DNA nucleobase properties and photoreactivity: Modeling environmental effects
Abstract The accurate ab initio quantum chemical (QM) method multiconfigurational second-order perturbation (CASSPT2)/complete active space self-consistent field (CASSCF) has been used in conjunction with molecular mechanics (MM) procedures to compute molecular properties and photoinduced reactivity of DNA/RNA nucleobases (NABs) in isolation and within a realistic environment, in which the double helix strand, the aqueous media, and the external counterions are included. It is illustrated that the use of an MM model is helpful both to account for short- and long-range effects of the system surrounding the QM molecular core and to provide the proper structural constraints that allow more acc…
On the role of the triplet state in the cis/trans isomerization of rhodopsin: A CASPT2//CASSCF study of a model chromophore
The possibility of population of the lowest-lying triplet state (T1) in the early events of the photochemical isomerization process of a model chromophore of Rhodopsin (Rh) has been analyzed using multireference perturbation theory (CASPT2//CASSCF) methods. It is shown that the characteristics of the isomerization process namely small S1−T1 gap, presence of hydrogen out of plane active vibrational modes, and existence of a dense manifold of vibrational states, render possible the fulfilment of the conditions needed for the population of T1. The possible consequences for the photochemistry and photophysics of Rh are also discussed. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem 111:3431–3…
Theoretical insight into the intrinsic ultrafast formation of cyclobutane pyrimidine dimers in UV-irradiated DNA: thymine versus cytosine.
The higher formation yields measured in the ultrafast photoinduced formation of cyclobutane thymine dimers (T T) with respect to those of cytosine (C C) are explained, on the basis of ab initio CASPT2 results, by the existence in thymine of more reactive orientations and a less efficient photoreversibility, whereas in cytosine the funnel toward the photolesion becomes competitive with that mediating the internal conversion of the excited-cytosine monomer.
Effect of opsin on the shape of the potential energy surfaces at the conical intersection of the Rhodopsin chromophore
Abstract In order to disentangle the role of the protein in the control of the photoisomerization of the chromophore of the visual pigment Rhodopsin, we compare the structure of the ground and excited potential energy surfaces of gas-phase and opsin-embedded 11- cis retinal chromophore at the corresponding (lowest energy) conical intersections. It is shown that, along the branching plane, the asymmetric opsin environment destabilizes one of the ground state relaxation channels emerging from the conical intersection. This suggests that opsin promotes the formation of the product (bathorhodopsin) via enhanced decay probability along the all- trans exit channel. In contrast, in the gas-phase n…
Do fluorescence and transient absorption probe the same intramolecular charge transfer state of 4-(dimethylamino)benzonitrile?
International audience; We present here the results of time-resolved absorption and emission experiments for 4-(dimethylamino)benzonitrile in solution, which suggest that the fluorescent intramolecular charge transfer (ICT) state may differ from the twisted ICT (TICT) state observed in transient absorption.
Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism
Proton/hydrogen-transfer processes have been broadly studied in the past 50 years to explain the photostability and the spontaneous tautomerism in the DNA base pairs. In the present study, the CASSCF/CASPT2 methodology is used to map the two-dimensional potential energy surfaces along the stretched NH reaction coordinates of the guanine–cytosine (GC) base pair. Concerted and stepwise pathways are explored initially in vacuo, and three mechanisms are studied: the stepwise double proton transfer, the stepwise double hydrogen transfer, and the concerted double proton transfer. The results are consistent with previous findings related to the photostability of the GC base pair, and a new contrib…
Intramolecular charge transfer and dual fluorescence of 4-(dimethylamino)benzonitrile: ultrafast branching followed by a two-fold decay mechanism.
International audience; In this contribution we present new experimental and theoretical results for the intramolecular charge transfer (ICT) reaction underlying the dual fluorescence of 4-(dimethylamino) benzonitrile ( DMABN), which indicate that the fully twisted ICT (TICT) state is responsible for the time-resolved transient absorption spectrum while a distinct partially twisted ICT (pTICT) structure is suggested for the fluorescent ICT state.
