Theoretical study of PdNi and PdCu clusters embedded on graphene modified by monovacancy and nitrogen doping.

The stability and reactivity of Pd4Ni4 and Pd4Cu4 clusters embedded on graphene modified by monovacancy and nitrogen doping were investigated using auxiliary density functional theory (ADFT) calculations. The most stable structure of the Pd4Ni4 cluster is found in high spin multiplicity, whereas the lowest stable energy structure of the Pd4Cu4 cluster is a close shell system. The interaction energies between the bimetallic clusters and the defective graphene systems are significantly higher than those reported in the literature for the Pd-based clusters deposited on pristine graphene. It is observed that the composites studied present a HOMO-LUMO gap less than 1 eV, which suggests that they may present a good chemical reactivity. Therefore, from the results obtained in this work it can be inferred that the single vacancy graphene and pyridinic N-doped graphene are potentially good support materials for Pd-based clusters.

Pd2 and CoPd dimers/N-doped graphene sensors with enhanced sensitivity for CO detection: A first-principles study.

CONTEXT: The detection and monitoring of CO gas are essential to avoid human health problems. Therefore, the CO adsorption on Pd2 and PdCo dimers deposited on pyridinic Nx-doped graphene (PNxG; x = 1 - 3) was investigated employing the auxiliary density functional theory. In the most stable arrangements for the Pd2 dimer supported on PNxG, a Pd atom is in the PNxG vacancy, and the other Pd atom is placed on C atoms. For the PdCo dimer deposited on PNxG, the most stable interaction is like Pd2 dimer supported on PNxG, but with the Co atom centered over the vacancy site. Concerning the stability of the Pd2 and PdCo dimers supported on PNxG, the interaction energies (Eint) of the PdCo dimer deposited on PNxG are higher than those obtained with the Pd2 dimer. Also, the Eint of Pd2 and PdCo dimers deposited on PNxG are higher than those supported on pristine graphene. The CO adsorption energies on Pd2/PNxG and PdCo/PNxG composites are higher than those reported in the literature for pristine graphene, showing that the Pd2/PNxG and PdCo/PNxG composites have a good sensitivity toward the CO molecule. METHODS: All electronic structure calculations were performed using the auxiliary density functional theory implemented in the deMon2k program. For exchange and correlation functional, the revised PBE was used. The Pd atoms were treated with an 18-electron QECP|SD basis set, while the remaining atoms were subjected to a DZVP-GGA basis set. The GEN-A2* auxiliary-function-set was used for all computations.

A first-principles study of Ni n Pd n (n = 1 - 5) clusters.

A first-principle investigation of structures and properties of Ni n Pd n (n=1-5) clusters is presented. For this study, the linear combination of Gaussian-type orbitals auxiliary density functional theory (LCGTO-ADFT) method has been employed. In order to determine the lowest energy structures, several isomers in different spin multiplicities were studied, for each cluster size. Initial structures, for which successive geometry optimization was computed without any constrain, were taken along Born-Oppenheimer molecular dynamics (BOMD) trajectories. To discriminate between minima and transition state structures, harmonic frequency analyses were performed at the optimized structures. Ground state structures, bond lengths, harmonic frequencies, dissociation energy, ionization potential, electron affinity and spin density plots are presented. This work demonstrates, that the Pd atoms prefer to allocate on the surface of the cluster structures whose core is formed by the 3d TM atoms type. Moreover, it has been observed that the ground-state structure spin multiplicity increases as the system size grows. The results of this study contribute to gain insight into how structures and energy properties change with cluster size in bimetallic Pd-based alloys.

Metadynamics combined with auxiliary density functional and density functional tight-binding methods: alanine dipeptide as a case study.

Application of ab initio molecular dynamics to study free energy surfaces (FES) is still not commonly performed because of the extensive sampling required. Indeed, it generally necessitates computationally costly simulations of more than several hundreds of picoseconds. To achieve such studies, efficient density functional theory (DFT) formalisms, based on various levels of approximate computational schemes, have been developed, and provide a good alternative to commonly used DFT implementations. We report benchmark results on the conformational change FES of alanine dipeptide obtained with auxiliary density functional theory (ADFT) and second- and third-order density functional tight-binding (DFTB) methods coupled to metadynamics simulations. The influence of an explicit water solvent is also studied with DFTB, which was made possible by its lower computational cost compared to ADFT. Simulations lengths of 2.1 and 15 ns were achieved with ADFT and DFTB, respectively, in a reasonably short computational time. ADFT leads to a free energy difference (ΔF eq-ax) of ∼ -3 kcal mol-1 between the two low energy conformers, C7eq and C7ax, which is lower by only 1.5 kcal mol-1 than the ΔF eq-ax computed with DFTB. The two minima in ADFT FES are separated by an energy barrier of 9 kcal mol-1, which is higher than the DFTB barriers by 2-4 kcal mol-1. Despite these small quantitative differences, the DFTB method reveals FES shapes, confor-mation geometries and energies of the stationary points in good agreement with these found with ADFT. This validates the promising applicability of DFTB to FES of reactions occurring in larger-size systems placed in complex environments.