Excited-state dynamics of isolated nucleic acid bases and their clusters

Structural Characterization of 6-Thioguanosine and Its Monohydrate in the Gas Phase

Detailed structural analysis of 6-thioguanosine (6TGs) in relation to its tautomerization and sugar conformation is performed in the gas phase using UV and IR spectroscopy combined with ab initio calculations. We have observed a thiol tautomer of 6TGs with its sugar moiety in the syn conformation that is stabilized by a strong intramolecular H-bonding between O5'H of the sugar and N3 atom of the guanine moiety. This observation is consistent with previous results for guanosine (Gs) in which the corresponding enol form is solely detected. We have also identified a monohydrate of 6TGs consisting of a thiol tautomer with the water linking guanine moiety and sugar OH group. It is demonstrated that hydration behavior of 6TGs is significantly different from that of Gs as a result of a weaker H-bonding ability of the thiol group.

Identification of an ultrafast internal conversion pathway of pyrazine by time-resolved vacuum ultraviolet photoelectron spectrum simulations

The internal conversion from the optically bright S₂ (¹B_2u, ππ*) state to the dark S₁ (¹B_3u, nπ*) state in pyrazine is a standard benchmark for experimental and theoretical studies on ultrafast radiationless decay. Since 2008, a few theoretical groups have suggested significant contributions of other dark states S₃ (¹A_u, nπ*) and S₄ (¹B_2g, nπ*) to the decay of S₂. We have previously reported the results of nuclear wave packet simulations [Kanno et al., Phys. Chem. Chem. Phys. 17, 2012 (2015)] and photoelectron spectrum calculations [Mignolet et al., Chem. Phys. 515, 704 (2018)] that support the conventional two-state picture. In this article, the two different approaches, i.e., wave packet simulation and photoelectron spectrum calculation, are combined: We computed the time-resolved vacuum ultraviolet photoelectron spectrum and photoelectron angular distribution for the ionization of the wave packet transferred from S₂ to S₁. The present results reproduce almost all the characteristic features of the corresponding experimental time-resolved spectrum [Horio et al., J. Chem. Phys. 145, 044306 (2016)], such as a rapid change from a three-band to two-band structure. This further supports the existence and character of the widely accepted pathway (S₂ → S₁) of ultrafast internal conversion in pyrazine.

Broadband cavity-enhanced ultrafast spectroscopy

Broadband ultrafast optical spectroscopy methods, such as transient absorption spectroscopy and 2D spectroscopy, are widely used to study molecular dynamics. However, these techniques are typically restricted to optically thick samples, such as solids and liquid solutions. In this article we discuss a cavity-enhanced ultrafast transient absorption spectrometer covering almost the entire visible range with a detection limit of ΔOD < 1 × 10-9, extending broadband all-optical ultrafast spectroscopy techniques to dilute beams of gas-phase molecules and clusters. We describe the technical innovations behind the spectrometer and present transient absorption data on two archetypical molecular systems for excited-state intramolecular proton transfer, 1'-hydroxy-2'-acetonapthone and salicylideneaniline, under jet-cooled and Ar cluster conditions.

Long living excited state of protonated adenosine unveiled by ultrafast fluorescence spectroscopy and density functional theoretical study

Adenosine (Ado) possesses ultrafast nonradiative dynamics accounting for its remarkably high photostability. The deactivation dynamics of Ado after protonation in an aqueous solution remains an elusive issue. Herein we report an investigation of the excited state dynamics of protonated Ado (AdoH⁺) performed using ultrafast time-resolved fluorescence spectroscopy combined with density functional theoretical calculation. The result obtained from comparison of conformers with protonation at different sites revealed that the syn-conformer with protonation occurring at the N3 position (syn-N3) is the predominant form of AdoH⁺ in the ground state, similar to that of Ado. In contrast, the fluorescence of AdoH⁺ with maximum intensity at 385 nm, significantly red-shifted from that of Ado, displaying decay dynamics composed of an ultrafast component with the lifetime of ∼0.5 ps and a slower one of ∼2.9 ns. The former is because of the decay of the syn-N3 conformer, similar to that reported for AdoH⁺ under the gas phase condition. The latter is due to the syn-N1 conformer formed via ultrafast proton transfer of the syn-N3. The excited state of syn-N1 has a peculiar nonplanar conformation over the purine molecule, which is responsible for the substantial Stokes shift showed in the fluorescence spectrum and correlates with a large energy barrier for nonradiative decay likely involving a reversed proton transfer. This study demonstrates the importance of protonation and solvent environment in altering dramatically the excited states of Ado, providing insight for better understanding nonradiative dynamics of both the monomeric bases and the oligomeric or polymeric DNAs.

