Hydration of guanine: Electronic singlet excited states for complexes with 19 and 27 water molecules

Ultraviolet Light Makes dGMP Floppy: Femtosecond Stimulated Raman Spectroscopy of 2'-Deoxyguanosine 5'-Monophosphate

The ultrafast dynamics of 2'-deoxyguanosine 5'-monophosphate after excitation with ultraviolet light has been studied with femtosecond transient absorption (TA) and femtosecond stimulated Raman spectroscopy (FSRS). TA kinetics and transient anisotropy spectra reveal a rapid relaxation from the Franck-Condon region, producing an extremely red-shifted stimulated emission band at ∼440 nm that is formed after 200 fs and subsequent relaxation for 0.8-1.5 ps, consistent with prior studies. Viscosity dependence shows that the initial relaxation, before 0.5 ps, is the same in water or viscous glycerol/water mixtures, but after 0.5 ps the dynamics significantly slow down in a viscous solution. This indicates that large amplitude structural changes occur after 0.5 ps following photoexcitation. FSRS obtained with both 480 and 600 nm Raman pump pulses observe very broad Raman peaks at 509 and 1530 cm^-1, as well as a narrower peak at 1179 cm^-1. All of the Raman peaks decay with 0.7-1.3 ps time constants. The 1530 cm^-1 peak also shows an increasing inhomogeneous linewidth over the first 0.3 ps. Our TA and FSRS data are consistent with a structurally inhomogeneous population in the S₁ (L_a) state and, in particular, with previous theoretical models in which out-of-plane distortion at C2 and the amine move the molecule toward a conical intersection with the ground state. These FSRS data are the first to directly observe the structural inhomogeneity imparted upon the excited-state population by the broad, flat potential energy surface of the S₁ (L_a) state.

Excited-state deactivation in 8-oxo-deoxyguanosine: comparison between anionic and neutral forms

Ab initio explorations of excited-state potential-energy surfaces show that a radiationless deactivation mechanism via intramolecular excited-state proton transfer is available in neutral 8-oxo-deoxyguanosine, whereas it is not available in the anionic form.

New size-expanded RNA nucleobase analogs: a detailed theoretical study

Fluorescent nucleobase analogs have attracted much attention in recent years due to their potential applications in nucleic acids research. In this work, four new size-expanded RNA base analogs were computationally designed and their structural, electronic, and optical properties are investigated by means of DFT calculations. The results indicate that these analogs can form stable Watson-Crick base pairs with natural counterparts and they have smaller ionization potentials and HOMO-LUMO gaps than natural ones. Particularly, the electronic absorption spectra and fluorescent emission spectra are calculated. The calculated excitation maxima are greatly red-shifted compared with their parental and natural bases, allowing them to be selectively excited. In gas phase, the fluorescence from them would be expected to occur around 526, 489, 510, and 462 nm, respectively. The influences of water solution and base pairing on the relevant absorption spectra of these base analogs are also examined.

Ultrafast Excited-State Deactivation of 8-Hydroxy-2'-deoxyguanosine Studied by Femtosecond Fluorescence Spectroscopy and Quantum-Chemical Calculations

The fluorescence properties of the 8-hydroxy-2'-deoxyguanosine (8-oxo-dG) in aqueous solution at pH 6.5 are studied by steady-state spectroscopy and femtosecond fluorescence up-conversion and compared with those of 2'-deoxyguanine (dG) and 2'-deoxyguanine monophosphate (dGMP). The steady-state fluorescence spectrum of 8-oxo-dG is composed of a broad band that peaks at 356 nm and extends over the entire visible spectral region, and its fluorescence quantum yield is twice that of dG/dGMP. After excitation at 267 nm, the initial fluorescence anisotropy at all wavelengths is lower than 0.1, giving evidence of an ultrafast internal conversion (<100 fs) between the two lowest excited ππ* states (Lb and La). The fluorescence decays of 8-oxo-dG are biexponential with an average lifetime of 0.7 ± 0.1 ps, which is about two times longer than that of dGMP. In contrast with dGMP, only a moderate dynamical shift (∼1400 vs 10,000 cm(-1)) of the fluorescence spectra of 8-oxo-dG is observed on the time scale of a few picoseconds without modification of the spectral shape. PCM/TD-DFT calculations, employing either the PBE0 or the M052X functionals, provide absorption spectra in good agreement with the experimental one and show that the deactivation path is similar to that proposed for dGMP, with a fast motion toward an energy plateau, where the purine ring keeps an almost planar geometry, followed by decay to S0, via out-of-the plane motion of amino substituent.

