Absorption and Fluorescence Spectra of Uracil in the Gas Phase and in Aqueous Solution: A TD-DFT Quantum Mechanical Study

Photophysics and photochemistry of a DNA-protein cross-linking model: a synergistic approach combining experiments and theory

The photophysical and photochemical properties of 5-benzyluracil and 5,6-benzyluracil, the latter produced by photocyclization of the former through irradiation with femtosecond UV laser pulses, are investigated both experimentally and theoretically. The absorption spectra of the two molecules are compared, and the principal electronic transitions involved are discussed, with particular emphasis on the perturbation induced on the two chromophore species (uracil and benzene) by their proximity. The photoproduct formation for different irradiation times was verified with high-performance liquid chromatography and nuclear magnetic resonance measurements. The steady-state fluorescence demonstrates that the fluorescence is a distinctive physical observable for detection and selective identification of 5- and 5,6-benzyluracil. The principal electronic decay paths of the two molecules, obtained through TDDFT calculations, explain the features observed in the emission spectra and the photoreactivity of 5-benzyluracil. The order of magnitude of the lifetime of the excited states is derived with steady-state fluorescence anisotropy measurements and rationalized with the help of the computational findings. Finally, the spectroscopic data collected are used to derive the photocyclization and fluorescence quantum yields. In obtaining a global picture of the photophysical and photochemical properties of the two molecules, our findings demonstrates that the use of 5-benzyluracil as a model system to study the proximity relations of a DNA base with a close-lying aromatic amino acid is valid at a local level since the main characteristics of the decay processes from the excited states of the uracil/thymine molecules remain almost unchanged in 5-benzyluracil, the main perturbation arising from the presence of the close-lying aromatic group.

Theoretical study on absorption and emission spectra of size-expanded Janus-type AT nucleobases and effect of base pairing

Fluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we design benzo- and naphtha-expanded Janus AT base analogues, using DFT, TDDFT, and CIS methods to investigate the structural and optical properties of the Janus AT base analogues (termed as J-AT, xJ-AT, yyJ-AT, BF, xBF and yyBF), and also consider the effect of base pairing. The results show that the Janus AT base analogues can pair with T and A simultaneously to form stable H-bonded WC base pairs. The ground state structure of J-AT is similar to BF, the size expansion is 2.42Å for the x-Janus AT bases and 4.86Å for the yy-Janus AT bases. The excited state geometries of J-AT and BF change dramatically, while the other bases are similar to the ground state geometries. The lowest excited singlet transitions of the Janus AT base analogues are predicted to be of ππ(*) character and mainly dominated by the configuration HOMO-LUMO. The maximum absorption wavelengths of size expansion Janus AT base analogues are greatly red shifted compared with J-AT (or BF). BF, xBF and yyJ-AT have larger oscillator strengths than J-AT, xJ-AT and yyBF. The emission wavelengths of the Janus AT base analogues also exhibit red shifts from x-Janus AT bases to yy-Janus AT bases. However, the emission wavelengths of J-AT and BF change greatly, which are coincident with the structures observed in the excited state geometries. With regard to the WC base pairs, the B3LYP functional reveals that the lowest energy transitions of some base pairs are charge transfer excitation, while the other base pairs are local excitation. The CAM-B3LYP functional predicts that all the lowest transitions are localized on the Janus AT bases, and show good agreement with the results of the M062X functional.

Low-lying excited-states of 5-benzyluracil

A numerical study is reported concerning the first and second singlet excited-states of 5-benzyluracil using the multireference self-consistent field (state-averaged CASSCF) method. The vertical excitation energies of low-lying excited-states were characterized using the SA-CASSCF method, as well as using higher-level methods, such as CASPT2, MRCI and EOM-CCSD. The local minima and conical intersections found on the potential energy surfaces (PESs) were characterized in terms of molecular geometry and natural population analysis. Different relaxation pathways on the PESs are identified and discussed by comparing with the similar pathways found for the individual monomers of uracil and benzene. The molecule can be thought of as a model system for the study of crosslink reaction between DNA and proteins induced by UV light.

