Adenine and 2-aminopurine: paradigms of modern theoretical photochemistry

Theoretical insight into photodeactivation mechanisms of adenine-uracil and adenine-thymine nucleobase pairs

In this work, several plausible intra- and intermolecular photoinduced processes of the Watson-Crick base pairs of adenine with uracil (A-U) or thymine (A-T) according to the results of spin component scaling variant of algebraic diagrammatic construction up to the second order [SCS-ADC(2)] calculations are discussed. Although widely explored, these systems lack complete characterization of possible intramolecular relaxation channels perturbed by intermolecular interactions. In particular, we address the still open debate on photodeactivation via purine-ring puckering at the C2 or C6-atom position of adenine. We also show that the presence of low-lying, long-lived 1nπ* states can be a significant factor in hindering relaxation via an electron-driven proton transfer process, as the population of these states can lead to an efficient intersystem crossing to a triplet manifold, the estimated rate of which is 1.6 × 1010 s-1 which exceeds the corresponding internal conversion to the ground state by an order of magnitude. Additionally, the SCS variant of the ADC(2) method is shown to provide a more balanced description of valence and charge-transfer excited states.

A DNA Aptamer for 2-Aminopurine: Binding-Induced Fluorescence Quenching

2-Aminopurine (2AP) is a fluorescent analog of adenine, and its unique properties make it valuable in various biochemical and biotechnological applications. Its fluorescence property probes local dynamics in DNA and RNA because stacking with the surrounding bases quench its fluorescence. 2AP-labeled DNA or RNA sequences have been used for the detection of genetic mutations, viral RNA, or other nucleic acid-based markers associated with diseases like cancer and infectious diseases. In this study, we isolated aptamers for 2AP using the library immobilization capture-SELEX technique. A dominating aptamer family was isolated after 15 rounds of selection. The Kd values for the most abundant 2AP1 aptamer are 209 nM in a fluorescence assay and 72 nM in an isothermal titration calorimetry test. A 32 nM 2AP limit of detection was tested based on its intrinsic fluorescence change upon aptamer binding. Additionally, we conducted some mutation analysis. Furthermore, we tested the selectivity of this aptamer and discovered that it can bind adenine and adenosine with approximately 100-fold lower affinity than 2AP.

DNA as a perfect quantum computer based on the quantum physics principles

DNA is a complex multi-resolution molecule whose theoretical study is a challenge. Its intrinsic multiscale nature requires chemistry and quantum physics to understand the structure and quantum informatics to explain its operation as a perfect quantum computer. Here, we present theoretical results of DNA that allow a better description of its structure and the operation process in the transmission, coding, and decoding of genetic information. Aromaticity is explained by the oscillatory resonant quantum state of correlated electron and hole pairs due to the quantized molecular vibrational energy acting as an attractive force. The correlated pairs form a supercurrent in the nitrogenous bases in a single band π -molecular orbital ( π -MO). The MO wave function ( Φ ) is assumed to be the linear combination of the n constituent atomic orbitals. The central Hydrogen bond between Adenine (A) and Thymine (T) or Guanine (G) and Cytosine (C) functions like an ideal Josephson Junction. The approach of a Josephson Effect between two superconductors is correctly described, as well as the condensation of the nitrogenous bases to obtain the two entangled quantum states that form the qubit. Combining the quantum state of the composite system with the classical information, RNA polymerase teleports one of the four Bell states. DNA is a perfect quantum computer.

Extreme ultraviolet time-resolved photoelectron spectroscopy of adenine, adenosine and adenosine monophosphate in a liquid flat jet

Time-resolved photoelectron spectroscopy using an extreme-ultraviolet (XUV) probe pulse was used to investigate the UV photoinduced dynamics of adenine (Ade), adenosine (Ado), and adenosine-5-monophosphate (AMP) in a liquid water jet. In contrast to previous studies using UV probe pulses, the XUV pulse at 21.7 eV can photoionize all excited states of a molecule, allowing for full relaxation pathways to be addressed after excitation at 4.66 eV. This work was carried out using a gas-dynamic flat liquid jet, resulting in considerably enhanced signal compared to a cylindrical jet. All three species decay on multiple time scales that are assigned based on their decay associated spectra; the fastest decay of ∼100 fs is assigned to ππ* decay to the ground state, while a smaller component with a lifetime of ∼500 fs is attributed to the nπ* state. An additional slower channel in Ade is assigned to the 7H Ade conformer, as seen previously. This work demonstrates the capability of XUV-TRPES to disentangle non-adiabatic dynamics in an aqueous solution in a state-specific manner and represents the first identification of the nπ* state in the relaxation dynamics of adenine and its derivatives.

