Highly emissive organic molecular crystals find applications in several areas, such as organic electronics, solar cells, and sensors. Understanding the excited-state mechanisms underlying these applications is essential for optimizing and controlling them effectively. Exciton models coupled with nonadiabatic dynamics, particularly quantum dynamics, provide crucial insights into photochemical and photophysical processes in molecular crystals. Nevertheless, there remains a lack of general tools and automated workflows to facilitate such simulations. In this paper, we present a computational strategy to investigate the photoactivated dynamics of organic molecular crystals, bridging methodologies traditionally used for molecular systems and materials science, with a particular focus on the interplay between local excitations and charge transfer (CT) processes. We have implemented an interface between the fromage and Overdia programs, enabling the construction of vibronic Hamiltonians for molecular crystals within an excited-state ONIOM(QM:QM') framework, incorporating long-range electrostatics through a RESP-based Ewald summation. Fragment-based diabatization provides a route to quantum dynamics simulations in weak-to-intermediate coupling regimes. The method was applied to the photophysics of dibenzo[g,p]chrysene (DBC) crystals using time-dependent DFT. The fromage/Overdia interface was employed to compute the couplings of local excitations and CT states for 18 unique DBC dimers in the crystal and to quantify the influence of electrostatic embedding, which was found to be modest (10-20%). Simulations on π-stacked dimers reproduced the small red shift observed experimentally from solution to crystal, attributed to electronic interactions among fixed monomers rather than crystal electrostatics. Quantum dynamics simulations revealed ultrafast population transfer from bright local excitations to CT states. This approach establishes a robust framework linking molecular and solid-state excited-state dynamics, with potential applications for studying excitations, defects, and impurities in molecular crystals.

We characterize the photoactivated processes in 2'-deoxyadenosine (dA) in aqueous solution by combining transient absorption spectroscopy with 30 fs resolution, quantum mechanical calculations, and quantum dynamical simulations. Using TD-DFT within a polarized continuum model, we map the lowest-lying excited states - two ππ* (La and Lb) and one nπ* (Sn) - identifying five low-energy basins and computing their absorption spectra. Nonadiabatic transitions among them are described through quantum dynamics propagations. The evolution of the experimental photoinduced bands is rationalized through comparison with computed spectra, avoiding global multiexponential fits, incompatible with the evolving electronic structure of the chromophore. The first 100 fs are governed by the Lb - La interplay. Subsequently, the wave packet undergoes nonradiative decay to the ground state or explores the nonplanar region of the La surface, whose lifetime is 470 fs. Sn is the longest living excited state, decaying with a time constant of 1 ps.

We here describe a procedure for the calculation of photoelectron spectra in solution, including vibrational and dynamical solvent effect. Steady state vibronic spectra are computed in harmonic approximation including the...

The potential of thienoguanosine (thG), an isomorphic fluorescent analogue of guanosine, was evaluated as a reporter for probing the structure and dynamics of hTel22, a human telomeric G-quadruplex (G4) sequence. Nine of the 12 guanines directly participating in G-tetrads were individually substituted with thG, and their impact on the hTel22 structure was examined by circular dichroism, thermal melting, and 1H NMR spectroscopy. In Na+ buffer, substitutions at external tetrads maintained the native antiparallel topology and thermal stability, while substitutions within the middle tetrad significantly disrupted the G4 structure. Molecular dynamics simulations supported that thG incorporation in external tetrads is well tolerated, whereas it alters base stacking and Na+ coordination in middle tetrad positions. In K+ buffer, external substitutions favored the antiparallel over the hybrid topology, resulting in a modest destabilization. thG-labeled sequences at external tetrads in both Na+ and K+ buffers exhibited high fluorescence quantum yields, long fluorescence lifetimes, and high sensitivity to local conformation. As an application, thG fluorescence signal proved instrumental in accurately characterizing the kinetics of Na+-induced G4 folding, enabling all kinetically resolved folding steps to be captured from a single fluorescence observable. Overall, thG serves as a remarkably sensitive, minimally perturbing fluorescent guanosine analogue for structural and dynamic studies of G4s. Moreover, its longest lifetime (18.5 to 28.5 ns), at least twice that in DNA duplexes, is suitable for time-gated detection with high signal-to-noise ratio and easy distinction of G4s from duplexes, offering a key advantage for G4-targeting drug discovery.

