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.

The dynamics of excited electronic states in self-assembled structures formed between silver-(I) ions and cytosine-containing DNA strands or monomeric cytosine derivatives were investigated by time-resolved infrared (TRIR) spectroscopy and quantum mechanical calculations. The steady-state and time-resolved spectra depend sensitively on the underlying structures, which change with pH and the nucleobase and silver ion concentrations. At pH similar to 4 and low dC(20) strand concentration, an intramolecularly folded i-motif is observed, in which protons, and not silver ions, mediate C-C base pairing. However, at the higher strand concentrations used in the TRIR measurements, dC(20) strands associate pairwise to yield duplex structures containing C-Ag+-C base pairs with a high degree of propeller twisting. UV excitation of the silver ion-mediated duplex produces a long-lived excited state, which we assign to a triplet excimer state localized on a pair of stacked cytosines. The computational results indicate that the propeller-twisted motifs induced by metal-ion binding are responsible for the enhanced intersystem crossing that populates the triplet state and not a generic heavy atom effect. Although triplet excimer states have been discussed frequently as intermediates in the formation of cyclobutane pyrimidine dimers, we find neither computational nor experimental evidence for cytosine-cytosine photoproduct formation in the systems studied. These findings provide a rare demonstration of a long-lived triplet excited state that is formed in a significant yield in a DNA duplex, demonstrating that supramolecular structural changes induced by metal ion binding profoundly affect DNA photophysics.

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.

Two-photon absorption (2PA) spectra of liquid cyclohexane and hexanes are reported for the energy range 6.4-8.5 eV (177-145 nm), providing detailed information about their electronic structures in bulk liquid. Using a broadband pump-probe fashion, we measured the continuous 2PA spectra by simultaneous absorption of a 266 nm (4.6 eV) pump photon and one UV-vis probe photon from the white-light continuum (1.8-3.9 eV). Theoretical one-photon absorption (1PA) and 2PA cross sections of isolated gas phase molecules are computed by the equation of motion coupled-cluster method with single and double substitutions (EOM-CCSD) to substantiate the assignment of the experimental spectra, and the natural transition orbital (NTO) analysis provides visualization of the participating orbitals in a transition. Our analysis suggests that upon solvation transitions at the lowest excitation energy involving promotion of electron to the 3s Rydberg orbitals are blue-shifted (∼0.55 eV for cyclohexane and ∼0.18 eV for hexanes) to a greater extent as compared to those involving other Rydberg orbitals, which is similar to the behavior observed for water and alcohols. All other transitions experience negligible (cyclohexane) or minor red-shift by ∼0.15-0.2 eV (hexane) upon solvation. In both alkanes, the spectra are entirely dominated by Rydberg transitions: the most intense bands in 1PA and 2PA spectra are due to the excitation of electrons to the Rydberg "p" and "d" type orbitals, respectively, although one transition terminating in the 3s Rydberg has significant 2PA strength. This work demonstrates that the gas phase electronic transition properties in alkanes are not significantly altered upon solvation. In addition, electronic structure calculations using an isolated-molecule framework appear to provide a reasonable starting point for a semiquantitative picture for spectral assignment and also to analyze the solvatochromic shifts for liquid phase absorption spectra.