Buffer-Dependent Photophysics of 2-Aminopurine: Insights into Fluorescence Quenching and Excited-State Interactions

2-Aminopurine (2AP) is the most widely used fluorescent nucleobase analogue in DNA and RNA research. Its unique photophysical properties and sensitivity to environmental changes make it a useful tool for understanding nucleic acid dynamics and DNA-protein interactions. We studied the effect of ions present in commonly used buffer solutions on the excited-state photophysical properties of 2AP. Fluorescence quenching was negligible for tris(hydroxymethyl)aminomethane (TRIS), but significant for phosphate, carbonate, 3-(N-morpholino) propanesulfonic acid (MOPS), and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffers. Results indicate that the two tautomers of 2AP (7H, 9H) are quenched by phosphate ions to different extents. Quenching by the H2PO4- ion is more pronounced for the 7H tautomer, while the opposite is true for the HPO42- ion. For phosphate ions, the results of the time-resolved fluorescence study cannot be explained using a simple collisional quenching mechanism. Instead, results are consistent with transient interactions between 2AP and the phosphate ions. We postulate that excited-state interactions between the 2AP tautomers and an H-bond acceptor (phosphate and carbonate) result in significant quenching of the singlet-excited state of 2AP. Such interactions manifest in biexponential fluorescence intensity decays with pre-exponential factors that vary with quencher concentration, and downward curvatures of the Stern-Volmer plots.

The tautomer-specific excited state dynamics of 2,6-diaminopurine using resonance-enhanced multiphoton ionization and quantum chemical calculations

2,6-Diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines.

Galván I, Rivalta I, Aquilante F, Garavelli M, Lindh R, Segarra-Martí J. Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.

Screening for Novel Fluorescent Nucleobase Analogues Using Computational and Experimental Methods: 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) as a Case Study

Novel fluorescent nucleic acid base analogues (FBAs) with improved optical properties are needed in a variety of biological applications. 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) is structural analogue of two existing highly fluorescent FBAs, 2-aminopurine (2AP) and 8-vinyladenine (8VA), and can therefore be expected to have similar base pairing as well as better optical properties compared to its counterparts. In order to determine the absorption and fluorescence properties of 2A6Cl8VP, as a first step, we used TD-DFT calculations and the polarizable continuum model for simulating the solvents and computationally predicted absorption and fluorescence maxima. To test the computational predictions, we also synthesized 2A6Cl8VP and measured its UV/vis absorbance, fluorescence emission, and fluorescence lifetime. The computationally predicted absorbance and fluorescence maxima of 2A6Cl8VP are in reasonable agreement to the experimental values and are significantly redshifted compared to 2AP and 8VA, allowing for its specific excitation. The fluorescence quantum yield of 2A6Cl8VP, however, is significantly lower than those of 2AP and 8VA. Overall, 2A6Cl8VP is a novel fluorescent nucleobase analogue, which can be useful in studying structural, biophysical, and biochemical applications.

Rationalizing the environment-dependent photophysical behavior of a DNA luminescent probe by classical and non-adiabatic molecular dynamics simulations

Environment-sensitive fluorescent nucleoside analogs are of utmost importance to investigate the structure of nucleic acids, their intrinsic flexibility, and sequence-specific DNA- and RNA-binding proteins. The latter play indeed a key role in transcription, translation as well as in the regulation of RNA stability, localization and turnover, and many other cellular processes. The sensitivity of the embedded fluorophore to polarity, hydration, and base stacking is clearly dependent on the specific excited-state relaxation mechanism and can be rationalized combining experimental and computational techniques. In this work, we elucidate the mechanisms leading to the population of the triplet state manifold for a versatile nucleobase surrogate, namely the 2-thienyl-3-hydroxychromone in gas phase, owing to non-adiabatic molecular dynamics simulations. Furthermore, we analyze its behavior in the B-DNA environment via classical molecular dynamics simulations, which evidence a rapid extrusion of the adenine facing the 2-thienyl-3-hydroxychromone nucleobase surrogate. Our simulations provide new insights into the dynamics of this family of chromophores, which could give rise to an integrated view and a fine tuning of their photochemistry, and namely the role of excited-state intramolecular proton transfer for the rational design of the next generation of fluorescent nucleoside analogs.

Chemiexcitation: Mammalian Photochemistry in the Dark†

Light is one way to excite an electron in biology. Another is chemiexcitation, birthing a reaction product in an electronically excited state rather than exciting from the ground state. Chemiexcited molecules, as in bioluminescence, can release more energy than ATP. Excited states also allow bond rearrangements forbidden in ground states. Molecules with low-lying unoccupied orbitals, abundant in biology, are particularly susceptible. In mammals, chemiexcitation was discovered to transfer energy from excited melanin, neurotransmitters, or hormones to DNA, creating the lethal and carcinogenic cyclobutane pyrimidine dimer. That process was initiated by nitric oxide and superoxide, radicals triggered by ultraviolet light or inflammation. Several poorly understood chronic diseases share two properties: inflammation generates those radicals across the tissue, and cells that die are those containing melanin or neuromelanin. Chemiexcitation may therefore be a pathogenic event in noise- and drug-induced deafness, Parkinson's disease, and Alzheimer's; it may prevent macular degeneration early in life but turn pathogenic later. Beneficial evolutionary selection for excitable biomolecules may thus have conferred an Achilles heel. This review of recent findings on chemiexcitation in mammalian cells also describes the underlying physics, biochemistry, and potential pathogenesis, with the goal of making this interdisciplinary phenomenon accessible to researchers within each field.