Ubiquitin-like, containing PHD and RING fingers domains 1 (UHRF1) plays a pivotal role in replicating DNA methylation patterns during cell division. Acting as a DNA reader, UHRF1, via its SET- and RING-associated (SRA) domain, recognizes hemi-methylated (HM) CpG sites and flips 5-methylcytosine (5mC) nucleobases. This flipping triggers DNA methyltransferase 1 (DNMT1) recruitment to methylate cytosine in the complementary strand. To investigate the SRA-induced base-flipping mechanism, we introduced thienoguanosine (thG), a fluorescent guanosine analogue, at four positions in HM and non-methylated duplexes. The interactions of these labelled duplexes with wild-type SRA and a G448D mutant (incapable of base-flipping) were monitored using a combination of stopped-flow fluorescence measurements, molecular dynamics simulations, and quantum mechanical calculations. We show that 5mC and C residues are flipped with similar rate constants. However, while C residues rapidly revert to their original state, enabling SRA to continue reading or dissociate, SRA complexes with flipped 5mC undergo a slow conformational rearrangement, leading to the final conformation crucial for DNMT1 recruitment. Taken together, our findings suggest that base flipping is used to discriminate 5mC from C residues, while the ensuing conformational rearrangement drives DNMT1 recruitment.

Here, we demonstrate through AFM imaging and CD spectroscopy that the binding of silver ions (Ag+) to poly(dGdC), a double-stranded (ds) DNA composed of two identical repeating strands, at a stoichiometry of one Ag+ per GC base pair induces a one-base shift of one strand relative to the other. This results in a ds nucleic acid-Ag+ conjugate consisting of alternating CC and GG base pairs coordinated by silver ions. The proposed organization of the conjugate is supported by the results of our Quantum Mechanical (QM) and Molecular Mechanics (MMs) calculations. The reduction of Ag+ ions followed by the partial oxidation of silver atoms yields a highly fluorescent conjugate emitting at 720 nm. This fluorescent behavior in conjugates of long, repetitive ds DNA (thousands of base pairs) with silver has never been demonstrated before. We propose that the poly(dGdC)-Ag conjugate functions as a dynamic system, comprising various small clusters embedded within the DNA and interacting with one another through energy transfer. This hypothesis is supported by the results of our QM and MMs calculations. Additionally, these DNA-silver conjugates, comprising silver nanoclusters, may possess conductive properties, making them potential candidates for use as nanowires in nanodevices and nanosensors.

We study the excited state absorption (ESA) properties of the four DNA bases (thymine, cytosine, adenine, and guanine) by different single reference quantum mechanical methods, i.e. equation of motion coupled cluster singles and doubles (EOM-CCSD), singles, doubles and perturbative triples (EOM-CC3), and time-dependent density functional theory (TD-DFT), with the long-range corrected CAM-B3LYP functional. Preliminary results at the Tamm-Dancoff (TDA) CAM-B3LYP level using the maximum overlap method (MOM) are reported for Thymine. In the gas phase, the three methods predict similar One Photon Absorption (OPA) spectra, which are also consistent with the experimental results and with the most accurate computational studies available in the literature. The ESA spectra are then computed for the pp  states (one for pyrimidine, two for purines) associated with the lowest energy absorption band, and for the close-lying np  state. The EOM-CC3, EOM-CCSD and CAM-B3LYP methods provide similar ESA spectral patterns, which are also in qualitative agreement with literature RASPT2 results. Once validated in the gas phase, TD-CAM-B3LYP has been used to compute the ESA in chloroform, including solvent effect by the polarizable continuum model (PCM). The predicted OPA and ESA spectra in chloroform are very similar to those in the gas phase, most of the bands shifting by less than 0.1 eV, with a small increase of the intensities and a moderate destabilization of the np  state. Finally, ESA spectra have been computed from the minima of the lowest energy pp  state, and are consistent with the available experimental transient absorption spectra of the nucleosides in solution, providing a final validation of our computational approach.