Excited-State Dynamics Affected by Switching of a Hydrogen-Bond Network in Hydrated Aminopyrazine Clusters

The cluster structures of hydrated aminopyrazines, APz-(H₂O)_n=2-4, in supersonic jets have been investigated measuring the size-selected electronic and vibrational spectra and determined with the aid of quantum chemical calculations. The APz-(H₂O)₂ structure is assigned as a cyclic N1 type where a homodromic hydrogen-bond chain starts from the amino group and ends at the 1-position nitrogen atom of the pyrazine moiety, corresponding to 2-aminopyridine-(H₂O)₂. On the other hand, APz-(H₂O)_n=3,4 has a linear hydrogen-bond network ending at the 4-position one (N4), which resembles 3-aminopyridine-(H₂O)_n=3,4. The hydrogen-bond network switching from the N1 type to the N4 one provides the accompanying red shifts of the S₁-S₀ electronic transition that are entirely consistent with those of the corresponding 2-aminopyridine and 3-aminopyridine clusters and also shows the drastically strengthened fluorescence intensity of origin bands in the electronic spectrum. The significant change in the excited-state dynamics is explored by the fluorescence lifetime measurement and the time-dependent density functional theory (TD-DFT) calculation. It is suggested that the drastic elongation of fluorescence lifetimes is due to the change in the electronic structure of the first excited state from nπ* to ππ*, resulting in the decreasing spin-orbit coupling to T₁ (ππ*).

An effective and facile synthesis of new blue fluorophores on the basis of an 8-azapurine core

A convenient synthesis of 2-aryl-2,4-dihydro-5H-[1,2,3]triazolo[4,5-d]pyrimidin-5-ones (DTPs) from 3,3-diamino-2-(arylazo)acrylonitriles through a versatile and readily accessible two-step procedure is described. Density functional theory (DFT) calculations were performed to explain the selectivity of the heterocyclization step, which predominantly afforded 6-amino-5-(arylazo)pyrimidin-2(1H)-thiones in chloroform or ethanol, and 2,3-dihydro-1,2,4-triazines in toluene or DMF. Novel 2-aryl-2,4-dihydro-5H-[1,2,3]triazolo[4,5-d]pyrimidin-5-ones were obtained in good yields and showed absorption in the ultraviolet region and good emission in the blue region. The photophysical properties of DTPs were better than those cited in select literature examples of 8-azapurines. Owing to the facile synthesis and good photophysical characteristics in an aqueous medium, the new DTPs should have potential applications as organic fluorophores in fluorescence imaging and materials science.

How nature covers its bases

The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.

Sub-50 fs excited state dynamics of 6-chloroguanine upon deep ultraviolet excitation

