (S2) behaves like the lower and more productive dark nπ* (S1) state because less potential energy along the planar bending mode is available to reach higher energy unproductive nπ*/S0 crossing regions, which are responsible for the lower quantum yield of the parent compound. The stabilization of the bright ππ* state and the consequent increase in isomerization efficiency may be regulated via the strength of push-pull substituents. Finally, the torsional mechanism is recognized here as the unique productive route because structures with bending values attributable to the inversion mechanism were never detected, out of the 280 ππ* time-dependent density functional theory (RASPT2-validated) dynamics simulations.

Modern quantum chemistry with [Open]Molcas.

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

Tailoring Spectral and Photochemical Properties of Bioinspired Retinal Mimics by in Silico Engineering.

Controlling the spectral tunability and isomerization activity is currently one of the hot topics in the design of photoreversible molecular switches for application in optoelectronic devices. The present work demonstrates how to manipulate the absorption of the retinal protonated Schiff base (rPSB) chromophore over the entire visible range by targeted functionalization of the retinal backbone. Moreover, a correlation between the vertical excitation energy and the profile of the potential energy surface of the bright excited state responsible for the photoreactivity of rPSB is established. This correlation was exploited to rank the functionalized rPSBs into different classes with characteristic photoisomerization activity. Eventually, the synergic effects of functionalization and of external electric fields in the range of a few MV cm-1 were applied to achieve reversable and regioselective control of the photoisomerization propensity of selected rPBS derivatives.

Observation of the Sub-100 Femtosecond Population of a Dark State in a Thiobase Mediating Intersystem Crossing.

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 ππ* 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.

Photoinduced formation mechanism of the thymine-thymine (6-4) adduct in DNA; a QM(CASPT2//CASSCF):MM(AMBER) study.

The UVB-induced photomechanism leading the carbonyl group of a thymine nucleobase to react with the carbon-carbon double bond of a consecutive thymine nucleobase in a DNA strand to form the thymine-thymine (6-4) photodamage adduct remains poorly understood. Key questions remain unanswered, concerning both the intrinsic features of the photoreaction (such as the contribution (or not) of triplet states, the nature of the involved states and the time-scale of the photoprocess) and the role played by the non-reactive surroundings of the two reactive pyrimidine nucleobases (such as the nature of the flanked nucleobases and the flexibility of the whole DNA molecule). A small number of theoretical studies have been carried out on the title photoreaction, most of which have used reduced model systems of DNA, consequently neglecting potential key parameters for the photoreaction such as the constraints due to the double strain structure and the presence of paired and stacked nucleobases. In the present contribution the photoactivation step of the title reaction has been studied in a DNA system, and in particular for a specific DNA hairpin for which the quantum yield of photodamage formation has been recently experimentally measured. The reaction has been characterized by carrying out high-level QM/MM computations, combining the CASPT2//CASSCF approach for the study of the reactive part (i.e. the two thymine molecules) with an MM-Amber treatment of the surrounding environment. The possibility of a reaction path along both the singlet and triplet manifolds has been characterized, the nature of the reactive states has been analyzed, and the role played by the flexibility of the whole system, which in turn determines the initial accessible geometrical conformations, has been evaluated, thus substantially contributing towards the elucidation of the photoreaction mechanism. On the basis of the obtained results, it can be observed that a charge-transfer state can decay from a pro-reactive initial structure towards a region of energy degeneracy with the ground state, from which the subsequent decay along the ground state hypersurface can lead to the photoreaction.

Multiple Electronic and Structural Factors Control Cyclobutane Pyrimidine Dimer and 6-4 Thymine-Thymine Photodimerization in a DNA Duplex.

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 (<0.3 eV) is associated to this path, likely contributing to the smaller quantum yield observed for this process. Eventually, a clear directionality is always shown by the electronic excitation characterizing the singlet photoactive state driving the photodimerization process: an exciton that is more localized on T3 and a 5'-T→3'-T charge transfer for CPD and oxetane formation, respectively, thus calling for specific electronic constraints.

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

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.

Reconciling TD-DFT and CASPT2 electronic structure methods for describing the photophysics of DNA.