Ultrafast Intersystem Crossing Dynamics of 6-Selenoguanine in Water

Rationalizing the photochemistry of nucleobases where an oxygen is replaced by a heavier atom is essential for applications that exploit near-unity triplet quantum yields. Herein, we report on the ultrafast excited-state deactivation mechanism of 6-selenoguanine (6SeGua) in water by combining nonadiabatic trajectory surface-hopping dynamics with an electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. We find that the predominant relaxation mechanism after irradiation starts on the bright singlet S₂ state that converts internally to the dark S₁ state, from which the population is transferred to the triplet T₂ state via intersystem crossing and finally to the lowest T₁ state. This S₂ → S₁ → T₂ → T₁ deactivation pathway is similar to that observed for the lighter 6-thioguanine (6tGua) analogue, but counterintuitively, the T₁ lifetime of the heavier 6SeGua is shorter than that of 6tGua. This fact is explained by the smaller activation barrier to reach the T₁/S₀ crossing point and the larger spin-orbit couplings of 6SeGua compared to 6tGua. From the dynamical simulations, we also calculate transient absorption spectra (TAS), which provide two time constants (τ₁ = 131 fs and τ₂ = 191 fs) that are in excellent agreement with the experimentally reported value (τ_exp = 130 ± 50 fs) (Farrel et al. J. Am. Chem. Soc. 2018, 140, 11214). Intersystem crossing itself is calculated to occur with a time scale of 452 ± 38 fs, highlighting that the TAS is the result of a complex average of signals coming from different nonradiative processes and not intersystem crossing alone.

2-Oxopurine Riboside: A Dual Fluorescent Analog and Photosensitizer for RNA/DNA Research

There is significant interest in developing suitable nucleoside analogs exhibiting high fluorescence and triplet yields to investigate the structure, dynamics, and binding properties of nucleic acids and promote selective photosensitized damage to DNA/RNA, respectively. In this study, steady-state, laser flash photolysis, time-resolved IR luminescence, and femtosecond broad-band transient absorption spectroscopies are combined with quantum chemical calculations to elucidate the excited-state dynamics of 2-oxopurine riboside in aqueous solution and to investigate its prospective use as a fluorescent or photosensitizer analog. The Franck-Condon population in the S₁ (ππ*) state decays through a combination of solvent and conformational relaxation to its minimum in 1.9 ps. The population trapped in the ¹ππ* minimum bifurcates to either fluoresce or intersystem cross to the triplet manifold within ca. 5 ns, while another fraction of the population decays nonradiatively to the ground state. It is demonstrated that 2-oxopurine riboside exhibits both high fluorescent (48%) and significant triplet (between 10% and 52%) yields, leading to a yield of singlet oxygen generation of 10%, making this nucleoside analog a dual fluorescent and photosensitizer analog for DNA and RNA research.

Fewest switches surface hopping with Baeck-An couplings

In the Baeck-An (BA) approximation, first-order nonadiabatic coupling vectors are given in terms of adiabatic energy gaps and the second derivative of the gaps with respect to the coupling coordinate. In this paper, a time-dependent (TD) BA approximation is derived, where the couplings are computed from the energy gaps and their second time-derivatives. TD-BA couplings can be directly used in fewest switches surface hopping, enabling nonadiabatic dynamics with any electronic structure methods able to provide excitation energies and energy gradients. Test results of surface hopping with TD-BA couplings for ethylene and fulvene show that the TD-BA approximation delivers a qualitatively correct picture of the dynamics and a semiquantitative agreement with reference data computed with exact couplings. Nevertheless, TD-BA does not perform well in situations conjugating strong couplings and small velocities. Considered the uncertainties in the method, TD-BA couplings could be a competitive approach for inexpensive, exploratory dynamics with a small trajectories ensemble. We also assessed the potential use of TD-BA couplings for surface hopping dynamics with time-dependent density functional theory (TDDFT), but the results are not encouraging due to singlet instabilities near the crossing seam with the ground state.