To fully exploit the potential of isothiazologuanosine (tzG), an isomorphic and isofunctional fluorescent analogue of guanosine, as a probe for DNA and RNA, we characterized its photophysics and in particular its excited-state reactions over a wide pH range (-0.6 to 12) and time scale (100 fs-100 ns) by combining transient absorption and time-correlated single photon counting measurements with quantum mechanical calculations. At acidic pH, the dominant ground-state species tzG-H1-H3+, where the N atoms in positions 1 and 3 are protonated, rapidly converts to the more stable tautomer tzG-H1-H7+ in its excited state. The latter then deprotonates to form the tzG-H1 neutral species with an excited-state pKa* value that differs by three pH units from the ground-state pKa value. The rate constants governing the excited-state reactions and the fluorescence lifetime of each species were all determined. With the exception of intramolecular and solvent relaxations, no excited-state reactions in the femtosecond to nanosecond time scale were, however, observed between the dominant tzG-H1 and tzG-H3 tautomers in equilibrium at neutral pH or for tzG-H1 deprotonation at high pH. Because of the distinct spectra, fluorescence quantum yields and lifetimes of its different protonated and deprotonated forms, tzG is highly responsive over a wide range of acidic (0-5) and basic pH values (8-10). The mechanisms revealed herein will be instrumental for tzG-labelled oligonucleotides in order to interpret proton transfer reactions as well as interactions with specific protein domains, which, due to local electrostatic changes and water exclusion effects, may shift the pKa values of tzG to a more physiologically relevant range.

Femtosecond fluorescence upconversion experiments were combined with CASPT2 and time dependent DFT calculations to characterize the excited state dynamics of the mutagenic etheno adduct 1,N2-etheno-2'-deoxyguanosine (ϵdG). This endogenously formed lesion is attracting great interest because of its ubiquity in human tissues and its highly mutagenic properties. The ϵdG fluorescence is strongly modified with respect to that of the canonical nucleoside dG, notably by an about 6-fold increase in fluorescence lifetime and quantum yield at neutral pH. In addition, femtosecond fluorescence upconversion experiments reveal the presence of two emission bands with maxima at 335 nm for the shorter-lived and 425 nm for the longer-lived. Quantum mechanical calculations rationalize these findings and provide absorption and fluorescence spectral shapes similar to the experimental ones. Two different bright minima are located on the potential energy surface of the lowest energy singlet excited state. One planar minimum, slightly more stable, is associated with the emission at 335 nm, whereas the other one, with a bent etheno ring, is associated with the red-shifted emission.

Let's shine! The 2'-deoxyguanosine etheno adduct exhibits enhanced emission features with respect to the canonical nucleobase. The peculiar fluorescence arising from two independent species was unveiled by upconversion fluorescence and rationalized by quantum mechanical calculations. More information can be found in the Research Article by R. Improta, V. Lhiaubet-Vallet and co-workers (DOI: 10.1002/chem.202401835). Artwork designed by Cora Pardo Asuncion.

Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the ions, make these structures interesting candidates in the context of using DNA in nanotechnology. Here, we report the formation and characterization of conjugates of long (kilo bases) homoguanine DNA strands with silver ions. We demonstrate using atomic force microscopy (AFM) and scanning tunneling microscope (STM) that binding of silver ions leads to folding of homoguanine DNA strands in a “hairpin” fashion to yield double-helical, left-handed molecules composed of G-G base pairs each stabilized by a silver ion. Further folding of the DNA–silver conjugate yields linear molecules in which the two halves of the double helix are twisted one against the other in a right-handed fashion. Quantum mechanical calculations on smaller molecular models support the helical twist directions obtained by the high resolution STM analysis. These long guanine-based nanostructures bearing a chain of silver ions have not been synthesized and studied before and are likely to possess conductive properties that will make them attractive candidates for nanoelectronics.

