Alberto Requena

Effects of hydration on the proton transfer mechanism in the adenine-thymine base pair.

We report the first density functional study of water catalytic effect in the double proton transfer (DPT) taking place in the adenine-thymine (AT) base pair. To gain more insight regarding the accuracy of several theoretical methods, the ability of various functionals and models for describing the geometry of this system has first been checked. According to our results, BP86/6-311++G(d,p) is the best option for describing the solvation effects in AT when applied to a two-water-molecule-featuring model. The two possible mechanisms for DPT in solution are explored: in the first one, water molecules only remain passive elements, whereas in the second one they are directly included in the reaction path. For the noncatalyzed mechanism, the stable structures constitute the canonical form of the base pair and the first proton transfer product. Nevertheless, by involving the two water molecules in the reaction, we found three stable species: canonical base pair, first proton transfer product, and double proton transfer product. Although the thermodynamic analysis confirms that AT does not contribute to spontaneous mutation through proton transfer catalyzed by surrounding water, our results suggest that microhydration may play a crucial role for DPT reaction in others DNA or RNA basis pair.

Intermolecular Proton Transfer in Microhydrated Guanine−Cytosine Base Pairs: a New Mechanism for Spontaneous Mutation in DNA

Accurate calculations of the double proton transfer (DPT) in the adenine-thymine base pair (AT) were presented in a previous work [J. Phys. Chem. A 2009, 113, 7892.] where we demonstrated that the mechanism of the reaction in solution is strongly affected by surrounding water. Here we extend our methodology to the guanine-cytosine base pair (GC), for which it turns out that the proton transfer in the gas phase is a synchronous concerted mechanism. The O(G)-H-N(C) hydrogen bond strength emerges as the key parameter in this process, to the extent that complete transfer takes place by means of this hydrogen bond. Since the main effect of the molecular environment is precisely to weaken this bond, the direct proton transfer is not possible in solution, and thus the tautomeric equilibrium must be assisted by surrounding water molecules in an asynchronous concerted mechanism. This result demonstrates that water plays a crucial role in proton reactions. It does not act as a passive element but actually catalyzes the DPT.

A theoretical study of the HgAr2(3P1←1S0) vibronic spectrum

A quantum mechanical calculation of the vibronic spectrum of the HgAr2 van der Waals cluster in the region of the Hg(3P1←1S0) electronic transition is presented and compared with experiments. The potential energy surfaces for the ground and excited states are obtained using available empirical Ar–Ar and Ar–Hg potentials. For the ground electronic state, the potential is written as a sum of pairwise Ar–Ar and Ar–Hg(1S0) interactions. On the contrary, for the electronically excited states correlating to Hg(3P1), an axis switching rotation has to be applied to each individual Ar–Hg(3P1; Ωe=0, ±1) interactions in order to define a common quantization axis. This results in a nonpairwise additive diabatic matrix Hamiltonian which after diagonalization provides the adiabatic excited potential energy surfaces. The vibrational wave functions associated to the ground and the first two (A and B+) adiabatic electronically excited states are obtained by variational techniques using basis sets along Jacobi coordinate...

Harmonic Models in Cartesian and Internal Coordinates to Simulate the Absorption Spectra of Carotenoids at Finite Temperatures

When large structural displacements take place between the ground state (GS) and excited state (ES) minima of polyatomic molecules, the choice of a proper set of coordinates can be crucial for a reliable simulation of the vibrationally resolved absorption spectrum. In this work, we study two carotenoids that undergo structural displacements from GS to ES minima of different magnitude, from small displacements for violaxanthin to rather large ones for β-carotene isomers. Their finite-temperature (77 and 300 K) spectra are simulated at the harmonic level, including Duschinsky effect, by time-dependent (TD) and time-independent (TI) approaches, using (TD)DFT computed potential energy surfaces (PES). We adopted two approaches to construct the harmonic PES, the Adiabatic (AH) and Vertical Hessian (VH) models and, for AH, two reference coordinate frames: Cartesian and valence internal coordinates. Our results show that when large displacements take place, Cartesian coordinates dramatically fail to describe curvilinear displacements and to account for the Duschinsky matrix, preventing a realistic simulation of the spectra within the AH model, where the GS and ES PESs are quadratically expanded around their own equilibrium geometry. In contrast, internal coordinates largely amend such deficiencies and deliver reasonable spectral widths. As expected, both coordinate frames give similar results when small displacements occur. The good agreement between VH and experimental line shapes indicates that VH model, in which GS and ES normal modes are both evaluated at the GS equilibrium geometry, is a good alternative to deal with systems exhibiting large displacements. The use of this model can be, however, problematic when imaginary frequencies arise. The extent of the nonorthogonality of the Dushinsky matrix in internal coordinates and its correlation with the magnitude of the displacement of the GS and ES geometries is analyzed in detail.