The solvent effect and identification of a weakly emissive state in nonradiative dynamics of guanine nucleosides and nucleotides--a combined femtosecond broadband time-resolved fluorescence and transient absorption study

A combined method of femtosecond broadband time-resolved fluorescence (fs-TRF) and transient absorption (fs-TA) was employed to investigate the excited state dynamics of 2'-deoxyguanosine (dG) and 2'-deoxyguanosine 5'-monophosphate (dGMP). Comparative fs-TRF and fs-TA measurements were conducted on dG and dGMP in neutral water, deuterated water, and methanol with excitation wavelengths of 245, 267 and 285 nm. Very similar results were observed with dG and dGMP. The data provide compelling evidence for the co-existence of two nonradiative pathways. One is the generally recognized Laππ* mediated channel, the other involves an unprecedented weakly emissive state which plays a significant role in the overall deactivation processes. The Laππ* channel features biphasic dynamics with time constants (τ1/τ2) of ~0.2/0.8 ps in water and ~0.25/1.0 ps in methanol. The biphasic decay arises due to a partial transfer with τ1 of the Laππ* population to the newly identified state followed by conversion in τ2 of the remaining Laππ* molecules into the electronic ground state. The channel mediated by the weakly emissive species shows solvent-dependent dynamics with time constants (τ3) of ~2.0 ps in water, ~2.3 ps in deuterated water, and ~4.1 ps in methanol. The species features absorption at UV wavelengths (~300-400 nm) and exhibits deeply red-shifted fluorescence (λmax ~ 520 nm) with polarization direction varied markedly from that of the Laππ* but close to the Lbππ*. This species acts as an effective quenching state to the radiative decay of the brightly emissive Laππ* and Lbππ*. It sets in promptly (<~50 fs) after the photoexcitation and is further populated through nonadiabatic coupling with the Laππ*. The overall involvement of this state is facilitated with excitation at high energy and is favoured in methanol over water. According to the spectral character and the solvent effect in particular the kinetic isotope effect, the species is tentatively associated to the πσ* state with charge transfer (CT) character which is considered to be preferentially stabilized by hydrogen-bonding between the guanine amino and surrounding solvent molecules. The result of this study leads to a dramatically different picture of guanine deactivation. It demonstrates a crucial role of the solvent in shaping the nonradiative dynamics of guanine nucleosides and nucleotides. The data presented are important for understanding the detailed photophysics of not only the monomeric guanine but also DNA assemblies that contain guanine in base pairs or have a guanine tetrad as the structural motif.

A theoretical study of hydration effects on structural stability and hydrogen-bonding dynamics of 2′-deoxyguanosine 5′-monophosphate with different negative charges

The effects of hydration on the ground-state structural stability and excited-state hydrogen-bonding dynamics of 2′-deoxyguanosine 5′-monophosphate (dGMP) carrying different negative charges were investigated with B3LYP/6–31+G(d,p) using density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods, respectively. Particularly, we not only considered the solvent effects by the polarizible continuum model (PCM), but also the first solvation shell was included explicitly. We demonstrated that the intramolecular hydrogen bond O2–H1···O3 will be weakened with the strengthening of the hydration. From the view of bond length, we can make a valid presumption that the site of negative charge will be the more preferable site of the hydration, and the preferable site may be changed because of the presence of other hydrogen bonds. Furthermore, we found that the first solvation shell had very little effect on the geometric structures except for the hydrogen bond P–O5···H5. By comparing the excitation energies, one important finding is that the changes in different electronic states are not obvious with the increase in n value when considering the PCM. Another finding is that the average interactions of hydrogen bonds may be strengthened with an increase of negative charge because of a decrease in excitation energies.

Excited-state dynamics of dGMP measured by steady-state and femtosecond fluorescence spectroscopy

The room-temperature fluorescence of 2'-deoxyguanosine 5'-monophosphate (dGMP) in aqueous solution is studied by steady-state and time-resolved fluorescence spectroscopy. The steady-state fluorescence spectrum of dGMP shows one band centered at 334 nm but has an extraordinary long red tail, extending beyond 700 nm. Both the fluorescence quantum yield and the relative weight of the 334 nm peak increase with the excitation wavelength. The initial fluorescence anisotropy after excitation at 267 nm is lower than 0.2 for all emission wavelengths, indicating an ultrafast S(2) --> S(1) internal conversion. The fluorescence decays depend strongly on the emission wavelength, getting longer with the wavelength. A rise time of 100-150 fs was observed for wavelengths longer than 450 nm, in accordance with a gradual red shift of the time-resolved spectra. The results are discussed in terms of a relaxation occurring mainly on the lowest excited (1)pi pi*-state surface toward a conical intersection with the ground state, in line with recent theoretical predictions. Our results show that the excited-state population undergoes a substantial "spreading out" before reaching the CI, explaining the complex dynamics observed.