Fewest switches surface hopping with Baeck-An couplings

In the Baeck-An (BA) approximation, first-order nonadiabatic coupling vectors are given in terms of adiabatic energy gaps and the second derivative of the gaps with respect to the coupling coordinate. In this paper, a time-dependent (TD) BA approximation is derived, where the couplings are computed from the energy gaps and their second time-derivatives. TD-BA couplings can be directly used in fewest switches surface hopping, enabling nonadiabatic dynamics with any electronic structure methods able to provide excitation energies and energy gradients. Test results of surface hopping with TD-BA couplings for ethylene and fulvene show that the TD-BA approximation delivers a qualitatively correct picture of the dynamics and a semiquantitative agreement with reference data computed with exact couplings. Nevertheless, TD-BA does not perform well in situations conjugating strong couplings and small velocities. Considered the uncertainties in the method, TD-BA couplings could be a competitive approach for inexpensive, exploratory dynamics with a small trajectories ensemble. We also assessed the potential use of TD-BA couplings for surface hopping dynamics with time-dependent density functional theory (TDDFT), but the results are not encouraging due to singlet instabilities near the crossing seam with the ground state.

Excited-state proton transfer in the 2-aminopyridine dimer: A surface hopping study

We present a theoretical investigation of the excited-state intermolecular proton transfer process in the 2-aminopyridine dimer. Prior experimental and theoretical studies on this doubly hydrogen bonded system have attributed an...

Excited State Deactivation Mechanisms of Protonated Adenine: a Theoretical study

Quantum chemical computational method as well as the adiabatic dynamics simulation have been employed to investigate the non-radiative relaxation mechanism of protonated 9H- and 7H-adenine (AH+). We have located three...

Adenine ultrafast photorelaxation via electron-driven proton transfer

Photorelaxation of adenine in water was reported to be ultrafast (within 180 fs) primarily due to radiationless relaxation. However, in the last two decades, several experimental and theoretical investigations on photoexcitation of adenine have revealed diverse types of decay mechanisms. Using time-dependent density functional excited-state nonadiabatic dynamics simulations we show that it is the water to adenine electron-driven proton transfer (EDPT) barrierless reaction responsible for the ultrafast component of the adenine relaxation, which, however, occurred only in the case of the 7H isomer of adenine with five water molecules. This result reveals a known reaction pathway, however not found in previous simulations, with inference for the ultrafast relaxation mechanisms of adenine reported in experiments. The 9H isomer of adenine with six water molecules relaxing in a water cluster followed the previously known structural distortion (C2) decay pathway. The observations of the adenine EDPT reaction with water provide the origin of the experimental ultrafast adenine decay component and present a possible method to tackle future computational challenges in molecular-level biological processes.

Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues

Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.

Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds

Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.

Ultrafast Dynamics of the Isolated Adenosine-5'-triphosphate Dianion Probed by Time-Resolved Photoelectron Imaging

The excited state dynamics of the doubly deprotonated dianion of adenosine-5'-triphosphate, [ATP-H₂]^2-, has been spectroscopically explored by time-resolved photoelectron spectroscopy following excitation at 4.66 eV. Time-resolved photoelectron spectra show that two competing processes occur for the initially populated ¹ππ* state. The first is rapid electron emission by tunneling through a repulsive Coulomb barrier as the ¹ππ* state is a resonance. The second is nuclear motion on the ¹ππ* state surface leading to an intermediate that no longer tunnels and subsequently decays by internal conversion to the ground electronic state. The spectral signatures of the features are similar to those observed for other adenine-derivatives, suggesting that this nucleobase is quite insensitive to the nearby negative charges localized on the phosphates, except of course for the appearance of the additional electron tunneling channel, which is open in the dianion.

Molecular Photochemistry: Recent Developments in Theory

Photochemistry is a fascinating branch of chemistry that is concerned with molecules and light. However, the importance of simulating light-induced processes is reflected also in fields as diverse as biology, material science, and medicine. This Minireview highlights recent progress achieved in theoretical chemistry to calculate electronically excited states of molecules and simulate their photoinduced dynamics, with the aim of reaching experimental accuracy. We focus on emergent methods and give selected examples that illustrate the progress in recent years towards predicting complex electronic structures with strong correlation, calculations on large molecules, describing multichromophoric systems, and simulating non-adiabatic molecular dynamics over long time scales, for molecules in the gas phase or in complex biological environments.

An nπ* gated decay mediates excited-state lifetimes of isolated azaindoles

Aiming to serve as a guide to understand the relaxation mechanisms of more complex aza-aromatic compounds, such as purine bases, we have studied the non-radiative channels of a set of azaindole structural isomers: 4-, 5-, 6- and 7-azaindole (AI). The relaxation of the isolated molecules, after excitation at the low energy portion of their spectra, has been tracked by femtosecond time-resolved ionization, and the decay paths have been obtained with MS-CASPT2//TD-DFT calculations. Although the ultrashort measured lifetimes for 5- and 6-AI are in contrast to the long-living excited state found in 7-AI, the calculations describe a common relaxation pathway. Along it, the initially excited ππ* states decay to the ground state through a conical intersection accessed through an nπ* state that functions as a gate state. The work reveals that the position of the nitrogen atoms in the purine ring determines the barrier to access the gate state and therefore, the rate of the non-radiative relaxation.