Epigenetic modifications impart important functionality to nucleic acids during gene expression but may increase the risk of photoinduced gene mutations. Thus, it is crucial to understand how these modifications affect the photostability of duplex DNA. In this work, the ultrafast formation (<20 ps) of a delocalized triplet charge transfer (CT) state spreading over two stacked neighboring nucleobases after direct UV excitation is demonstrated in a DNA duplex, d(G5fC)9•d(G5fC)9, made of alternating guanine (G) and 5-formylcytosine (5fC) nucleobases. The triplet yield is estimated to be 8 ± 3%, and the lifetime of the triplet CT state is 256 ± 22 ns, indicating that epigenetic modifications dramatically alter the excited state dynamics of duplex DNA and may enhance triplet state-induced photochemistry.

RG1 is a quadruplex-forming sequence in the SARS-CoV-2 genome proposed as possible therapeutic target for COVID-19. We demonstrate that the dominant conformation of RG1 under physiological conditions differs from the parallel quadruplex previously assumed. Through comprehensive investigations employing CD, UV, NMR, DSC, gel electrophoresis, MD simulations, in silico spectroscopy and the use of truncated RG1 sequences, we have identified this stable conformation as an RNA G-triplex composed of two G-triads. We believe this previously unreported RNA structure could serve as a novel therapeutic target. Our findings open new avenues for further studies on the presence and biological role of RNA G-triplexes in vivo.

Study of alternating DNA GC sequences by different time-resolved spectroscopies has provided fundamental information on the interaction between UV light and DNA, a process of great biological importance. Multiple decay paths have been identified, but their interplay is still poorly understood. Here, we characterize the photophysics of GC-DNA by integrating different computational approaches, to study molecular models including up to 6 bases described at a full quantum mechanical level. Quantum dynamical simulations, exploiting a nonadiabatic linear vibronic coupling (LVC) model, coupled with molecular dynamics sampling of the initial structures of a (GC)5 DNA duplex, provide new insights into the photophysics in the sub-picosecond time-regime. They indicate a substantial population transfer, within 50 fs, from the spectroscopic states towards G -> C charge transfer states involving two stacked bases (CTintra), thus explaining the ultrafast disappearance of fluorescence. This picture is consistent with that provided by quantum mechanical geometry optimizations, using time dependent-density functional theory and a polarizable continuum model, which we use to parametrize the LVC model and to map the main excited state deactivation pathways. For the first time, the infrared and excited state absorption signatures of the various states along these pathways are comprehensively mapped. The computational models suggest that the main deactivation pathways, which, according to experiment, lead to ground state recovery on the 10-50 ps time scale, involve CTintra followed by interstrand proton transfer from the neutral G to C-. Our calculations indicate that CTintra is populated to a larger extent and more rapidly in GC than in CG steps and suggest the likely involvement of monomer-like and interstrand charge transfer decay routes for isolated and less stacked CG steps. These findings underscore the importance of the DNA sequence and thermal fluctuations for the dynamics. They will also aid the interpretation of experimental results on other sequences. We disentangle the photophysical processes triggered in a representative DNA sequence by absorption of UV light, giving new molecular insights on the sub picosecond component of phenomena with great biological importance.