Towards the understanding at the molecular level of the structured-water absorption and fluorescence spectra: a fingerprint of π-stacked water
An intriguing absorption peak around ∼270 nm (4.59 eV) has been recurrently recorded in aqueous solutions of salts, sugars, amino acids, in the free-solute zone (exclusion zone) adjacent to various hydrophilic surfaces, as well as a transient in the conversion process of ice to water. The corresponding associated fluorescence has been observed in the interval 480–490 nm (2.58–2.53 eV). The spectroscopic features have been related to the presence of structured water but its nature remains incompletely understood. On the basis of high-level ab initio computations, the main absorption feature of structured water is assigned to the presence of two π-stacked ground-state water molecules, prefera…
Single-electron self-exchange between cage hydrocarbons and their radical cations in the gas phase.
We show that the radical cations of adamantane (C(10)H(16)(*+), 1H(*+)) and perdeuteroadamantane (C(10)D(16)(*+), 1D(*+)) are stable species in the gas phase. The radical cation of adamantylideneadamantane (C(20)H(28)(*+), 2H(*+)) is also stable (as in solution). By using the natural (13)C abundances of the ions, we determine the rate constants for the reversible isergonic single-electron transfer (SET) processes involving the dyads 1H(*+)/1H, 1D(*+)/1D and 2H(*+)/2H. Rate constants for the reaction 1H(*+)+1D 1H+1D(*+) are also determined and Marcus' cross-term equation is shown to hold in this case. The rate constants for the isergonic processes are extremely high, practically collision-co…
A theoretical study on the thermal ring opening rearrangement of 1H-bicyclo[3.1.0]hexa-3,5-dien-2-one: a case of two state reactivity
The molecular mechanism of the thermal rearrangement of singlet 1H-bicyclo[3.1.0]hexa-3,5-dien-2-one to give triplet 4-oxocyclohexa-2,5-dienylidene has been investigated using density functional theory (B3LYP and M05-2X functionals) as well as ab initio CASSCF and CASPT2 multiconfigurational methods. The reactant has a singlet ground state while the product can be found in three low lying electronic states P((3)B(1)), P((1)B(1)), and P((1)A'). Therefore, the molecular mechanism of this ring opening rearrangement may involve up to three different potential energy surfaces of two spin multiplicities: two singlet (closed shell, CS, and open shell, OS) and one triplet. The stationary points on …
Toward Understanding the Photochemistry of Photoactive Yellow Protein: A CASPT2/CASSCF and Quantum Theory of Atoms in Molecules Combined Study of a Model Chromophore in Vacuo.
Photochemical processes that take place in biological molecules have become an increasingly important research topic for both experimentalists and theoreticians. In this work, we report the reaction mechanism of a model of the photoactive yellow protein (PYP) chromophore in vacuo. The results obtained here, using a strategy based on the simultaneous use of the minimum energy path concept and the quantum theory of atoms in molecules applied to this excited state process, suggest a possible way in which the protein could increase the efficiency of the reaction. The role played by other electronic states of the same and different spin multiplicities in the reaction process is also analyzed, wi…
A theoretical study of the intramolecular charge transfer in 4-(dimethylamino)benzethyne
We have investigated the non-adiabatic relaxation processes occurring in the singlet manifold of 4-(dimethylamino)benzethyne (DMABE){,} a molecule isoelectronic with 4-(dimethylamino)benzonitrile (DMABN) but lacking its characteristic dual fluorescence{,} using multireference perturbation theory methods. The results obtained point out to the existence of a two-fold decay mechanism in which the population of the initially accessed La state bifurcates towards a locally excited (LE) and a [small pi][sigma]* state. Further relaxation to an emitting intramolecular charge transfer (ICT) state is impeded due to the presence of pronounced energy barriers along their associated potential energy surf…