Emilio Martínez-Núñez

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.

Semiempirical Hamiltonian for Simulation of Azobenzene Photochemistry

We present a semiempirical Hamiltonian that provides an accurate description of the first singlet and triplet potential energy surfaces of azobenzene for use in direct simulations of the excited-state dynamics. The parameterization made use of spectroscopic and thermochemical data and the best ab initio results available to date. Two-dimensional potential energy surfaces based on constrained geometry optimizations are presented for the states that are most relevant for the photochemistry of azobenzene, namely, S(0), S(1), and S(2). In order to run simulations of the photodynamics of azobenzene in hydrocarbons or hydroxylic solvents, we determined the interactions of methane and methanol with the azo group by ab initio calculations and fitted the interactions with a QM/MM interaction Hamiltonian.

An automated method to find transition states using chemical dynamics simulations

A procedure to automatically find the transition states (TSs) of a molecular system (MS) is proposed. It has two components: high‐energy chemical dynamics simulations (CDS), and an algorithm that analyzes the geometries along the trajectories to find reactive pathways. Two levels of electronic structure calculations are involved: a low level (LL) is used to integrate the trajectories and also to optimize the TSs, and a higher level (HL) is used to reoptimize the structures. The method has been tested in three MSs: formaldehyde, formic acid (FA), and vinyl cyanide (VC), using MOPAC2012 and Gaussian09 to run the LL and HL calculations, respectively. Both the efficacy and efficiency of the method are very good, with around 15 TS structures optimized every 10 trajectories, which gives a total of 7, 12, and 83 TSs for formaldehyde, FA, and VC, respectively. The use of CDS makes it a powerful tool to unveil possible nonstatistical behavior of the system under study.

Quasiclassical dynamics simulation of the collision-induced dissociation of Cr(CO)6+ with Xe

Quasiclassical trajectory calculations are employed to investigate the dynamics of collision-induced dissociation (CID) of Cr(CO)6 + with Xe atoms at collision energies ranging from 1.3 to 5.0 eV. The trajectory simulations show that direct elimination of CO ligands, during the collision, becomes increasingly important as the collision energy increases. In a significant number of cases, this shattering mechanism is accompanied with a concomitant formation of a transient Xe-Cr(CO)x +(x<6) complex. The calculated results are in very good agreement with the experimental results presented previously [F. Muntean and P. B. Armentrout, J. Chem. Phys. 115, 1213 (2001)]. In particular, the computed cross sections and scattering maps for the product ions Cr(CO)x +(x=3-5) compare very favorably with the reported experimental data. However, in contrast with the conclusions of the previous study, the present calculations suggest that CID dynamics for this system exhibits a significant impulsive character rather than proceeding via a complex surviving more than a rotational period.

Dynamics of CO2 Scattering off a Perfluorinated Self-Assembled Monolayer. Influence of the Incident Collision Energy, Mass Effects, and Use of Different Surface Models †

The dynamics of collisions of CO2 with a perfluorinated alkanethiol self-assembled monolayer (F-SAM) on gold were investigated by classical trajectory calculations using explicit atom (EA) and united atom (UA) models to represent the F-SAM surface. The CO2 molecule was directed perpendicularly to the surface at initial collision energies of 1.6, 4.7, 7.7, and 10.6 kcal/mol. Rotational distributions of the scattered CO2 molecules are in agreement with experimental distributions determined for collisions of CO2 with liquid surfaces of perfluoropolyether. The agreement is especially good for the EA model. The role of the mass in the efficiency of the energy transfer was investigated in separate simulations in which the mass of the F atoms was replaced by either that of hydrogen or chlorine, while keeping the potential energy function unchanged. The calculations predict the observed trend that less energy is transferred to the surface as the mass of the alkyl chains increases. Significant discrepancies were found between results obtained with the EA and UA models. The UA surface leads to an enhancement of the energy transfer efficiency in comparison with the EA surface. The reason for this is in the softer structure of the UA surface, which facilitates transfer from translation to interchain vibrational modes.

