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.

Cycloaddition reactions via "on water" protocol reactions: A density functional theory study.

In this work, the reactions of quadricyclane with dimethyl azodicarboxylate (DMAD) and of quadricyclane with diethyl azodicarboxylate (DEAD) in gas phase and in water environments were studied by a first-principles investigation within the framework of auxiliary density functional theory (ADFT). For these type of organic reactions is known that water is required to accelerate them. Since the reason of why this occur is still unknown, this work aims to gain insight into this reaction mechanism. For this investigation, the generalized gradient approximation as well as a hybrid functional were employed. The obtained optimized structures for the reactants, of the products and of the transition states are reported, together with the corresponding frequency analysis results and the reaction profiles. Along the proposed concerted reaction mechanism, a critical points search of the electron density and a charge analysis were performed. The calculated potential energy barriers of these reactions in gas phase and in water environments are compared. In agreement with experiment, the obtained results indicate that both reactions occur faster in water than in gas phase. This study shows that there is a change in the polarity of the two most important carbon atoms of the formed compounds along the reactions and that the decrease of the activation energy barrier which occurs in liquid phase in these reactions is because the structures of the main transition states are stabilized by the water environment. Therefore, the here obtained results demonstrate the important role played by the water-molecule framework into the activation energy barrier and structures of the molecules that participate in the DMAD and DEAD cycloaddition reactions.

Cartesian constraints in QM/MM optimizations.

With the rise of quantum mechanical/molecular mechanical (QM/MM) methods, the interest in the calculation of molecular assemblies has increased considerably. The structures and dynamics of such assemblies are usually governed to a large extend by intermolecular interactions. As a result, the corresponding potential energy surfaces are topological rich and possess many shallow minima. Therefore, local structure optimizations of QM/MM molecular assemblies can be challenging, in particular if optimization constraints are imposed. To overcome this problem, structure optimization in normal coordinate space is advocated. To do so, the external degrees of freedom of a molecule are separated from the internal ones by a projector matrix in the space of the Cartesian coordinates. Here we extend this approach to Cartesian constraints. To this end, we devise an algorithm that adds the Cartesian constraints directly to the projector matrix and in this way eliminates them from the reduced coordinate space in which the molecule is optimized. To analyze the performance and stability of the constrained optimization algorithm in normal coordinate space, we present constrained minimizations of small molecular systems and amino acids in gas phase as well as water employing QM/MM constrained optimizations. All calculations are performed in the framework of auxiliary density functional theory as implemented in the program deMon2k.

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.

Isomerization Reactions of the Cu15V+ Cluster: A Density Functional Theory Study.

The investigation of the chemical reactivity of complex systems such as transition metal clusters is a very complicated task because often the structures of the corresponding transition states are far from being intuitive. Bimetallic transition metal clusters represent a particular class of complex systems. In this work, density functional theory (DFT) is applied to study the isomerization reactions of the Cu15V+ cluster. Full geometry optimizations of dozens of initial structures taken along Born-Oppenheimer molecular dynamics (BOMD) trajectories were performed using a quasi-Newton method in a reduced space Cartesian coordinate system that works considering the internal degrees of freedom. Harmonic frequencies calculations were performed at the optimized structures. To study the isomerization reactions between the obtained stable isomers, a hierarchical transition state algorithm has been applied to locate the transition states of this cluster. The found transition states were than connected with the corresponding minimum structures by calculating the intrinsic reaction coordinates. This work demonstrates the capability of the applied method to study non-intuitive rearrangement mechanisms in complex finite systems and to create networks between minima and transition state structures on their potential energy surface.

Hybrid ADFT Study of the C104 and C106 IPR Isomers.

This work presents a hybrid auxiliary density functional theory (ADFT) study of the neutral and hexaanionic C104 and C106 fullerenes with the aim to determine their ground state structures. To this end, all C104 and C106 fullerene structures that obey the isolated pentagon rule (IPR) were optimized with the Perdew-Burke-Ernzerhof generalized gradient approximation followed by a single-point energy calculation with the PBE0 hybrid functional. Our studies show that this composite approach yields relative energies of giant fullerenes that are accurate to around 1 kcal/mol. As a result, the ground states of C104, C1046-, and C1066- can be assigned to the isomers 234:Cs, 821:D2, and 891:Cs, respectively. On the other hand, the energetically lowest lying IPR isomers of C106, 331:Cs, 1194:C2, 534:C1 are separated by less than 1 kcal/mol which makes an unequivocal ground state assignment by hybrid DFT methods impossible. To guide future experiments, we also report the simulated IR and Raman spectra of the most stable neutral and hexaanionic C104 and C106 fullerenes.