DNA strands are polymeric ligands that both protect and tune molecular-sized silver cluster chromophores. We studied single-stranded DNA C4AC4TC3XT4 with X = guanosine and inosine that form a green fluorescent Ag10 6+ cluster, but these two hosts are distinguished by their binding sites and the brightness of their Ag10 6+ adducts. The nucleobase subunits in these oligomers collectively coordinate this cluster, and fs time-resolved infrared spectra previously identified one point of contact between the C2-NH2 of the X = guanosine, an interaction that is precluded for inosine. Furthermore, this single nucleobase controls the cluster fluorescence as the X = guanosine complex is ∼2.5× dimmer. We discuss the electronic relaxation in these two complexes using transient absorption spectroscopy in the time window 200 fs-400 µs. Three prominent features emerged: a ground state bleach, an excited state absorption, and a stimulated emission. Stimulated emission at the earliest delay time (200 fs) suggests that the emissive state is populated promptly following photoexcitation. Concurrently, the excited state decays and the ground state recovers, and these changes are ∼2× faster for the X = guanosine compared to the X = inosine cluster, paralleling their brightness difference. In contrast to similar radiative decay rates, the nonradiative decay rate is 7× higher with the X = guanosine vs inosine strand. A minor decay channel via a dark state is discussed. The possible correlation between the nonradiative decay and selective coordination with the X = guanosine/inosine suggests that specific nucleobase subunits within a DNA strand can modulate cluster-ligand interactions and, in turn, cluster brightness.

2'-Deoxy-5-formylcytidine (5fdCyd), a naturally occurring nucleoside found in mammalian DNA and mitochondrial RNA, exhibits important epigenetic functionality in biological processes. Because it efficiently generates triplet excited states, it is an endogenous photosensitizer capable of damaging DNA, but the intersystem crossing (ISC) mechanism responsible for ultrafast triplet state generation is poorly understood. In this study, time-resolved mid-IR spectroscopy and quantum mechanical calculations reveal the distinct ultrafast ISC mechanisms of 5fdCyd in water versus acetonitrile. Our experiment indicates that in water, ISC to triplet states occurs within 1 ps after 285 nm excitation. PCM-TD-DFT computations suggest that this ultrafast ISC is mediated by a singlet state with significant cytosine-to-formyl charge-transfer (CT) character. In contrast, ISC in acetonitrile proceeds via a dark (1)n pi* state with a lifetime of similar to 3 ps. CT-induced ISC is not favored in acetonitrile because reaching the minimum of the gateway CT state is hampered by intramolecular hydrogen bonding, which enforces planarity between the aldehyde group and the aromatic group. Our study provides a comprehensive picture of the non-radiative decay of 5fdCyd in solution and new insights into the factors governing ISC in biomolecules. We propose that the intramolecular CT state observed here is a key to the excited-state dynamics of epigenetic nucleosides with modified exocyclic functional groups, paving the way to study their effects in DNA strands.

DNA-templated silver clusters are chromophores in which the nucleobases encode the cluster spectra and brightness. We describe the coordination environments of two nearly identical Ag106+ clusters that form with 18-nucleotide strands CCCCA CCCCT CCCX TTTT, with X = guanosine and inosine. For the first time, femtosecond time-resolved infrared (TRIR) spectroscopy with visible excitation and mid-infrared probing is used to correlate the response of nucleobase vibrational modes to electronic excitation of the metal cluster. A rich pattern of transient TRIR peaks in the 1400-1720 cm-1 range decays synchronously with the visible emission. Specific infrared signatures associated with the single guanosine/inosine along with a subset of cytidines, but not the thymidines, are observed. These fingerprints suggest that the network of bonds between a silver cluster adduct and its polydentate DNA ligands can be deciphered to rationally tune the coordination and thus spectra of molecular silver chromophores.

To better understand the nexus between structure and photophysics in metallo-DNA assemblies, the parallel-stranded duplex formed by the all-cytosine oligonucleotide, dC(20), and silver nitrate was studied by circular dichroism (CD), femtosecond transient absorption spectroscopy, and time-dependent-density functional theory calculations. Silver(I) ions mediate Cytosine-Cytosine (CC) base pairs by coordinating to the N3 atoms of two cytosines. Although these silver(I) mediated CC base pairs resemble the proton-mediated CC base pairs found in i-motif DNA at first glance, a comparison of experimental and calculated CD spectra reveals that silver ion-mediated i-motif structures do not form. Instead, the parallel-stranded duplex formed between dC(20) and silver ions is proposed to contain consecutive silver-mediated base pairs with high propeller twist-like ones seen in a recent crystal structure of an emissive, DNA-templated silver cluster. Femtosecond transient absorption measurements with broadband probing from the near UV to the near IR reveal an unusually long-lived (>10 ns) excited state in the dC(20) silver ion complex that is not seen in dC(20) in single-stranded or i-motif forms. This state is also absent in a concentrated solution of cytosine-silver ion complexes that are thought to assemble into planar ribbons or sheets that lack stacked silver(I) mediated CC base pairs. The large propeller twist angle present in metal-mediated base pairs may promote the formation of long-lived charged separated or triplet states in this metallo-DNA.