Solvation Structures and Deactivation Pathways of Luminescent Isothiazole-Derived Nucleobases: tz, tz, and tz

The photophysical relaxation pathways of ^tzA, ^tzG, and ^tzI luminescent nucleobases were investigated with the MS-CASPT2 quantum-chemical method and double-ζ basis sets (cc-pVDZ) in gas and condensed phases (1,4-dioxane and water) with the sequential Monte Carlo/CASPT2 and free energy gradient (FEG) methods. Solvation shell structures, in the ground and excited states, were examined with the pairwise radial distribution function (G(r)) and solute-solvent hydrogen-bond networks. Site-specific hydrogen bonding analysis evidenced relevant changes between both electronic states. The three luminescent nucleobases share a common photophysical pattern, summarized as the lowest-lying ¹(ππ*) bright state that is populated directly after the absorption of radiation and evolves barrierless to the minimum energy structure, from where the excess of energy is released by fluorescence. From the ¹(ππ*)_min region, the conical intersection with the ground state ((ππ*/GS)_CI) is not accessible due to the presence of high energetic barriers. By combining the present results with those reported earlier by us for the pyrimidine fluorescent nucleobases, we present a comprehensive description of the photophysical properties of this important class of new fluorescent nucleosides.

Excited State Dynamics of 8-Vinyldeoxyguanosine In Aqueous Solution Studied by Time-Resolved Fluorescence Spectroscopy and Quantum Mechanical Calculations

The fluorescent base guanine analog, 8-vinyl-deoxyguanosine (8vdG), is studied in solution using a combination of optical spectroscopies, notably femtosecond fluorescence upconversion and quantum chemical calculations, based on time-dependent density functional theory (TD-DFT) and including solvent effect by using a mixed discrete-continuum model. In all investigated solvents, the fluorescence is very long lived (3-4 ns), emanating from a stable excited state minimum with pronounced intramolecular charge-transfer character. The main non-radiative decay channel features a sizeable energy barrier and it is affected by the polarity and the H-bonding properties of the solvent. Calculations provide a picture of dynamical solvation effects fully consistent with the experimental results and show that the photophysical properties of 8vdG are modulated by the orientation of the vinyl group with respect to the purine ring, which in turn depends on the solvent. These findings may have importance for the understanding of the fluorescence properties of 8vdG when incorporated in a DNA helix.

FUS Recognizes G Quadruplex Structures Within Neuronal mRNAs

Fused in sarcoma (FUS), identified as the heterogeneous nuclear ribonuclear protein P2, is expressed in neuronal and non-neuronal tissue, and among other functions, has been implicated in messenger RNA (mRNA) transport and possibly local translation regulation. Although FUS is mainly localized to the nucleus, in the neurons FUS has also been shown to localize to the post-synaptic density, as well as to the pre-synapse. Additionally, the FUS deletion in cultured hippocampal cells results in abnormal spine and dendrite morphology. Thus, FUS may play a role in synaptic function regulation, mRNA localization, and local translation. Many dendritic mRNAs have been shown to form G quadruplex structures in their 3'-untranslated region (3'-UTR). Since FUS contains three arginine-glycine-glycine (RGG) boxes, an RNA binding domain shown to bind with high affinity and specificity to RNA G quadruplex structures, in this study we hypothesized that FUS recognizes these structural elements in its neuronal mRNA targets. Two neuronal mRNAs found in the pre- and post-synapse are the post-synaptic density protein 95 (PSD-95) and Shank1 mRNAs, which encode for proteins involved in synaptic plasticity, maintenance, and function. These mRNAs have been shown to form 3'-UTR G quadruplex structures and were also enriched in FUS hydrogels. In this study, we used native gel electrophoresis and steady-state fluorescence spectroscopy to demonstrate specific nanomolar binding of the FUS C-terminal RGG box and of full-length FUS to the RNA G quadruplex structures formed in the 3'-UTR of PSD-95 and Shank1a mRNAs. These results point toward a novel mechanism by which FUS targets neuronal mRNA and given that these PSD-95 and Shank1 3'-UTR G quadruplex structures are also targeted by the fragile X mental retardation protein (FMRP), they raise the possibility that FUS and FMRP might work together to regulate the translation of these neuronal mRNA targets.