Vibrational predissociation of the I2⋯Ne2 cluster: A molecular dynamics with quantum transitions study

The MDQT (molecular dynamics with quantum transitions) method of Tully is applied to the vibrational predissociation of a Van der Waals cluster containing a diatomic molecule and two rare gas atoms, I2⋯Ne2. The vibrational degree of freedom of the diatomic is treated quantum mechanically using DVR (discrete variable representation) while all the other degrees of freedom are treated classically. The results are in very good agreement with the experimentally measured lifetimes and product state distributions. In particular, the final vibrational state distribution of I2, which could not be satisfactorily reproduced in quasiclassical studies, is well described. Based on these results a different kinetic scheme for interpreting the vibrational predissociation in this system is proposed. In addition, this work shows that the method is very promising for the study of clusters containing more rare gas atoms.

About the overestimation of the basis set superposition error on interaction energy calculations for van der Waals systems

A procedure to estimate the basis set superposition error is proposed avoiding the overestimation of the counterpoise correction in the van der Waals interactions. Numerical calculations were carried out in the Ne ⋅⋅⋅ Ne complex at the SCF level.

The Ehrenfest method with quantum corrections to simulate the relaxation of molecules in solution: equilibrium and dynamics.

The use of the Ehrenfest method to simulate the relaxation of molecules in solution is explored. Using the cyanide ion dissolved in water as a test model, the independent trajectory (IT) and the bundle of trajectories (BT) approximations are shown to provide very different results for the time evolution of the vibrational populations of the solute. None of these approximations reproduce the Boltzmann equilibrium vibrational populations accurately. A modification of the Ehrenfest method based on the use of quantum correction factors is thus proposed to solve this problem. The simulations carried out using the modified Ehrenfest method provide IT and BT relaxation times which are closer to each other and which agree quite well with previous hybrid perturbative results.

Intramolecular vibrational redistribution and fragmentation dynamics of I2 ⋯ Nen (n=2–6) clusters

Intramolecular vibrational energy redistribution and fragmentation dynamics in I2(B,v=22) ⋯ Nen (n=2–6) and I2(B,v=21) ⋯ Nen (n=2–5) clusters is studied by hybrid quantum/classical techniques and the results are compared with experiments. A vibrational version of the molecular dynamics with quantum transitions (MDQT) treatment is used in which the vibrational degree of freedom of I2 is treated quantum mechanically while all the other degrees of freedom are treated classically. The potential energy surface is represented as a sum of pairwise interactions with parameters taken from the literature. The calculated product state distributions are in very good agreement with the experiments. Fragmentation lifetimes were also calculated and agree reasonably well with those measured in time-dependent experiments. Fragmentation proceeds via sequential ejection of Ne monomers through three different mechanisms: (i) sequential intramolecular vibrational redistribution plus vibrational predissociation (in which the I...

Instantaneous normal modes, resonances, and decay channels in the vibrational relaxation of the amide I mode of N-methylacetamide-D in liquid deuterated water

A nonequilibrium molecular dynamics (MD) study of the vibrational relaxation of the amide I mode of deuterated N-methylacetamide (NMAD) in aqueous (D(2)O) solution is carried out using instantaneous normal modes (INMs). The identification of the INMs as they evolve over time, which is necessary to analyze the energy fluxes, is made by using a novel algorithm which allows us to assign unequivocally each INM to an individual equilibrium normal mode (ENM) or to a group of ENMs during the MD simulations. The time evolution of the energy stored in each INM is monitored and the occurrence of resonances during the relaxation process is then investigated. The decay of the amide I mode, initially excited with one vibrational quantum, is confirmed to fit well to a biexponential function, implying that the relaxation process involves at least two mechanisms with different rate constants. By freezing the internal motions of the solvent, it is shown that the intermolecular vibration-vibration channel to the bending modes of the solvent is closed. The INM analysis reveals then the existence of a major and faster decay channel, which corresponds to an intramolecular vibrational redistribution process and a minor, and slower, decay channel which involves the participation of the librational motions of the solvent. The faster relaxation pathway can be rationalized in turn using a sequential kinetic mechanism of the type P-->M+L-->L, where P (parent) is the initially excited amide I mode, and M (medium) and L (low) are specific midrange and lower-frequency NMAD vibrational modes, respectively.

Hybrid quantum/classical simulation and kinetic study of the vibrational predissociation of Cl2⋯Nen (n=2, 3)

A hybrid quantum/classical method is applied to the vibrational predissociation of van der Waals clusters containing a diatomic molecule and several rare gas atoms, Cl2⋯Nen (n=2, 3). The vibrational degree of freedom of the diatomic is treated quantum mechanically while all the other degrees of freedom are treated classically. A kinetic mechanism is proposed in order to interpret the dynamics in terms of the following elementary steps; vibrational predissociation (VP), intramolecular vibrational redistribution (IVR), and evaporative cooling (EC). The resulting lifetimes are in very good agreement with the experimental linewidth measurements of Janda and co-workers, and with the quantum mechanical reduced-dimension results of Le Quere and Gray on Cl2⋯Ne2. The final rotational state distributions agree very well with the experimental results and exhibit a quasistatistical behavior. The final vibrational distributions reproduce the main experimental features.