Liquid phase charge-transfer-to-solvent (CTTS) transitions are important, as they serve as photochemical routes to solvated electrons. In this work, broadband deep-ultraviolet electronic sum frequency generation (DUV-ESFG) and two-photon absorption (2PA) spectroscopic techniques were used to assign and compare the nature of the aqueous iodide CTTS excitations at the air/water interface and in bulk solution. In the one-photon absorption (1PA) spectrum, excitation to the 6s Rydberg-like orbital (5p → 6s) gives rise to a pair of spin-orbit split iodine states, 2P3/2 and 2P1/2. In the 2PA spectra, the lower-energy 2P3/2 peak is absent and the observed 2PA peak, which is ∼0.14 eV blue-shifted relative to the upper 2P1/2 CTTS peak seen in 1PA, arises from 5p → 6p electronic promotion. The band observed in the ESFG spectrum is attributed to mixing of excited states involving 5p → 6p and 5p → 6s promotions caused by both vibronic coupling and the external electric field generated by asymmetric interfacial solvation.

Two-photon absorption (2PA) spectroscopy in the range from 7 to 10 eV provides new insight on the electronic structure of liquid water. Continuous 2PA spectra are obtained via the pump-probe technique, using broadband probe pulses to record the absorption at many wavelengths simultaneously. A preresonance enhancement of the absolute 2PA cross section is observed when the pump-photon energy increases from 4.6 to 6.2 eV. The absorption cross section also depends on the relative polarization of the pump and probe photons. The variation of the polarization ratio across the spectrum reveals a detailed picture of the 2PA and indicates that at least four different transitions play a role below 10 eV. Theoretical polarization ratios for the isolated molecule illustrate the value of the experimental polarization measurement in deciphering the 2PA spectrum and provide the framework for a simple simulation of the liquid spectrum. A more comprehensive model goes beyond the isolated molecule picture and connects the 2PA spectrum with previous one-photon absorption, photoelectron, and x-ray absorption spectroscopy measurements of liquid water. Previously unresolved, overlapping transitions are assigned for the first time. Finally, the electronic character of the vertical excited states is related to the energy-dependent ionization mechanism of liquid water.

Changing the solvent from H2O to D2O dramatically affects the branching of the initial excited electronic states in an alternating G·C DNA duplex into two distinct decay channels. The slower, multisite PCET channel that deactivates more than half of all excited states in D2O becomes six times weaker in H2O.

Supramolecular assemblies form when silver nitrate is added to an aqueous solution of adenine (Ade) or 2-aminopurine (2AP) in a 2:1 mole ratio. Atomic force microscopy images reveal nanofibers that are ∼30 nm in diameter and micrometers in length in the dried film formed from a room-temperature solution. Femtosecond broadband transient absorption spectroscopy was used to investigate the dynamics of excited states formed by UV excitation of the nanofibers in room-temperature aqueous solutions in an effort to learn how nonradiative decay pathways of the uncomplexed nucleobases are altered in the silver-ion-mediated assemblies. The changes in the spectroscopy and dynamics of Ade and 2AP upon forming nanofibers with silver ions closely parallel the ones seen when these bases are organized into DNA strands. The similarities strongly suggest that these structures feature extensive π-π stacking interactions between nucleobases. The results show that time-resolved spectroscopy combined with growing understanding of the photophysics of DNA strands can deliver new insights into the properties of metal-nucleobase nanoassemblies.