Time-dependent density functional theory (TD-DFT) and multiconfigurational second-order perturbation theory (CASPT2) are two of the most widely used methods to investigate photoinduced dynamics in DNA-based systems. These methods sometimes give diverse dynamics in physiological environments usually modeled by quantum mechanics/molecular mechanics (QM/MM) protocol. In this work, we demonstrate for the uridine test case that the underlying topology of the potential energy surfaces of electronic states involved in photoinduced relaxation is similar in both electronic structure methods. This is verified by analyzing surface-hopping dynamics performed at the QM/MM level on aqueous solvated uridine at TD-DFT and CASPT2 levels. By constraining the dynamics to remain on π π * state we observe similar fluctuations in energy and relaxation lifetimes in surface-hopping dynamics in both TD-DFT and experimentally validated CASPT2 methods. This finding calls for a systematic comparison of the ES potential energy surfaces of DNA and RNA nucleosides at the single- and multi-reference levels of theory. The anomalous long excited state lifetime at the TD-DFT level is explained by n π * trapping due to the tendency of TD-DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of the π π * state leading to a wrong π π * / n π * energetic order. A study of the FC energetics suggests that improving the description of the surrounding environment through polarizable embedding or by the expansion of QM layer with hydrogen-bonded waters helps restore the correct state order at TD-DFT level. Thus by combining TDDFT with an accurate modeling of the environment, TD-DFT is positioned as the standout protocol to model photoinduced dynamics in DNA-based aggregates and multimers.

The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter.

Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electronically conjugated chemical compounds. The origin of this phenomenon has remained elusive so far. In the present study, we identify a mechanism underlying this new type of fluorescence in different biological aggregates. By employing non-adiabatic ab initio molecular dynamics simulations combined with a data-driven approach, we characterize the typical ultrafast non-radiative relaxation pathways active in non-fluorescent peptides. We show that the key vibrational mode for the non-radiative decay towards the ground state is the carbonyl elongation. Non-aromatic fluorescence appears to emerge from blocking this mode with strong local interactions such as hydrogen bonds. While we cannot rule out the existence of alternative non-aromatic fluorescence mechanisms in other systems, we demonstrate that this carbonyl-lock mechanism for trapping the excited state leads to the fluorescence yield increase observed experimentally, and set the stage for design principles to realize novel non-invasive biocompatible probes with applications in bioimaging, sensing, and biophotonics.

The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry.

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.

Primary headache: role of investigations in a cohort of young children and adolescents.

BACKGROUND: We report a study conducted in children and adolescents who are affected by primary headaches. The aim was to establish the most useful investigations for diagnosing headaches. METHODS: The current study involved 300 consecutively hospitalized children and adolescents selected according to the criteria of the second edition of the International Classification of Headache Disorders. The following examinations were performed in all patients: full ophthalmologic; brain magnetic resonance imaging (MRI); electroencephalography; echocardiogram; and electrocardiogram. Dental, otorhinolaryngology, echocardiography of the supra-aortic trunks, abdominal ultrasound, and visual- and auditory-evoked potentials were carried out in patients according to the clinical signs associated with headache. RESULTS: In a large number of cases routine laboratory analysis and neurophysiologic investigations were within the normal value when neurologic examination was normal. Electroencephalography, ophthalmologic studies and cerebral MRI are advisable as they can reveal precocious pathologic events, even in the absence of evident or alarming clinical signs. CONCLUSION: As widely reported in the literature, most of these investigations may be of little clinical value, but the authors reasoned that electroencephalography, ophthalmologic investigations and a cerebral MRI may be noteworthy because such studies may reveal a precocious pathologic event which can change the prognostic value of the headache. In addition, negative results on cerebral MRI may relieve the anxiety of parents and in turn may positively influence the clinical course of headache in children and adolescents.

Unified Description of Ultrafast Excited State Decay Processes in Epigenetic Deoxycytidine Derivatives.

Epigenetic DNA modifications play a fundamental role in modulating gene expression and regulating cellular and developmental biological processes, thereby forming a second layer of information in DNA. The epigenetic 2'-deoxycytidine modification 5-methyl-2'-deoxycytidine, together with its enzymatic oxidation products (5-hydroxymethyl-2'-deoxycytidine, 5-formyl-2'-deoxycytidine, and 5-carboxyl-2'-deoxycytidine), are closely related to deactivation and reactivation of DNA transcription. Here, we combine sub-30-fs transient absorption spectroscopy with high-level correlated multiconfigurational CASPT2/MM computational methods, explicitly including the solvent, to obtain a unified picture of the photophysics of deoxycytidine-derived epigenetic DNA nucleosides. We assign all the observed time constants and identify the excited state relaxation pathways, including the competition of intersystem crossing and internal conversion for 5-formyl-2'-deoxycytidine and ballistic decay to the ground state for 5-carboxy-2'-deoxycytidine. Our work contributes to shed light on the role of epigenetic derivatives in DNA photodamage as well as on their possible therapeutic use.