José Manuel Vásquez-Pérez

The discovery of unexpected isomers in sodium heptamers by Born–Oppenheimer molecular dynamics

This work presents a density functional study of neutral, cationic, and anionic sodium cluster heptamers. The cluster structures were optimized with the local density approximation as well as with the generalized gradient approximation. For the neutral and cationic clusters new unexpected isomers are found closed in energy to the well known ground state structures. In the case of the neutral heptamer the new isomer was first noticed by inspection of a first-principles Born-Oppenheimer molecular dynamics (BOMD) simulations at 300 K. A structure alignment algorithm is presented which facilitates the discovery of new structures from such BOMD simulations. With this algorithm the structural evolution of the two low-lying isomers of the neutral, cationic, and anionic heptamer was analyzed at different temperatures. This work demonstrates the capability of reasonably long (approximately 100 ps) first-principles BOMD simulations to explore the potential energy landscape of metallic clusters.

Transition-State Searches in Metal Clusters by First-Principle Methods

Elucidation of the chemical reactivity of metal clusters is often cumbersome due to the nonintuitive structures of the corresponding transition states. In this work, a hierarchical transition-state algorithm as implemented in the deMon2k code has been applied to locate transition states of small sodium clusters with 6-10 atoms. This algorithm combines the so-called double-ended interpolation method with the uphill trust region method. The minimum structures needed as input were obtained from Born-Oppenheimer molecular dynamics simulations. To connect the found transition states with the corresponding minimum structures, the intrinsic reaction coordinates were calculated. This work demonstrates how nonintuitive rearrangement mechanisms can be studied in metal clusters.

Metal cluster structures and properties from Born-Oppenheimer molecular dynamics

Density functional theory (DFT) Born-Oppenheimer molecular dynamics (BOMD) simulations of metal clusters are presented. The calculations have been performed with the deMon2k [1] code employing all-electron basis sets and local and non-local functionals. The capability to perform reasonable long (∼ 100 ps) first-principle BOMD simulations in order to explore potential energy landscape of metallic clusters will be presented [2,3]. The evolution of the cluster structures and properties, such as polarizability and heat capacity, with temperature is discussed.

First Principles Computational Biochemistry with deMon2k

Abstract: The growth of computational power, provided by new hardware technologies and the development of better theoretical methods and algorithms, allows more than ever an improvement in the reliability of computational predictions in medical sciences, along with a better understanding of the underlying molecular mechanisms. However, one limitation of computational chemistry approaches in the field of biological systems is the complexity of the molecules and the environment in which such molecules are to be studied. Important issues such as the determination of molecular properties which depend on the electronic structure face a considerable challenge when all-electron methodologies are required in the investigation. The most rigorous and sophisticated electronic structure methodologies, like density functional theory (DFT), are usually overwhelmed by the molecular size of most pharmacological targets. However, important implementations were recently achieved by the developers group of the computational chemistry code deMon2k. Knowing that the computation of electrostatic interaction integrals is an important bottleneck in all-electron calculations three new implementations have been worked out in order to eliminate such bottleneck. These implementations allow deMon2k now to explore biological and pharmacological systems in the framework of all-electron DFT methodologies.