We here study the effect that a lowering of the pH has on the excited state processes of cytidine and a cytidine/cytidine pair in solution, by integrating time-dependent density functional theory and CASSCF/CASPT2 calculations, and including solvent by a mixed discrete/continuum model. Our calculations reproduce the effect of protonation at N3 on the steady-state infrared and absorption spectra of a protonated cytidine (CH+ ), and predict that an easily accessible non-radiative deactivation route exists for the spectroscopic state, explaining its sub-ps lifetime. Indeed, an extremely small energy barrier separates the minimum of the lowest energy bright state from a crossing region with the ground electronic state, reached by out-of-plane motion of the hydrogen substituents of the CC double bond, the so-called ethylenic conical intersection typical of cytidine and other pyrimidine bases. This deactivation route is operative for the two bases forming an hemiprotonated cytidine base pair, [CH·C]+ , the building blocks of I-motif secondary structures, whereas interbase processes play a minor role. N3 protonation disfavors instead the nπ* transitions, associated with the long-living components of cytidine photoactivated dynamics.

Application of fluorescence techniques to investigate molecular interactions with nucleic acids is complicated by their poor emission, making the substitution of natural nucleobases by fluorescent nucleoside analogues (FNAs) a useful strategy. A breakthrough in fluorescent nucleoside analogues has been the development of thienoguanosine (thG) and isothiazologuanosine (tzG), two isosteric mimics of guanosine (G). Due to its N7 atom needed in Hoogsteen base pairs and enzyme recognition, tzG is also an isofunctional G surrogate. Herein, we integrated fluorescence spectroscopy measurements with quantum mechanical (QM) calculations to characterize the mechanisms underlying tzG photophysics in different solvents. In dioxane and ethyl acetate, tzG existed primarily as a H1 keto-amino tautomer with short fluorescence lifetime (r - 2 ns) and low quantum yield (O - 0.10). In buffer, the H1 tautomer (O = 0.36, r = 8.84 ns) coexisted with a weakly emissive H3 keto-amino tautomer. The two tautomers were also observed in methanol, but with a 30% decrease in O and r values for the major H1 tautomer. QM calculations suggested that the main non-radiative pathway of tzG-H1 involves NS bond loosening and is responsible for the more solvent-sensitive O and r values compared to thG. This pathway is much more efficient for tzG-H3, for which an additional pathway to a dark n pi* state and a large coupling with triplet states further explain its very low emission. This study lays the ground for rationally using tzG as a sensitive FNA.

In this study, we exploit a recently developed fragment diabatization-based excitonic model, FrDEx, to simulate the electronic circular dichroism (ECD) spectra of three guanine-rich DNA sequences arranged in guanine quadruple helices with different topologies: thrombin binding aptamer (antiparallel), c-Myc promoter (parallel), and human telomeric sequence (3+1 hybrid). Starting from time-dependent density functional theory (TD-DFT) calculations with the M052X functional, we apply our protocol to parameterize the FrDEX Hamiltonian, which accounts for electron density overlap and includes both the coupling with charge transfer transitions and the effect of the surrounding bases on the local excitation of each chromophore. The TD-DFT/M052X spectral shapes are in good agreement with the experimental ones, the main source of discrepancy being related to the intrinsic error on the computed transition energies of guanine monomer. FrDEx spectra are fairly close to the reference TD-DFT ones, allowing a significant advance with respect to a more standard excitonic Hamiltonian. We also show that the ECD spectra are sensitive to the inclusion of the inner K + cation in the calculation.

I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)+ pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH+), which are currently drawing great attention due to their biological relevance and promising nanotechnological properties. It is important to characterize the processes occurring in I-motifs following irradiation by UV light because they can lead to harmful consequences for genetic code and because optical spectroscopies are the most-used tools to characterize I-motifs. By using time-dependent DFT calculations, we here provide the first comprehensive picture of the photoactivated behavior of the (CH·C)+ core of I-motifs, from absorption to emission, while also considering the possible photochemical reactions. We reproduce and assign their spectral signatures, i.e., infrared, absorption, fluorescence and circular dichroism spectra, disentangling the underlying chemical–physical effects. We show that the main photophysical paths involve C and CH+ bases on adjacent steps and, using this basis, interpret the available time-resolved spectra. We propose that a photodimerization reaction can occur on an excited state with strong C→CH+ charge transfer character and examine some of the possible photoproducts. Based on the results reported, some future perspectives for the study of I-motifs are discussed.