Hydration-Dependent Structural Deformation of Guanine in the Electronic Singlet Excited State

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.

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.

Mode-specific vibrational relaxation of photoexcited guanosine 5'-monophosphate and its acid form: a femtosecond broadband mid-IR transient absorption and theoretical study

UV-pump/broadband-mid-IR-probe transient absorption (TA) experiments and ab initio quantum mechanical (QM) calculations were used to investigate the photophysics in heavy water of the neutral and acid forms of guanosine 5'-monophosphate (GMP and GMPD(+), respectively). Excited GMP undergoes ultrafast internal conversion (IC) and returns to the electronic ground state in less than one picosecond with a large amount of excess vibrational energy. The spectroscopic signals are dominated by vibrational cooling - a process in which the solute dissipates vibrational energy to the solvent. For neutral GMP, cooling proceeds with a time constant of 3 ps. Following IC, at least some medium-frequency modes such as the carbonyl stretch and an in-plane ring vibration are excited, suggesting that the vibrational energy distribution is non-statistical. This is consistent with predicted structural changes upon passage through the S1/S0 conical intersection. GMPD(+) differs from GMP by a single deuteron at the N7 position, but has a dramatically longer lifetime of 200 ps. Vibrational cooling of the S1 state of GMPD(+) was monitored via several medium-frequency modes that were assigned using QM calculations. These medium-frequency modes are also vibrationally excited in a non-statistical fashion. Excitation of these modes is in line with the change in geometry at the S1 minimum of GMPD(+) predicted by QM calculations. Furthermore, these modes relax at different rates, fully consistent with QM calculations, which predict that excited vibrational states of the carbonyl stretch couple strongly to the D2O solvent and thus deactivate via intermolecular energy transfer (IET). In contrast, the ring stretch couples strongly to other ring modes of the guanine chromophore and appears to decay via intramolecular vibrational energy redistribution (IVR).

Time-dependent density functional theory study on the electronic excited-state hydrogen bonding dynamics of BHC-nicotinamide in MeOH solution

The density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods were performed to investigate the electronic excited-state hydrogen bonding dynamics of the hydrogenbonded complex formed by BHC-nicotinamide (BHCN) and methanol (MeOH). The ground-state geometry optimizations, electronic transition energies, corresponding oscillation strengths of the low-lying electronically excited states, and the optimized S1 excited-state geometry for the isolated BHCN and MeOH monomers, the hydrogen-bonded BHCN–MeOH dimers, and BHCN–2MeOH trimer complexes have been calculated by using the DFT and TDDFT methods, respectively. We have demonstrated that the intermolecular hydrogen bond C10=O14···H40−O39−Me is weaker than C16=O17···H46−O45−Me in the hydrogen-bonded dimers and trimer no matter whether in the ground state or the excited state. In addition, our results are consistent with the relationship between the electronic spectral shifts and excited-state hydrogen bonding dynamics: hydrogen bond strengthening can induce the relative electronic spectra redshift, whereas a blueshift will be induced. In addition, we focused our attention on the frontier molecular orbital and the results could reasonably explain the hydrogen bond strengthening or weakening mechanism.

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.

TIME-DEPENDENT DENSITY FUNCTIONAL THEORY STUDY ON DYNAMICS OF HYDROGEN BONDING IN EXCITED STATES OF TRANS-ACETANILIDE IN METHANOL SOLVENT

The hydrogen-bonding dynamics in both singlet and triplet excited states of the trans-acetanilide ( AA ) in methanol ( MeOH ) solvent was investigated using the time-dependent density functional theory (TDDFT) method. Geometric optimizations of the hydrogen-bonded AA–MeOH complexes considered here as well as the isolated AA and MeOH molecules were performed using density functional theory (DFT) method. At the same time, the TDDFT method was performed to calculate the electronic transition energies and corresponding oscillation strengths of all the compounds in the low-lying electronically excited states. In this study, only the intermolecular hydrogen bonds C=O⋯H–O and N–H⋯O–H can be formed. A theoretical forecast that changes of hydrogen bonds in the low-lying electronic excited states was proposed. We discussed not only ground-state geometric structures and electronic excitation energies but also frontier molecular orbitals and electron density transition. The intermolecular hydrogen bonds between AA and MeOH molecules play an important role in the geometric structures and electronic excitation energies. Zhao et al. have put forward the relationship between the electronic spectra and hydrogen bonding dynamics for the first time. According to Zhao's rule, a redshift of the relevant electronic spectra will appear if hydrogen bond is strengthened, while the hydrogen bond weakening can make an electronic spectra shift to blue.

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.

Photoinduced dynamics of guanosine monophosphate in water from broad-band transient absorption spectroscopy and quantum-chemical calculations

Guanosine monophosphate (GMP) in aqueous solutions has been studied with femtosecond broad-band transient absorption spectroscopy and by quantum-mechanical calculations. The sample was excited at 267 or 287 nm and probed between 270 and 1000 nm with 100 fs resolution, for various pH values between 2 and 7. At pH 2, when the guanine ring is ground-state protonated (GMPH(+)), we observe isosbestic behavior indicating state-to-state relaxation. The relaxation is biexponential, tau(1) = 0.4 ps, tau(2) = 2.2 ps, and followed by slower internal conversion with tau(3) = 167 ps. For nonprotonated GMP in the pH range 7-4, we find biexponential decay in the region 400-900 nm (tau(1) = 0.22 ps, tau(2) = 0.9 ps), whereas, between 270 and 400 nm, the behavior is triexponential with one growing, tau(1) = 0.25 ps, and two decaying, tau(2) = 1.0 ps, tau(3) = 2.5 ps, components. The excited-state evolution is interpreted with the help of quantum-chemical calculations, performed at the time-dependent PBE0 level accounting for bulk solvent effects and specific solvation. The computed dynamics involves L(a) and L(b) bright excited states, whereas the n(0)pi* and pisigma* dark excited states play a minor role. Independent of the pH, the photoinduced evolution involves ultrafast L(b)-->L(a) conversion (tau(ba) << 100 fs) and exhibits the presence of a wide planar plateau on L(a). For neutral GMP a barrierless path connects this region to a conical intersection (CI) with the ground state, giving an account of the ultrafast decay of this species. For protonated GMPH(+) the system evolves into a stable minimum L(a min) characterized by out-of-plane displacement of NH and CH groups, which explains the longer (167 ps) fluorescence lifetime.