Ultrafast Fluorescence Signals from β-Dihydronicotinamide Adenine Dinucleotide: Resonant Energy Transfer in the Folded and Unfolded Forms

β-Dihydronicotinamide adenine dinucleotide (NADH) plays a critical role in biological redox processes. Inside the cell, NADH can be in a folded or an unfolded conformation, depending on the chemical environment that surrounds it. It is known that selective excitation of adenine in NADH can induce energy transfer events from this nucleotide to the reduced nicotinamide chromophore. From the anticipated time scales, this process must compete with adenine's internal conversion channel, which is known to occur in the sub-picosecond time scale. In this work, we studied the dynamics of the excited states of both chromophores in NADH through the time resolution of the spontaneous emission from both nucleotides. Through these experiments, we extend the knowledge about the competition between the different photophysical channels both in the folded and unfolded states. The study involved the folded and unfolded states of NADH by experiments in water and methanol solutions. Our femtosecond fluorescence results were complemented by the first nuclear magnetic resonance through space magnetization transfer measurements on NADH, which establish the solvent-dependent folded versus unfolded states. We determined the dynamics of the excited states by direct excitation of dihydronicotinamide at 380 nm and adenine at 266 nm. From this, we were able to measure for the folded state, a time constant of 90 fs for energy transfer. Additionally, we determined that even in what is referred to as an unfolded state in methanol, non-negligible excitation transfer events do take place. Spontaneous emission anisotropy measurements were used in order to confirm the presence of a minor energy transfer channel in the methanol solutions where the unfolded state dominates.

First-principles characterization of the singlet excited state manifold in DNA/RNA nucleobases

TD-DFT characterization of the high-energy singlet excited state manifold of the canonical DNA/RNA nucleobasesin vacuumis assessed against RASPT2 reference computations for reliable simulations of linear and non-linear electronic spectra.

Conical Intersections at the Nanoscale: Molecular Ideas for Materials

The ability to predict and describe nonradiative processes in molecules via the identification and characterization of conical intersections is one of the greatest recent successes of theoretical chemistry. Only recently, however, has this concept been extended to materials science, where nonradiative recombination limits the efficiencies of materials for various optoelectronic applications. In this review, we present recent advances in the theoretical study of conical intersections in semiconductor nanomaterials. After briefly introducing conical intersections, we argue that specific defects in materials can induce conical intersections between the ground and first excited electronic states, thus introducing pathways for nonradiative recombination. We present recent developments in theoretical methods, computational tools, and chemical intuition for the prediction of such defect-induced conical intersections. Through examples in various nanomaterials, we illustrate the significance of conical intersections for nanoscience. We also discuss challenges facing research in this area and opportunities for progress.

FMRP - G-quadruplex mRNA - miR-125a interactions: Implications for miR-125a mediated translation regulation of PSD-95 mRNA

Fragile X syndrome, the most common inherited form of intellectual disability, is caused by the CGG trinucleotide expansion in the 5'-untranslated region of the Fmr1 gene on the X chromosome, which silences the expression of the fragile X mental retardation protein (FMRP). FMRP has been shown to bind to a G-rich region within the PSD-95 mRNA, which encodes for the postsynaptic density protein 95, and together with microRNA-125a to mediate the reversible inhibition of the PSD-95 mRNA translation in neurons. The miR-125a binding site within the PSD-95 mRNA 3'-untranslated region (UTR) is embedded in a G-rich region bound by FMRP, which we have previously demonstrated folds into two parallel G-quadruplex structures. The FMRP regulation of PSD-95 mRNA translation is complex, being mediated by its phosphorylation. While the requirement for FMRP in the regulation of PSD-95 mRNA translation is clearly established, the exact mechanism by which this is achieved is not known. In this study, we have shown that both unphosphorylated FMRP and its phosphomimic FMRP S500D bind to the PSD-95 mRNA G-quadruplexes with high affinity, whereas only FMRP S500D binds to miR-125a. These results point towards a mechanism by which, depending on its phosphorylation status, FMRP acts as a switch that potentially controls the stability of the complex formed by the miR-125a-guided RNA induced silencing complex (RISC) and PSD-95 mRNA.

Excited-State Dynamics of Thienoguanosine, an Isomorphic Highly Fluorescent Analogue of Guanosine

Thienoguanosine (^th G) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, ^th G exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto-amino tautomers. We herein investigate the photophysics of ^th G in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5-20.5 and 7-13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of ^th G, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.