The photophysical properties of natural nucleobases and their respective nucleotides are ascribed to the sub-picosecond lifetime of their first singlet states in the UV-B region (260-350 nm). Electronic transitions of the ππ* type, which are stronger than those in the UV-B region, lie at the red edge of the UV-C range (100-260 nm) in all isolated nucleobases. The lowest energetic excited states in the UV-B region of nucleobases have been investigated using a plethora of experimental and theoretical methods in gas and solution phases. The sub-picosecond lifetime of these molecules is not a general attribute of all nucleobases but specific to the five primary nucleobases and a few xanthine and methylated derivatives. To determine the overall UV photostability, we aim to understand the effect of more energetic photons lying in the UV-C region on nucleobases. To determine the UV-C initiated photophysics of a nucleobase system, we chose a halogen substituted purine, 6-chloroguanine (6-ClG), that we had investigated previously using resonance Raman spectroscopy. We have performed quantitative measurements of the resonance Raman cross-section across the Bb absorption band (210-230 nm) and constructed the Raman excitation profiles. We modeled the excitation profiles using Lee and Heller's time-dependent theory of resonance Raman intensities to extract the initial excited state dynamics of 6-ClG within 30-50 fs after photoexcitation. We found that imidazole and pyrimidine rings of 6-ClG undergo expansion and contraction, respectively, following photoexcitation to the Bb state. The amount of distortions of the excited state structure from that of the ground state structure is reflected by the total internal reorganization energy that is determined at 112 cm(-1). The contribution of the inertial component of the solvent response towards the total reorganization energy was obtained at 1220 cm(-1). In addition, our simulation also yields an instantaneous response of the first solvation shell within an ultrafast timescale of less than 30 fs following photoexcitation.

Ionization-Induced Structural Changes in Uracil Dimers and Their Spectroscopic Signatures

The electronic structure of the three representative isomers of the ionized uracil dimers is characterized by high-level electronic structure calculations. Noncovalent interactions between the fragments lower the vertical ionization energies by 0.13-0.35 eV, the largest drop being observed for the stacked and the T-shaped isomers. The initial hole is delocalized in the stacked and the H-bonded isomers and is localized in the T-shaped one. The ionization induces significant structural relaxation and increases the binding energies. The stacked dimer cation relaxes to the symmetric structure bound by 22.7 kcal/mol. The T-shaped dimer cation has a binding energy of 25.1 kcal/mol. Thus, the relative order of the stacked and T-shaped isomers is reversed upon ionization. Finally, the H-bonded isomer, which relaxes to the proton-transferred structure, is bound by 37.0 kcal/mol. The electronic spectra of all three isomers characterized at the vertical and the relaxed geometries show different patterns, which may be exploited in spectroscopic probing of ionization-induced dynamics in these species.

8-Azapurines as isosteric purine fluorescent probes for nucleic acid and enzymatic research

The 8-azapurines, and their 7-deaza and 9-deaza congeners, represent a unique class of isosteric (isomorphic) analogues of the natural purines, frequently capable of substituting for the latter in many biochemical processes. Particularly interesting is their propensity to exhibit pH-dependent room-temperature fluorescence in aqueous medium, and in non-polar media. We herein review the physico-chemical properties of this class of compounds, with particular emphasis on the fluorescence emission properties of their neutral and/or ionic species, which has led to their widespread use as fluorescent probes in enzymology, including enzymes involved in purine metabolism, agonists/antagonists of adenosine receptors, mechanisms of catalytic RNAs, RNA editing, etc. They are also exceptionally useful fluorescent probes for analytical and clinical applications in crude cell homogenates.

Excited-state proton transfer and phototautomerism in nucleobase and nucleoside analogs: a mini-review

Intermolecular excited-state proton transfer (ESPT) has been observed in several fluorescent nucleobase and/or nucleoside analogs. In the present work, some new examples of ESPT in this class of compounds are presented together with a brief recapitulation of the previously published data. The nucleobases, nucleosides, and their analogs contain many basic and acidic centers and therefore their ESPT behavior may be complex. To interpret the complex data, it is usually necessary to determine the microscopic pK* values for each (or most) of the possible ESPT centers. Typical approach to solve this problem is by analysis of the alkyl derivatives, in which the possibility of the ESPT is reduced. Of particular interest are examples of "phototautomerization via the cation," observed in several systems, which in the neutral media do not undergo ESPT. Protonation of the molecule in the ground state facilitates the two-step phototautomerism in several systems, including formycin A and 2-amino-8-azadenine. Fluorescence of the nucleobase and nucleoside analogs undergoing ESPT is usually solvent-, isotope-, and buffer-ion sensitive, and in some systems the ESPT can be promoted by environmental factors, e.g., the presence of buffer ions. This sensitivity to the microenvironment parameters makes the ESPT systems potentially useful for biological applications.