A theoretical study on the structure, intramolecular interactions, and detonation performance of hydrazinium dinitramide

The structures of hydrazinium dinitramide (HDN) in the gas phase and in aqueous solution have been studied at different levels of theory by using quantum chemistry. The intramolecular hydrogen-bond interactions in HDN were studied by employing the quantum theory of atoms in molecules (QTAIM), as well as those in ammonium dinitramide (ADN), hydrazinium nitroformate (HNF), and ammonium nitroformate (ANF) for comparison. The results showed that HDN possessed the strongest hydrogen bonds, with the largest hydrogen-bond energy (-47.95 kJ mol(-1)) and the largest total hydrogen-bond energy (-60.29 kJ mol(-1)). In addition, the charge transfer between the cation and the anion, the binding energy, the energy difference between the frontier orbitals, and the second-order perturbation energy of HDN were all the largest among the investigated compounds. These strongest intramolecular interactions accounted for the highest decomposition temperature of HDN among all four compounds. The IR spectra in the gas phase and in aqueous solution were very different and showed the significant influence of the solvent. The UV spectrum showed the strongest absorption at about 253 nm. An orbital-interaction diagram demonstrated that the transition of electrons mainly happened inside the anion of HDN. The detonation velocity (D=8.34 km s(-1)) and detonation pressure (P=30.18 GPa) of HDN were both higher than those of ADN (D=7.55 km s(-1) and P=24.83 GPa). The composite explosive HDN/CL-20 with the weight ratio wCL-20 /wHDN =0.388:0.612 showed the best performance (D=9.36 km s(-1) , P=39.82 GPa), which was close to that of CL-20 (D=9.73 km s(-1), P=45.19 GPa) and slightly better than that of the composite explosive ADN/CL-20 (wCL-20 /wADN =0.298:0.702, D=9.34 km s(-1), P=39.63 GPa).

Solvent induced shifts in the UV spectrum of amides

Solvent effects on the electronic spectra of formamide and trans-N-methylacetamide are studied using four different levels of theory: singly excited configuration interaction (CIS), equations of motion coupled-cluster theory with singles and doubles (EOM-CCSD), completely renormalized coupled-cluster theory with singles and doubles with perturbative triple excitations (CR-EOM-CCSD(T)), and time-dependent density functional theory (TDDFT), employing small clusters of water molecules. The simulated electronic spectrum is obtained via molecular dynamics simulations with 100 waters modeled with the effective fragment potential method and exhibits a blue-shift and red-shift, respectively, for the n → π* and πnb → π* vertical excitation energies, in good agreement with the experimental electronic spectra of amides.

Ab initio study of the solvent H-bonding effect on ESIPT reaction and electronic transitions of 3-hydroxychromone derivatives

The electronic transitions occurring in 4-(N,N-dimethylamino)-3-hydroxyflavone (DMAF) and 2-furanyl-3-hydroxychromone (FHC) were investigated using the TDDFT method in aprotic and protic solvents. The solvent effect was incorporated into the calculations via the PCM formalism. The H-bonding between solute and protic solvent was taken into account by considering a molecular complex between these molecules. To examine the effect of the H-bond on the ESIPT reaction, the absorption and emission wavelengths as well as the energies of the different states that intervene during these electronic transitions were calculated in acetonitrile, ethanol and methanol. The calculated positions of the absorption and emission wavelengths in various solvents were in excellent agreement with the experimental spectra, validating our approach. We found that in DMAF, the hydrogen bonding with protic solvents makes the ESIPT reaction energetically unfavourable, which explains the absence of the ESIPT tautomer emission in protic solvents. In contrast, the excited tautomer state of FHC remains energetically favourable in both aprotic and protic solvents. Comparing our calculations with the previously reported time-resolved fluorescence data, the ESIPT reaction of DMAF in aprotic solvents is reversible because the emitting states are energetically close, whereas in FHC, ESIPT is irreversible because the tautomer state is below the corresponding normal state. Therefore, the ESIPT reaction in DMAF is controlled by the relative energies of the excited states (thermodynamic control), while in FHC the ESIPT is controlled probably by the energetic barrier (kinetic control).

Resonance Raman and density functional study of the excited state structural dynamics of 3-amino-2-cyclohexen-1-one in water and acetonitrile solvents

FT-Raman and/or FT-IR spectra of 3-amino-2-cyclohexen-1-one (ACyO) in solid state and/or in solvents of water and acetonitrile were obtained. Density functional theory calculations were done to help elucidate the vibrational band assignments. The A-band resonance Raman spectra of ACyO were acquired in water and acetonitrile solvents to examine the excited state structural dynamics and the state-mixing or curve-crossing tuned by solvents. A preliminary resonance Raman intensity analysis using the time-dependent wave-packet theory and simple model was done for ACyO in acetonitrile solvent. Resonance Raman spectroscopic probing of the excited state curve-crossing or state-mixing was proposed.

