Enrique Abad

C6H6/Au(111): Interface dipoles, band alignment, charging energy, and van der Waals interaction

We analyze the benzene/Au(111) interface taking into account charging energy effects to properly describe the electronic structure of the interface and van der Waals interactions to obtain the adsorption energy and geometry. We also analyze the interface dipoles and discuss the barrier formation as a function of the metal work-function. We interpret our DFT calculations within the induced density of interface states (IDIS) model. Our results compare well with experimental and other theoretical results, showing that the dipole formation of these interfaces is due to the charge transfer between the metal and benzene, as described in the IDIS model.

Reaction mechanism of monoamine oxidase from QM/MM calculations.

The flavoenzyme monoamine oxidase (MAO) is essential for the enzymatic decomposition of neurotransmitters. While it is commonly accepted that the rate limiting step of the reaction is the stereoselective abstraction of a hydrogen from the substrate, the precise mechanism is unknown. We modeled the reaction of human MAO-B with benzylamine by means of QM/MM calculations based on density functional theory. Oxidation of the unprotonated substrate was found to proceed with rates in good agreement with experimental values, while the protonated substrate does not react at room temperature. Our results support a concerted asynchronous polar nucleophilic mechanism. The lone pair of the amine-nitrogen interacts with a carbon atom of the flavin cofactor. During the reaction, this lone pair, as well as a proton, are transferred to the cofactor. Analysis of the electronic structure during the reaction rules out a radical mechanism.

Nonadiabatic Ensemble Simulations of cis-Stilbene and cis-Azobenzene Photoisomerization

Structurally, stilbene and azobenzene molecules exist in closed and open cis and trans forms, which are able to transform into each other under the influence of light (photoisomerization). To accurately simulate the photoisomerization processes, one must go beyond ground-state (Born-Oppenheimer) calculations and include nonadiabatic coupling between the electronic and vibrational states. We have successfully implemented nonadiabatic couplings and a surface-hopping algorithm within a density functional theory approach that utilizes local orbitals. We demonstrate the effectiveness of our approach by performing molecular dynamics simulations of the cis-trans photoisomerization in both azobenzene and stilbene upon excitation into the S1 state. By generating an ensemble of trajectories, we can gather characteristic transformation times and quantum yields that we will discuss and compare with ultrafast spectroscopic experiments.

Influence of the environment on the oxidative deamination of p-substituted benzylamines in monoamine oxidase.

The flavin-containing enzyme monoamine oxidase (MAO) is essential for the enzymatic decomposition of amine neurotransmitters. The exact mechanism of the oxidative deamination of amines to aldehydes by the enzyme has not yet been fully understood despite extensive research on the area. The rate limiting step is the reductive half-reaction where the Hα together with two electrons of the amine substrate is transferred to the flavin cofactor. However, it is still not known whether the hydrogen is transferred as a proton or a hydride. Experimental results cannot be fully explained by either of those mechanisms. In our previous work, theoretical results based on QM/MM calculations of the full enzyme show an intermediate situation between these two cases. In this paper, we report on an in-depth computational analysis concerning the role of the enzymatic environment for the reaction mechanism of human MAO-B with different p-substituted benzylamines as substrates. Our results show that steric and electrostatic effects from the active site environment turn the mechanism closer to an asynchronous polar nucleophilic mechanism. We found indications that the protein environment of MAO-A enhances the polar nucleophilic character of the mechanism compared to that of MAO-B.

Barrier height formation in organic blends/metal interfaces: case of tetrathiafulvalene-tetracyanoquinodimethane/Au(111).

The interface between the tetrathiafulvalene/tetracyanoquinodimethane (TTF-TCNQ) organic blend and the Au(111) metal surface is analyzed by Density Functional Theory calculations, including the effect of the charging energies on the molecule transport gaps. Given the strong donor and acceptor characters of the TTF and TCNQ molecules, respectively, there is a strong intermolecular interaction, with a relatively high charge transfer between the two organic materials, and between the organic layer and the metal surface. We find that the TCNQ LUMO peak is very close to the Fermi level; due to the interaction with the metal surface, the organic molecular levels are broadened, creating an important induced density of interface states (IDIS). We show that the interface energy level alignment is controlled by the charge transfer between TTF, TCNQ, and Au, and by the molecular dipoles created in the molecules because of their deformations when adsorbed on Au(111). A generalization of the Unified-IDIS model, to explain how the interface energy levels alignment is achieved for the case of this blended donor/acceptor organic layer, is presented by introducing matrix equations associated with the Charge Neutrality Levels of both organic materials and with their intermixed screening properties.