Quasiclassical trajectory study of the collision-induced dissociation of CH3SH++Ar

Quasiclassical trajectory calculations were carried out to study the dynamics of energy transfer and collision-induced dissociation (CID) of CH(3)SH(+) + Ar at collision energies ranging from 4.34 to 34.7 eV. The relative abundances calculated for the most relevant product ions are found to be in good agreement with experiment, except for the lowest energies investigated. In general, the dissociation to form CH(3)(+) + SH is the dominant channel, even though it is not among the energetically favored reaction pathways. The results corroborate that this selective dissociation observed upon collisional activation arises from a more efficient translational to vibrational energy transfer for the low-frequency C-S stretching mode than for the high-frequency C-H stretching modes, together with weak couplings between the low- and high-frequency modes of vibration. The calculations suggest that CID takes place preferentially by a direct CH(3)(+) + SH detachment, and more efficiently when the Ar atom collides with the methyl group-side of CH(3)SH(+).

Ab Initio and RRKM Study of the HCN/HNC Elimination Channels from Vinyl Cyanide

Ab initio CCSD and CCSD(T) calculations with the 6-311+G(2d,2p) and the 6-311++G(3df,3pd) basis sets were carried out to characterize the vinyl cyanide (C(3)H(3)N) dissociation channels leading to hydrogen cyanide (HCN) and its isomer hydrogen isocyanide (HNC). Our computations predict three elimination channels giving rise to HCN and another four channels leading to HNC formation. The relative HCN/HNC branching ratios as a function of internal energy of vinyl cyanide were computed using RRKM theory and the kinetic Monte Carlo method. At low internal energies (120 kcal/mol), the total HCN/HNC ratio is about 14, but at 148 kcal/mol (193 nm) this ratio becomes 1.9, in contrast with the value 124 obtained in a previous ab initio/RRKM study at 193 nm (Derecskei-Kovacs, A.; North, S. W. J. Chem. Phys.1999, 110, 2862). Moreover, our theoretical results predict a ratio of rovibrationally excited acetylene over total acetylene of 3.3, in perfect agreement with very recent experimental measurements (Wilhelm, M. J.; Nikow, M.; Letendre, L.; Dai, H.-L. J. Chem. Phys.2009, 130, 044307).

Acceleration of Classical Mechanics by Phase Space Constraints.

In this article phase space constrained classical mechanics (PSCCM), a version of accelerated dynamics, is suggested to speed up classical trajectory simulations of slow chemical processes. The approach is based on introducing constraints which lock trajectories in the region of the phase space close to the dividing surface, which separates reactants and products. This results in substantial (up to more than 2 orders of magnitude) speeding up of the trajectory simulation. Actual microcanonical rates are calculated by introducing a correction factor equal to the fraction of the phase volume which is allowed by the constraints. The constraints can be more complex than previously used boosting potentials. The approach has its origin in Intramolecular Dynamics Diffusion Theory, which shows that the majority of nonstatistical effects are localized near the transition state. An excellent agreement with standard trajectory simulation at high energies and Monte Carlo Transition State Theory at low energies is demonstrated for the unimolecular dissociation of methyl nitrite, proving that PSCCM works both in statistical and nonstatistical regimes.

Dynamics calculations for the Cl+C2H6 abstraction reaction: Thermal rate constants and kinetic isotope effects

Thermal rate constants and H/D kinetic isotope effects for the Cl+C2H6→HCl+C2H5 reaction were computed by microcanonical variational transition state theory on a high-level ab initio potential energy surface (PES). The calculations show that the reaction proceeds through a “loose” transition state, and so the consideration of variational effects is important. The PES presents a van der Waals minimum in the products side. The calculations indicate that this minimum has no effect in the forward reaction and little effect in the reverse reaction for temperatures above room temperature. The analysis of the kinetic isotope effects shows that the contribution due to tunneling is fairly small, but with an important role played by the variational effects. Classical trajectory calculations were also performed on a semiempirical PES, which was parametrized from own ab initio calculations. This method was utilized to compare the HCl relative velocity distribution with those obtained experimentally. The results show ...

Ab Initio Calculations on the Vinyl Fluoride Fragmentation Reactions

High level ab initio calculations for the fragmentation reactions of vinyl fluoride were performed. The relative energies calculated at the QCISD(T)/6-311G(2d,2p) level of theory, corrected with MP2/6-311G(2d,2p) zero-point energies (ZPEs), differ significantly from those obtained previously at a lower level of theory. The calculations suggest that both the threeand four-center HF elimination processes are likely to occur, with the three-center elimination favored over the four-center at high energies.