Influence of spin multiplicity on the melting of Na55(+).

The influence of spin multiplicity on the melting of the Na55(+) cluster has been investigated by means of all-electron Kohn-Sham Born-Oppenheimer molecular dynamics simulations. On the basis of the quantitative agreement between the experimental and theoretical melting temperature and latent heat a detailed analysis of the cluster dynamics was performed. This analysis showed a significant structure deformation of the cluster that is inconsistent with the geometrical shell closing concept. In subsequent structure optimizations a high-spin ground state in perfect icosahedral symmetry was found for the Na55(+) cluster. The Born-Oppenheimer molecular dynamics of this high-spin Na55(+) cluster indicates a particular thermal stability of the icosahedral cluster structure. A new electronic mechanism, named subshell closing, is suggested as the origin for this enhanced thermal stability of the icosahedral cluster structure. This mechanism is a natural extension of the common jellium model. By its nature, the subshell closing mechanism is general for finite systems and expected to be found in many other clusters for which the jellium model is applicable.

Contribution of high-energy conformations to NMR chemical shifts, a DFT-BOMD study.

This paper highlights the relevance of including the high-energy conformational states sampled by Born-Oppenheimer molecular dynamics (BOMD) in the calculation of time-averaged NMR chemical shifts. Our case study is the very flexible glycerol molecule that undergoes interconversion between conformers in a nonrandom way. Along the sequence of structures from one backbone conformer to another, transition states have been identified. The three (13)C NMR chemical shifts of the molecule were estimated by averaging their calculated values over a large set of BOMD snapshots. The simulation time needed to obtain a good agreement with the two signals present in the experimental spectrum is shown to be dependent on the atomic orbital basis set used for the dynamics, with a necessary longer trajectory for the most extended basis sets. The large structural deformations with respect to the optimized conformer geometries that occur along the dynamics are related to a kinetically driven conformer distribution. Calculated conformer type populations are in good agreement with experimental gas phase microwave results.

Structural changes of Pd13 upon charging and oxidation/reduction.

First-principle generalized gradient corrected density functional calculations have been performed to study the stability of cationic and anionic Pd(13) (+∕-), and neutral Pd(13)O(2) clusters. It is found that while cationic Pd(13) (+) favors a C(s) geometry similar to the neutral Pd(13), both anionic Pd(13)(-) and neutral Pd(13)O(2) favor a compact ~I(h) structure. A detailed analysis of the electronic structure shows that the stabilization of the delocalized 1P and 2P cluster orbitals, and the hybridization of the 1D orbitals with the oxygen atomic p orbitals play an important role in the energetic ordering of C(s) and ~I(h) isomers. A structural oscillation is predicted during an oxidation/reduction cycle of Pd(13) in which small energy barriers between 0.3 and 0.4 eV are involved.

Theoretical study of the structure and properties of Na-MOR and H-MOR zeolite models.

This work presents calculated structural parameters and energetic properties of Na- and H-mordenites (MORs) using cluster models with more than 400 atoms. These state of the art calculations were performed within the framework of density functional theory, using both the local density approximation and the generalized gradient approximation, employing all-electron basis sets. The most populated T3, T4, and T1 Al sites have been investigated using two different MOR models, each containing two isolated Al sites. A detailed analysis of the structures, three-dimensional contours of molecular electrostatic potential, binding energies of Na cations and protons, and BrØnsted O-H harmonic frequencies are presented. These properties are compared with available experimental results. The structural changes among Si/Al substitution as well as Na/H exchange are discussed.

Density Functional Study of 2-[(R-Phenyl)amine]-1,4-naphthalenediones.

The molecular and electronic structures of a series of 2-[(R-phenyl)amine]-1,4-naphthalenediones (R = m-Me, p-Me, m-Et, p-CF3, p-Hex, p-Et, m-F, m-Cl, p-OMe, p-COMe, p-Bu, m-COOH, p-Cl, p-COOH, p-Br, m-NO2, m-CN, and p-NO2) and their anions are investigated in the framework of density functional theory. The calculations are of all-electron type using a double zeta valence polarization basis set optimized for density functional theory methods. The theoretical study shows that all compounds are nonplanar. The nonplanarity can be rationalized in terms of occupied π orbitals. A linear correlation between the measured half-wave potentials and the calculated gas-phase electron affinities is found. It holds for local as well as generalized gradient corrected functionals. Structural parameters, harmonic vibrational frequencies, and adiabatic and vertical electron affinities as well as orbital and spin density plots of the studied compounds are presented.