The photophysics of several mono- and oligonucleotides were investigated in a deep eutectic solvent for the first time. The solvent glyceline, prepared as a 1 : 2 mole ratio mixture of choline chloride and glycerol, was used to study excited-state deactivation in a non-aqueous solvent by the use of steady-state and time-resolved spectroscopy. DNA strands in glyceline retain the secondary structures that are present in aqueous solution to some degree, thus enabling a study of the effects of solvent properties on the excited states of stacked bases and stacked base pairs. The excited-state lifetime of the mononucleotide 5'-AMP in glyceline is 630 fs, or twice as long as in aqueous solution. Even slower relaxation is seen for 5'-TMP in glyceline, and a possible triplet state with a lifetime greater than 3 ns is observed. Circular dichroism spectra show that the single strand (dA)18 and the duplex d(AT)9·d(AT)9 adopt similar structures in glyceline and in aqueous solution. Despite having similar conformations in both solvents, femtosecond transient absorption experiments reveal striking changes in the dynamics. Excited-state decay and vibrational cooling generally take place more slowly in glyceline than in water. Additionally, the fraction of long-lived excited states in both oligonucleotide systems is lower in glyceline than in aqueous solution. For a DNA duplex, water is suggested to favor decay pathways involving intrastrand charge separation, while the deep eutectic solvent favors interstrand deactivation channels involving neutral species. Slower solvation dynamics in the viscous deep eutectic solvent may also play a role. These results demonstrate that the dynamics of excitations in stacked bases and stacked base pairs depend not only on conformation, but are also highly sensitive to the solvent.

The catechol functional group plays a major role in the chemistry of a wide variety of molecules important in biology and technology. In eumelanin, intermolecular hydrogen bonding between these functional groups is thought to contribute to UV photoprotective and radical buffering properties, but the mechanisms are poorly understood. Here, aggregates of 4‐ t ‐butylcatechol are used as model systems to study how intermolecular hydrogen bonding influences photochemical pathways that may occur in eumelanin. Ultrafast UV ‐visible and mid‐ IR transient absorption measurements are used to identify the photochemical processes of 4‐ t ‐butylcatechol monomers and their hydrogen‐bonded aggregates in cyclohexane solution. Monomer photoexcitation results in hydrogen atom ejection to the solvent via homolytic O‐H bond dissociation with a time constant of 12 ps, producing a neutral semiquinone radical with a lifetime greater than 1 ns. In contrast, intermolecular hydrogen bonding interactions within aggregates retard O‐H bond photodissociation by over an order of magnitude in time. Excited state structural relaxation is proposed to slow O‐H dissociation, allowing internal conversion to the ground state to occur in hundreds of picoseconds in competition with this channel. The semiquinone radicals formed in the aggregates exhibit spectral broadening of both their electronic and vibrational transitions.

To better understand how the solvent influences excited-state deactivation in DNA strands, femtosecond time-resolved IR (fs-TRIR) pump-probe measurements were performed on a d(AT)9·d(AT)9 duplex dissolved in a deep eutectic solvent (DES) made from choline chloride and ethylene glycol in a 1:2 mol ratio. This solvent, known as ethaline, is a member of a class of ionic liquids capable of solubilizing DNA with minimal disruption to its secondary structure. UV melting analysis reveals that the duplex studied here melts at 18 °C in ethaline compared to 50 °C in aqueous solution. Ethaline has an excellent transparency window that facilitates TRIR measurements in the double-bond stretching region. Transient spectra recorded in deuterated ethaline at room temperature indicate that photoinduced intrastrand charge transfer occurs from A to T, yielding the same exciplex state previously detected in aqueous solution. This state decays via charge recombination with a lifetime of 380 ± 10 ps compared to the 300 ± 10 ps lifetime measured earlier in D2O solution. The TRIR data strongly suggest that the long-lived exciplex forms exclusively in the solvated duplex, and not in the denatured single strands, which appear to have little, if any, base stacking. The longer lifetime of the exciplex state in the DES compared to aqueous solution is suggested to arise from reduced stabilization of the charge transfer state, resulting in slower charge recombination on account of Marcus inverted behavior.