Charging energy and barrier height of pentacene on Au(111): A local-orbital hybrid-functional density functional theory approach

We analyze the pentacene/Au(111) interface by means of density functional theory (DFT) calculations using a new hybrid functional; in our approach we introduce, in a local-orbital formulation of DFT, a hybrid exchange potential, and combine it with a calculation of the molecule charging energy to properly describe the transport energy gap of pentacene on Au(111). Van der Waals forces are taken into account to obtain the adsorption geometry. Interface dipole potentials are also calculated; it is shown that the metal/pentacene energy level alignment is determined by the potential induced by the charge transfer between the metal surface and the organic material, as described by the induced density of interface states model. Our results compare well with the experimental data.

Nonlinear reactive systems on a lattice viewed as Boolean dynamical systems.

We present a stochastic, time-discrete Boolean model that mimics the mesoscopic dynamics of the desorption reactions A+A-->A+S and A+A-->S+S in a one-dimensional lattice. In the continuous-time limit, we derive a hierarchy of dynamical equations for the subset of moments involving contiguous lattice sites. The solution of the hierarchy allows to compute the exact dynamics of the mean coverage for both microscopic and coarse-grained initial conditions, which turn out to be different from the mean field predictions. The evolution equations for the mean coverage and the second-order moments are shown to be equivalent to those provided by a time-continuous master equation. The important role of higher-order fluctuations is brought out by the failure of a truncation scheme retaining only two-particle fluctuation correlations.

Calculation of non-adiabatic coupling vectors in a local-orbital basis set.

Most of todays molecular-dynamics simulations of materials are based on the Born-Oppenheimer approximation. There are many cases, however, in which the coupling of the electrons and nuclei is important and it is necessary to go beyond the Born-Oppenheimer approximation. In these methods, the non-adiabatic coupling vectors are fundamental since they represent the link between the classical atomic motion of the nuclei and the time evolution of the quantum electronic state. In this paper we analyze the calculation of non-adiabatic coupling vectors in a basis set of local orbitals and derive an expression to calculate them in a practical and computationally efficient way. Some examples of the application of this expression using a local-orbital density functional theory approach are presented for a few simple molecules: H3, formaldimine, and azobenzene. These results show that the approach presented here, using the Slater transition-state density, is a very promising way for the practical calculation of non-adiabatic coupling vectors for large systems.

Efficiency of encounter-controlled reaction between diffusing reactants in a finite lattice: topology and boundary effects

The role of dimensionality (Euclidean vs. fractal), spatial extent, boundary effects and system topology on the efficiency of diffusion-reaction processes involving two simultaneously diffusing reactants is analyzed. We present numerically exact values for the mean time to reaction, as gauged by the mean walklength before reactive encounter, obtained via application of the theory of finite Markov processes, and via Monte Carlo simulation. As a general rule, we conclude that for sufficiently large systems, the efficiency of diffusion-reaction processes involving two synchronously diffusing reactants (two-walker case) relative to processes in which one reactant of a pair is anchored at some point in the reaction space (one-walker plus trap case) is higher, and is enhanced the lower the dimensionality of the system. This differential efficiency becomes larger with increasing system size and, for periodic systems, its asymptotic value may depend on the parity of the lattice. Imposing confining boundaries on the system enhances the differential efficiency relative to the periodic case, while decreasing the absolute efficiencies of both two-walker and one-walker plus trap processes. Analytic arguments are presented to provide a rationale for the results obtained. The insights afforded by the analysis to the design of heterogeneous catalyst systems is also discussed.

Synchronous vs. asynchronous dynamics of diffusion-controlled reactions

An analytical method based on the classical ruin problem is developed to compute the mean reaction time between two walkers undergoing a generalized random walk on a 1d lattice. At each time step, either both walkers diffuse simultaneously with probability p (synchronous event) or one of them diffuses while the other remains immobile with complementary probability (asynchronous event). Reaction takes place through same site occupation or position exchange. We study the influence of the degree of synchronicity p of the walkers and the lattice size N on the global reactions efficiency. For odd N, the purely synchronous case (p=1) is always the most effective one, while for even N, the encounter time is minimized by a combination of synchronous and asynchronous events. This new parity effect is fully confirmed by Monte Carlo simulations on 1d lattices as well as for 2d and 3d lattices. In contrast, the 1d continuum approximation valid for sufficiently large lattices predicts a monotonic increase of the efficiency as a function of p. The relevance of the model for several research areas is briefly discussed.