Computational modeling of photoexcitation in DNA single and double strands

The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.

Excited-state hydrogen atom abstraction initiates the photochemistry of β-2'-deoxycytidine

Understanding the effects of ultraviolet radiation on nucleotides in solution is an important step towards a comprehensive description of the photochemistry of nucleic acids and their constituents. Apart from having implications for mutagenesis and DNA photoprotection mechanisms, the photochemistry of cytidines is a central element in UV-assisted syntheses of pyrimidine nucleotides under prebiotically plausible conditions. In this contribution, we present UV-irradiation experiments of β-2'-deoxycytidine in aqueous solution involving H-D exchange followed by NMR spectroscopic analysis of the photoproducts. We further elucidate the outcome of these experiments by means of high-level quantum chemical calculations. In particular, we show that prolonged UV-irradiation of cytidine may lead to H-C1' hydrogen atom abstraction by the carbonyl oxygen atom of cytosine. This process may enable photoanomerisation and nucleobase loss, two previously unexplained photoreactions observed in pyrimidine nucleotides.

Nucleic acid ion structures in the gas phase

Nucleic acids are diverse polymeric macromolecules that are essential for all life forms. These biomolecules possess a functional three-dimensional structure under aqueous physiological conditions. Mass spectrometry-based approaches have on the other hand opened the possibility to gain structural information on nucleic acids from gas-phase measurements. To correlate gas-phase structural probing results with solution structures, it is therefore important to grasp the extent to which nucleic acid structures are preserved, or altered, when transferred from the solution to a fully anhydrous environment. We will review here experimental and theoretical approaches available to characterize the structure of nucleic acids in the gas phase (with a focus on oligonucleotides and higher-order structures), and will summarize the structural features of nucleic acids that can be preserved in the gas phase on the experiment time scale.

Excited states of proton-bound DNA/RNA base homodimers: pyrimidines

We are presenting the electronic photofragment spectra of the protonated pyrimidine DNA base homodimers. Only the thymine dimer exhibits a well structured vibrational progression, while the protonated monomer shows broad vibrational bands. This shows that proton bonding can block some nonradiative processes present in the monomer.

Solvent effects on the ultrafast nonradiative deactivation mechanisms of thymine in aqueous solution: excited-state QM/MM molecular dynamics simulations

On-the-fly excited-state quantum mechanics/molecular mechanics molecular dynamics (QM/MM-MD) simulations of thymine in aqueous solution are performed to investigate the role of solvent water molecules on the nonradiative deactivation process. The complete active space second-order perturbation theory (CASPT2) method is employed for a thymine molecule as the QM part in order to provide a reliable description of the excited-state potential energies. It is found that, in addition to the previously reported deactivation pathway involving the twisting of the C-C double bond in the pyrimidine ring, another efficient deactivation pathway leading to conical intersections that accompanies the out-of-plane displacement of the carbonyl group is observed in aqueous solution. Decay through this pathway is not observed in the gas phase simulations, and our analysis indicates that the hydrogen bonds with solvent water molecules play a key role in stabilizing the potential energies of thymine in this additional decay pathway.

The effect of dimerization on the excited state behavior of methylated xanthine derivatives: a computational study

The behavior of monomers and dimers of methylated xanthine derivatives in their excited states is investigated by means of the ADC(2), CASSCF, and CASPT2 methods. The results of the calculations of stationary points in the ground and excited states, minima on the S0/S1 crossing seams and the relaxation pathways are used to provide the interpretation of experimental observations of the monomer xanthine derivatives. The effect of dimerization on the excited state properties is studied for various relative orientations of the monomers in the dimer complexes in comparison with the relevant monomer species. A significant stabilization in the excited state minima of dimers is observed. These can act as trapping sites. Various types of conical intersections, with both localized and delocalized characters of wavefunctions, have been found, mainly energetically above the lowest bright excited state in the FC region. In addition, structures with the bonds formed between the two monomers were also found on the crossing seams. The possibility of ultrafast relaxation via these conical intersections is discussed.