The photophysical properties of the natural pigment violacein extracted from an Antarctic organism adapted to high exposure levels of UV radiation were measured in a combined steady-state and time-resolved spectroscopic study for the first time. In the low-viscosity solvents methanol and acetone, violacein exhibits low fluorescence quantum yields on the order of 10-4, and femtosecond transient absorption measurements reveal excited-state lifetimes of 3.2 ± 0.2 and 4.5 ± 0.2 picoseconds in methanol and acetone, respectively. As solvent viscosity is increased, both the fluorescence quantum yield and excited-state lifetime of this intensely colored pigment increase dramatically and stimulated emission decays 30-fold more slowly in glycerol than in methanol at room temperature. Excited-state deactivation is suggested to occur via a molecular-rotor mechanism in which torsion about an interring bond leads to a conical intersection with the ground state.

Photophysical investigations of the canonical nucleobases that make up DNA and RNA during the past 15 years have revealed that excited states formed by the absorption of UV radiation decay with subpicosecond lifetimes (i.e., <10(-12) s). Ultrashort lifetimes are a general property of absorbing sunscreen molecules, suggesting that the nucleobases are molecular survivors of a harsh UV environment. Encoding the genome using photostable building blocks is an elegant solution to the threat of photochemical damage. Ultrafast excited-state deactivation strongly supports the hypothesis that UV radiation played a major role in shaping molecular inventories on the early Earth before the emergence of life and the subsequent development of a protective ozone shield. Here, we review the general physical and chemical principles that underlie the photostability, or "UV hardiness", of modern nucleic acids and discuss the possible implications of these findings for prebiotic chemical evolution. In RNA and DNA strands, much longer-lived excited states are observed, which at first glance appear to increase the risk of photochemistry. It is proposed that the dramatically different photoproperties that emerge from assemblies of photostable building blocks may explain the transition from a world of molecular survival to a world in which energy-rich excited electronic states were eventually tamed for biological purposes such as energy transduction, signaling, and repair of the genetic machinery.

UV radiation creates excited electronic states in DNA that can decay to mutagenic photoproducts. When excited states return to the electronic ground state, photochemical injury is avoided. Understanding of the available relaxation pathways has advanced rapidly during the past decade, but there has been persistent uncertainty, and even controversy, over how to compare results from transient absorption and time-resolved emission experiments. Here, emission from single- and double-stranded AT DNA compounds excited at 265 nm was studied in aqueous solution using the time-correlated single photon counting technique. There is quantitative agreement between the emission lifetimes ranging from 50 to 200 ps and ones measured in transient absorption experiments, demonstrating that both techniques probe the same excited states. The results indicate that excitations with lifetimes of more than a few picoseconds are weakly emissive excimer and charge transfer states. Only a minute fraction of excitations persist beyond 1 ns in AT DNA strands at room temperature.

The excited-state dynamics of two cyclic DNA miniduplexes, each containing just two base pairs, are investigated using time-resolved infrared spectroscopy. As in longer DNA duplexes, intrastrand electron transfer induced by UV excitation triggers interstrand proton transfer in the alternating miniduplex containing two out-of-phase G·C base pairs. The resulting excited state decays on a time scale of several tens of picoseconds. This state is absent when one of the two G residues is substituted by 8-oxo-7,8-dihydroguanine, a modification that is suggested to disrupt base stacking, while maintaining base pairing. These findings demonstrate that a nucleobase tetramer arranged as two stacked base pairs accurately captures the interplay between intrastrand and interstrand decay channels. The similar signals seen in the miniduplexes and longer sequences suggest that excited states in the latter rapidly localize on two adjacent base pairs.