Antonio Fernández-Ramos

Improved algorithm for corner-cutting tunneling calculations

We present an improved version of the large-curvature tunneling method that more accurately treats the anharmonic potentials encountered along low-energy corner-cutting tunneling paths. The method is illustrated by applications to the reaction CH3+H2→CH4+H and to the double proton transfer in formamidine hydrate.

Proton tunnelling in polyatomic molecules: A direct-dynamics instanton approach

In this review we discuss a recently introduced method of calculating hydrogen tunnelling rates and tunnelling splittings in medium and large molecules. It is a non-empirical, direct-dynamics method that uses ab initio quantum-chemical output as input data for the calculation of dynamic properties by means of the instanton approach. This approach is based on the recognition that there is a single path that dominates the tunnelling rate. This so-called instanton trajectory is the path that minimizes the classical action. Although it is very difficult to calculate this trajectory for multidimensional systems, it will be shown that the corresponding instanton action, which is the quantity of practical interest, can be obtained with sufficient accuracy to reproduce experimental observations without the explicit evaluation of the instanton trajectory. In this approximation scheme the instanton action is calculated from the one-dimensional action through the introduction of appropriate correction terms for all ...

A direct-dynamics study of the zwitterion-to-neutral interconversion of glycine in aqueous solution

The mechanism of interconversion between the neutral and zwitterionic forms of glycine in aqueous solution is studied theoretically. It is argued that indirect transfer via a water bridge is a plausible alternative to the generally assumed direct transfer mechanism. The argument is based on model calculations in which the system glycine-water is represented by a 1:6 supermolecule embedded in a dielectric continuum. Optimized geometries and vibrational frequencies are obtained at the Hartree–Fock level with a 6-31G* basis set, and at the second-order Mo/ller–Plesset frozen-core level with the 6-31+G* basis set for the neutral and zwitterionic forms, and for their transition state. At both levels the energetics are corrected by single-point quadratic configuration interaction calculations, including single and double substitutions with frozen-core inner-shell orbitals. Both models reproduce the observed endothermicity of the transfer better than models that use only a limited number of discrete water molecu...

A direct-dynamics study of proton transfer through water bridges in guanine and 7-azaindole

To evaluate the efficiency of bridges of water molecules as proton conduits, multidimensional ab initio proton transfer rate constants are reported for complexes of guanine and 7-azaindole with one and two water molecules. These water molecules form hydrogen-bonded bridges between functional groups involved in tautomerization via proton transfer and catalyze this transfer. Structures and energies of the relevant stationary configurations are optimized at the second-order Moller–Plesset level and vibrational force fields are evaluated at the Hartree–Fock level. The proton transfer rate constants, calculated with the instanton method, show the effect of the structure and strength of the hydrogen bonds, reflected in couplings between the tunneling mode and the other vibrations of the complexes. The results indicate that strongly hydrogen-bonded, strain-free water bridges can serve as very efficient proton conduits.

Tunneling dynamics of double proton transfer in formic acid and benzoic acid dimers

Direct dynamics calculations based on instanton techniques are reported of tunneling splittings due to double proton transfer in formic and benzoic acid dimers. The results are used to assign the observed splittings to levels for which the authors of the high-resolution spectra could not provide a definitive assignment. In both cases the splitting is shown to be due mainly to the zero-point level rather than to the vibrationally or electronically excited level whose spectrum was investigated. This leads to zero-point splittings of 375 MHz for (DCOOH)(2) and 1107 MHz for the benzoic acid dimer. Thus, contrary to earlier calculations, it is found that the splitting is considerably larger in the benzoic than in the formic acid dimer. The calculations are extended to solid benzoic acid where the asymmetry of the proton-transfer potential induced by the crystal can be overcome by suitable doping. This has allowed direct measurement of the interactions responsible for double proton transfer, which were found to be much larger than those in the isolated dimer. To account for this observation both static and dynamic effects of the crystal forces on the intradimer hydrogen bonds are included in the calculations. The same methodology, extended to higher temperatures, is used to calculate rate constants for HH, HD, and DD transfers in neat benzoic acid crystals. The results are in good agreement with reported experimental rate constants measured by NMR relaxometry and, if allowance is made for small structural changes induced by doping, with the transfer matrix elements observed in doped crystals. Hence the method used allows a unified description of tunneling splittings in the gas phase and in doped crystals as well as of transfer rates in neat crystals.