Excited-state calculations with TD-DFT: from benchmarks to simulations in complex environments

In this perspective, we present an overview of recent progress on Time-Dependent Density Functional Theory (TD-DFT) with a specific focus on its accuracy and on models able to take into account environmental effects, including complex media. To this end, we first summarise recent benchmarks and define an average TD-DFT accuracy in reproducing excitation energies when a conventional approach is used. Next, coupling of TD-DFT with models able to account for different kinds of interactions between a central chromophore and nearby chemical objects (solvent, organic cage, metal as well as semi-conducting surface) is investigated. Examples of application to excitation properties are presented, allowing to briefly describe several recent computational strategies. In addition, an extension of TD-DFT to describe a phenomenon involving interacting chromophores, e.g. the electronic energy transfer (EET), is presented to illustrate that this methodology can be applied to processes beyond the vertical excitation. This perspective therefore aims to provide to non-specialists a flavour of recent trends in the field of simulations of excited states in "realistic" situations.

Environmental effects in computational spectroscopy: accuracy and interpretation

Spectroscopic techniques are valuable tools for understanding the structure and dynamics of complex systems, such as biomolecules or nanomaterials. Most of the current research is devoted to the development of new experimental techniques for improving the intrinsic resolution of different spectra. However, the subtle interplay of several different effects acting at different length and time scales still makes the interpretation and analysis of such spectra a very difficult task. In this respect, computational spectroscopy is becoming a needful and versatile tool for the assignment and interpretation of experimental spectra. It is in fact possible nowadays to model with relatively high accuracy the physical-chemical properties of complex molecules in different environments, and to link spectroscopic evidence directly to the structural and dynamical properties of optically or magnetically active solvated probes. In this Review, significant steps toward the simulation of entire spectra in condensed phases are presented together with some basic aspects of computational spectroscopy, which highlight how intramolecular and intermolecular degrees of freedom influence several spectroscopic parameters.

Vibronic model for the quantum dynamical study of the competition between bright and charge-transfer excited states in single-strand polynucleotides: the adenine dimer case

A simple vibronic model aimed at investigating the interplay between bright excitonic states and dark charge-transfer (CT) states in stacked adenine (Ade) nucleobases is presented. Two orbitals (the HOMO and the LUMO) for each Ade site have been included in the electronic Hamiltonian, whose parameters have been fitted to reproduce the main features of the absorption spectra of two stacked 9-methyladenine (9Me-A) molecules, computed in aqueous solution at the PCM/TD-PBE0 level. Three modes for each adenine unit have been included in the Hamiltonian, to describe the main structural changes among the different excited state minima of the adenine stacked dimer, as described at the TD-DFT level. The developed vibronic Hamiltonian (four electronic states and six nuclear coordinates) has been adopted to perform quantum dynamical calculations of a photoexcited Ade stacked dimer, utilizing the multiconfigurational time-dependent Hartree method. The obtained results indicate that the transfer between the bright excitonic state and the CT state is fast and effective.

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.

UV-vis spectra of the anticancer camptothecin family drugs in aqueous solution: specific spectroscopic signatures unraveled by a combined computational and experimental study

The ultraviolet-visible absorption spectrum of camptothecin (CPT) has been been recorded in aqueous solution at pH 5.3, where the equilibrium among the different CPT forms is shifted toward the lactonic one. Time-dependent density functional theory (TD-DFT) computations lead to a remarkable reproduction of the experimental spectrum only upon addition of explicit water molecules in interaction with specific moieties of the camptothecin molecule. Molecular dynamics (MD) simulations enforcing boundary periodic conditions for CPT embedded with 865 water molecules, with a force field derived from DFT computations, show that the experimental spectrum is due to the contributions of CPT molecules with different solvation patterns. A similar solvent effect is observed for several CPT derivatives, including the clinically relevant SN-38 and topotecan drugs. The quantitative agreement between TD-DFT/MD computations and experimental data allow us to identify specific spectroscopic signatures diagnostic of the drug environment and to develop procedures that can be used to monitor the drug-DNA/protein interaction.