Photochemical Relaxation Pathways of 9 H-8-Azaguanine and 8 H-8-Azaguanine

The photochemical reaction path approach, the MS-CASPT2 quantum-chemical method, and double-ζ basis sets (cc-pVDZ) were used to study 9 H-8-azaguanine and 8 H-8-azaguanine relaxation pathways. Several potential energy hypersurfaces were characterized by means of equilibrium geometries, surface crossings (conical intersections and singlet-triplet intersystem crossings), minimum energy paths, and linear interpolation in internal coordinates. The 9 H-8-azaguanine main photochemical event begins with the direct population of the ¹(ππ* L_a) state, which evolves toward a conical intersection with the ground state after surmounting a small energy barrier, explaining why it is nonfluorescent. For 8 H-8-azaguanine, two relaxation mechanisms are possible, depending on the excitation energy. If the S₁ ¹(ππ*) state is initially populated (lower-energy region), the system evolves barrierless to the S₁ ¹(ππ*)_min region, from where the excess energy is released. If the ¹(ππ* L_a) state is populated (higher-energy radiation), the system will encounter conical intersections with the S₂ ¹(n_Oπ*) and S₁ ¹(ππ*) states before evolving to the ¹(ππ* L_a)_min region, from where a conical intersection with the ground state is accessible, favoring radiationless deactivation to the ground state. However, because a fraction of the population can be transferred from ¹(ππ* L_a) to the S₁ ¹(ππ*) state, emission from the S₁ ¹(ππ*)_min region is also expected, although weaker than it would be if the S₁ ¹(ππ*) state were populated directly. Irrespective of the excitation energy, the emissive state is the same and a single fluorescence band is observed, with the strongest emission occurring upon excitation in the lower-energy region, as observed experimentally. Therefore, our computational study corroborates experimental results, attributing the emission of the neutral form of 8-azaguanine in solution to the presence of the minor 8 H-8-azaguanine tautomer, while the 9 H-8-azaguanine major tautomer is nonfluorescent.

Direct observation of an intramolecular charge transfer state in epigenetic nucleobase N6-methyladenine

N6-Methyladenine (6MeAde), the most abundant internal modification in mRNA, has proved to be an important epigenetic biomarker for gene regulation just like 5-methylcytosine in DNA. Recently, a unique UV-induced response of 6MeAde was reported, which makes it instructive and intriguing to reveal the excited state relaxation mechanism in this methylated adenine and its derivatives. In this work, we investigated 6MeAde and its ribose species N6-methyladenosine (6MeAdo) by using femtosecond time-resolved fluorescence up-conversion (FUC) and broadband transient absorption (TA) spectroscopy. Both 6MeAde and 6MeAdo exhibit a hundreds of femtoseconds lifetime, which originates from the efficient depletion of the ππ* (La) state. A several picoseconds lifetime is also observed and it should be attributed to the ππ* (Lb) state. Surprisingly, dual peak fluorescence emission is observed in 6MeAde and the long wavelength emission is ascribed to an intramolecular charge transfer (ICT) state. The lifetime of this ICT state is determined to be 107 ps. The kinetic isotope effect shows that the ICT state is closely associated with the solute-solvent H-bonding in aqueous solution. In 6MeAdo, the ICT state is apparently quenched and adenine-like excited state dynamics suggests that DNA/RNA containing such modification could still possess excellent photostability under UV irradiation. Our results contain an important insight for understanding excited state properties in epigenetic modified DNA/RNA.

pH Controlled Intersystem Crossing and Singlet Oxygen Generation of 8-Azaadenine in Aqueous Solution

Azabases are intriguing DNA and RNA analogues and have been used as effective antiviral and anticancer medicines. However, photosensitivity of these drugs has also been reported. Here, pH-controlled intersystem crossing (ISC) process of 9H 8-azaadenine (8-AA) in aqueous solution is reported. Broadband transient absorption measurements reveal that the hydrogen atom at N9 position can greatly affect ISC of 8-AA and ISC is more favorable when 8-AA is in its neutral form in aqueous solution. The initial excited ππ* (S₂ ) state evolves through ultrafast internal conversion (IC) (4.2 ps) to the lower-lying nπ* state (S₁ ), which further stands as a door way state for ISC with a time constant of 160 ps. The triplet state has a lifetime of 6.1 μs. On the other hand, deprotonation at N9 position promotes the IC from the ππ* (S₂ ) state to the ground state (S₀ ) and the lifetime of the S₂ state is determined to be 10 ps. The experimental results are further supported by time-dependent density functional theory (TDDFT) calculations. Singlet oxygen generation yield is measured to be 13.8 % for the neutral 8-AA while the deprotonated one exhibit much lower yield (<2 %), implying that this compound could be a potential pH-sensitized photodynamic therapy agent.

Mechanisms of photoreactivity in hydrogen-bonded adenine-H2O complexes

The mechanisms of photoinduced reactions of adenine with water molecules in hydrogen-bonded adenine-water complexes were investigated with ab initio wave-function-based electronic-structure calculations. Two excited-state electron/proton transfer reaction mechanisms have been characterized: H-atom abstraction from water by photoexcited adenine as well as H-atom transfer from photoexcited adenine or the (adenine+H) radical to water. In the water-to-adenine H-atom transfer reaction, an electron from one of the p orbitals of the water molecule fills the hole in the n (π) orbital of the nπ* (ππ*) excited state of adenine, resulting in a charge-separated electronic state. The electronic charge separation is neutralized by the transfer of a proton from the water molecule to adenine, resulting in the (adenine+H)OH biradical in the electronic ground state. In the adenine-to-water H-atom transfer reaction, πσ* states localized at the acidic sites of adenine provide the mechanism for the photoejection of an electron from adenine, which is followed by proton transfer to the hydrogen-bonded water molecule, resulting in the (adenine-H)H3O biradical. The energy profiles of the photoreactions have been computed as relaxed scans with the ADC(2) electronic-structure method. These reactions, which involve the reactivity of adenine with hydrogen-bonded water molecules, compete with the well-established intrinsic excited-state deactivation mechanisms of adenine via ring-puckering or ring-opening conical intersections. By providing additional decay channels, the electron/proton exchange reactions with water can account for the observed significantly shortened excited-state lifetime of adenine in aqueous environments. These findings indicate that adenine possibly was not only a photostabilizer at the beginning of life, but also a primordial photocatalyst for water splitting.