Ab initio studies on the photophysics of uric acid and its monohydrates: role of the water molecule

The photophysical behavior of three lowest-energy tautomers of uric acid and seven most stable isomers of uric acid monohydrate is comprehensively studied by ab initio calculations. Ground-state energies are calculated with the CCSD(T) method, while excitation and ionization energies as well as excited-state potential energy profiles of photoinduced processes are calculated with the CC2 method. For the (1)ππ* state, it is found that the excitation energy of the monohydrate cluster is significantly lower than that of isolated uric acid when the water molecule is hydrogen-bonded at a specific carbonyl group. The calculated excited-state potential energy profiles suggest that some monohydrate isomers can undergo a migration of the water molecule from one site to another site in the (1)ππ* state with a small energy barrier. It is also found for both uric acid and its monohydrate that nonradiative decay via the NH bond dissociation in the (1)πσ* state is likely to occur at higher excitation energies. On the basis of the computational results, possible mechanisms for the absence of specific isomers of uric acid monohydrate from the resonant two-photon ionization spectrum are discussed.

Excited states of protonated DNA/RNA bases

The excited state lifetime of protonated DNA/RNA bases is strongly dependent on the tautomeric form.

Coupled-cluster and density functional theory studies of the electronic 0–0 transitions of the DNA bases

The 0–0 transitions of the electronic excitation spectra of the lowest tautomers of the four nucleotide (DNA) bases have been studied using linear-response approximate coupled-cluster singles and doubles (CC2) calculations.

ABSORPTION SPECTRA OF NUCLEIC ACID BASES IN WATER ENVIRONMENT: INSIGHTS INTO FROM COMBINED QM/MM AND CLUSTER-CONTINUUM MODEL CALCULATIONS

Electronic spectra of uracil, thymine, adenine, guanine, and cytosine in the gas phase and aqueous solution have been studied by extensive time-dependent density functional calculations. Calculations show that the Quantum mechanics/molecular mechanics (QM/MM) geometry optimization based on the molecular dynamics (MD) equilibrated configuration can locate an optimal solvated cluster for the base solvation, and the combined QM/MM and cluster-continuum computational protocol is capable of handling the solvent effect on the excited states of nucleic acid bases and providing realistic absorption spectra in water environment with relatively low computational costs. Generally, the vertical excitation energies in aqueous solution by PCM/TD-X3LYP calculations show excellent agreement with the experimental observations and the maximum deviation is less than 0.2 eV. The present results reveal that the hydrogen bond network around the excited-state base and its dipole moment change may remarkably modify the absorption spectra of nucleic acid bases in aqueous solution.

Controlling Glycosyl Bond Conformation of Guanine Nucleosides: Stabilization of the anti Conformer in 5'-O-Ethylguanosine

Nucleosides that consist of base and sugar moieties can adopt two main conformations, syn and anti, about the glycosidic bond. We have investigated the conformational properties of guanine nucleosides in the gas phase by using laser desorption combined with IR-UV double resonance spectroscopy. In guanosine, syn conformation is preferred as a result of internal hydrogen bonding between the 5'-OH group of the sugar and the N3 site of the guanine moiety. We have therefore employed a chemically modified nucleoside 5'-O-ethylguanosine, in which possible glycosyl bond conformations are restricted upon ethylation of the 5'-OH group. The result shows that anti conformer is stabilized by the formation of hydrogen bonding involving the 2'-OH group.

Gas-phase isolation of diethyl guanosine 5'-monophosphate and its conformational assignment

We show that intact neutral molecules of guanosine 5'-monophosphate can be vaporized by laser desorption when its phosphate group is esterified. The UV and IR spectroscopic measurements of this nucleotide reveal the existence of a novel internal hydrogen-bonding conformation of the phosphate group and guanine moiety.