Daniel G. Trabada

Weak dimers and soft phonons on the β-SiC(100) surface

We study the β-SiC(100) [Formula: see text] reversible phase transition, using first-principles molecular dynamics simulations to search for the ground state atomic structure as well as to investigate the dynamics of this surface. We find that this surface consists of weakly bonded asymmetric Si dimers that exhibit a complex atomic motion, associated with a surface soft phonon. This soft phonon is strongly coupled to the electrons in dangling bond states close to the Fermi level, explaining the observed insulator-metal transition. We identify the dynamical processes responsible for the phase transition and predict that this surface should undergo another reversible phase transition at low T.

A practical quantum mechanics molecular mechanics method for the dynamical study of reactions in biomolecules

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.

A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.

Metallization of the potassium overlayer on the β-SiC(100) c(4 × 2) surface

We present new data on the potassium-induced semiconducting to metallic transition of the silicon-terminated β-SiC(100) c(4 × 2) surface, resulting from density functional theory simulations. We have analysed many different SiC(100)-K surface topologies, corresponding to K coverages ranging from 0.08 to 1.25 monolayers (ML), paying special attention to the 2/3 ML and 1 ML cases where a metal-insulator transition has been reported to occur. We find that the SiC(100)-K surface is metallic in all the cases. In spite of that, the potassium layer shows a very low density of states in the semiconductor gap up to potassium coverages of ~1 ML, beyond which the potassium layer undergoes a transition to metallic behaviour, explaining the experimental observation. We propose a new atomic model for the surface reconstruction of the 1 ML case which is lower in total energy than the previously suggested model based on linear potassium chains.