Tracking the origin of photostability in purine nucleobases: the photophysics of 2-oxopurine

Molding purine PES through functionalization: whilst purine C₂-substitution maintains the features of the spectroscopic PES of the heterocycle, C₆-functionalization reshapes its topography leading to photostable systems.

Highly efficient surface hopping dynamics using a linear vibronic coupling model

We report an implementation of the linear vibronic coupling (LVC) model within the surface hopping dynamics approach and present utilities for parameterizing this model in a blackbox fashion. This results in an extremely efficient method to obtain qualitative and even semi-quantitative information about the photodynamical behavior of a molecule, and provides a new route toward benchmarking the results of surface hopping computations. The merits and applicability of the method are demonstrated in a number of applications. First, the method is applied to the SO2 molecule showing that it is possible to compute its absorption spectrum beyond the Condon approximation, and that all the main features and timescales of previous on-the-fly dynamics simulations of intersystem crossing are reproduced while reducing the computational effort by three orders of magnitude. The dynamics results are benchmarked against exact wavepacket propagations on the same LVC potentials and against a variation of the electronic structure level. Four additional test cases are presented to exemplify the broader applicability of the model. The photodynamics of the isomeric adenine and 2-aminopurine molecules are studied and it is shown that the LVC model correctly predicts ultrafast decay in the former and an extended excited-state lifetime in the latter. Futhermore, the method correctly predicts ultrafast intersystem crossing in the modified nucleobase 2-thiocytosine and its absence in 5-azacytosine while it fails to describe the ultrafast internal conversion to the ground state in the latter.

Time-resolved photoelectron spectroscopy of adenosine and adenosine monophosphate photodeactivation dynamics in water microjets

The excited state relaxation dynamics of adenosine and adenosine monophosphate were studied at multiple excitation energies using femtosecond time-resolved photoelectron spectroscopy in a liquid water microjet. At pump energies of 4.69-4.97 eV, the lowest ππ^* excited state, S₁, was accessed and its decay dynamics were probed via ionization at 6.20 eV. By reversing the role of the pump and probe lasers, a higher-lying ππ^* state was excited at 6.20 eV and its time-evolving photoelectron spectrum was monitored at probe energies of 4.69-4.97 eV. The S₁ ππ^* excited state was found to decay with a lifetime ranging from ∼210 to 250 fs in adenosine and ∼220 to 250 fs in adenosine monophosphate. This lifetime drops with increasing pump photon energy. Signal from the higher-lying ππ^* excited state decayed on a time scale of ∼320 fs and was measureable only in adenosine monophosphate.

Efficient intersystem crossing in 2-aminopurine riboside probed by femtosecond time-resolved transient vibrational absorption spectroscopy

The photophysical dynamics of 2-aminopurine, a fluorescent analogue of the canonical nucleobase adenine, has been studied by femtosecond transient vibrational absorption spectroscopy.

Electronic structure and absorption spectra of fluorescent nucleoside analogues

This work presents a systematic investigation of the electronic and conformational properties of five new fluorescent nucleobases belonging to the alphabet based on the isothiazole[4,3-d]pyrimidine molecule, very recently synthesized. This is of particular importance in the characterization of the main electronic aspects of these fluorescent nucleosides. The solvent effects of 1,4-dioxane and water were included combining the Sequential Monte Carlo/CASPT2 and the Free Energy Gradient (FEG) methods. For comparison, the Polarizable Continuum method was also used. The geometries of all compounds were optimized in solvent with the largest effects observed in water using the average solvent electrostatic configuration (ASEC) and the FEG approaches. Statistical analysis of the solute-solvent hydrogen bonds is performed and their effect on the absorption spectra analyzed. The dipole moments were calculated and the value obtained from the ASEC-FEG method in water follows the same trend as the natural canonical bases (adenine → uracil → guanine → cytosine). The theoretical results for the absorption spectra obtained from CASPT2(18,13) calculations using the geometries obtained with the ASEC-FEG procedure are in very good agreement with the experimental data. A detailed elucidation of the main aspects of the absorption spectra of the five new fluorescent nucleoside analogues is successfully attempted.