Least-Action Tunneling Transmission Coefficient for Polyatomic Reactions.

We present a new least-action variational approximation for tunneling in polyatomic reactions based on the procedure developed by Garrett and Truhlar for atom-diatom reactions. (63) The method calculates the semiclassical ground-state tunneling probability at every tunneling energy by minimizing the value of imaginary action integral along a family of paths ranging from the minimum energy path to the straight path. The method is illustrated by applications to two hydrogen-atom abstraction reactions from methane using analytical potential energy surfaces.

DFT conformational study of cysteine in gas phase and aqueous solution

Abstract Different conformers of cysteine in gas phase are investigated at the DFT B3LYP/6-31G∗ and B3LYP/6-311++G∗∗ levels. The effect of the solvent is simulated by using the Onsager and polarizable continuum (PCM) models within the self-consistent reaction field method (SCRF) at the B3LYP/6-31G∗ level. Specifically, five neutral forms, two anions and one zwitterion were analysed. Both, in gas phase and solution the most stable normal form has the carboxyl group directed toward the amino group. In accord with the experiment, the PCM model predicts that the most stable structure in solution is a zwitterion, a species that does not exist or has a very small stability in gas phase. A major stabilization in solution is also predicted for the zwitterionic form of anionic cysteine. Thus the PCM model renders correct stability order of the different conformers in solution, while the Onsager model does not, which is due to the underestimation of the electrostatic contributions to the solute–solvent interaction for the zwitterions.

High-level direct-dynamics variational transition state theory calculations including multidimensional tunneling of the thermal rate constants, branching ratios, and kinetic isotope effects of the hydrogen abstraction reactions from methanol by atomic hydrogen

We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical variational transition state theory (CVT) with the microcanonically optimized multidimensional tunneling (μOMT) transmission coefficient (CVT/μOMT) to study both the CH(3)OH+H→CH(2)OH+H(2) (R1) reaction and the CH(3)OH+H→CH(3)O+H(2) (R2) reaction. The CVT/μOMT calculations show that reaction R1 dominates in the whole range 298≤T (K)≤2500 and that anharmonic effects on the torsional mode about the C-O bond are important, mainly at high temperatures. The activation energy for the total reaction sum of R1 and R2 reactions changes substantially with temperature and, therefore, the use of straight-line Arrhenius plots is not valid. We recommend the use of new expressions for the total R1 + R2 reaction and for the R1 and R2 individual reactions.

Mode-specific tunneling splittings in 9-hydroxyphenalenone: Comparison of two methods for direct tunneling dynamics

A benchmark comparison is presented of two direct dynamics methods for proton tunneling, namely variational transition-state theory with semiclassical tunneling corrections (VTST/ST) and the instanton method. The molecules chosen for the comparison are 9-hydroxyphenalenone-d0 and -d1, which have 64 vibrational degrees of freedom and show large tunneling splittings for the zero-point level and several vibrationally excited levels of the electronic ground state. Some of the excited-level splittings are larger and some smaller than the zero-level splitting, illustrating the multidimensional nature of the tunneling. Ab initio structure and force field calculations at the Hartree–Fock/6-31G** level are carried out for the two stationary points of the tunneling potential, viz. the equilibrium configuration and the transition state. The VTST/ST calculations are based on both the small- and the large-curvature approximation; the additional quantum-chemical calculations required at intermediate points of the poten...

Dynamics of the water-catalyzed phototautomerization of 7-azaindole

Multidimensional ab initio proton tunneling rate constants are reported for the tautomerization of singlet-excited 7-azaindole complexed with water, represented by discrete water molecules with and without a dielectric continuum. The results are compared with experimental observations in cold beams and in room-temperature aqueous solutions. For complexes with one and two water molecules, potential-energy surfaces are calculated at the complete active space multiconfiguration self-consistent-field [CASSCF(8,8)] level. For comparison with solution data, the structures are reoptimized inside a spherical cavity according to the Onsager model. To compare the effect of the dielectric with that of a secondary solvent shell, the structure of 1:1 and 1:2 complexes solvated by four and three additional water molecules so as to form 1:5 complexes, are optimized at the CASSCF(8,8) level with single-point Onsager corrections. Based on these potential-energy surfaces, temperature-dependent multidimensional proton trans...