Carlos A. Gonzalez

The injecting energy at molecule/metal interfaces: Implications for conductance of molecular junctions from an ab initio molecular description

To study the electronic transport of molecular wire circuits, we present a time-independent scattering formalism which includes an ab initio description of the molecular electronic structure. This allows us to obtain the molecule–metal coupling description at the same level of theory. The conductance of junction α, α′ xylyl dithiol and benzene-1,4-dithiol between gold electrodes is obtained and compared with available experimental data. The conductance depends dramatically on the relative position of the Fermi energy of the metal with respect to the molecular levels. We obtain an estimate for the injecting energy of the electron onto the molecule by varying the distance between the molecule and the attached gold clusters. Contrary to the standard assumption, we find that the injecting energy lies close to the molecular highest occupied molecular orbital, rather than in the middle of the gap; it is just the work function of the bulk metal. Finally, the adequacy of the widely used extended Huckel method for...

A natural orbital diagnostic for multiconfigurational character in correlated wave functions

The natural orbitals and their corresponding occupation numbers are constructed for several interesting problems to demonstrate that the existence of negative natural orbital occupation numbers for single reference correlation methods provides a simple diagnostic for the need for a multiconfigurational description of the wave function.

Electronic spectra and photophysics of the two stable conformers of anthracene dimer: evaluation of an ab initio structure prediction

Abstract It is shown that the spectral features and excited-state dynamics of the two Van der Waals dimers of anthracene, generated by supersonic free expansion, can be accounted for if the dimers have the crossed (D 2d ) and the parallel-displaced (C 2h ) structures predicted by an ab initio calculation with MP2 correlation.

The importance of global minimization and adequate theoretical tools for cluster optimization: the Ni6 cluster case

A Monte Carlo simulated annealing (MCSA) algorithm using parallel processing has been employed in quantum parametric method in order to full optimize the Ni6 cluster. Results obtained from this procedure show that the same trend is reproduced by standard DFT optimization calculations. However, results do not correspond with the octahedral geometry reported in several theoretical DFT calculations and for classical global minimization techniques. Different structures close in energy are found here, as the most stable ones: pentagonal pyramid (PPY) and capped trigonal bipyramid (CTB).

Fundamental properties of parametric functionals in quantum chemistry

Abstract A theoretical interpretation and justification of the basic approaches proposed in parametrical methods is presented in this paper. The idea of providing a fundamental understanding of these methods can be considered as a guide for further development in this area. The application of functional analysis concepts to understanding the nature of parametric functionals in terms of the Riesz and Weiestrasss theorems is discussed. In addition, applications of virial and hypervirial theorems to constrain the type of functional and the parameters used in these methods is addressed. A justification of the use of a single determinantal wavefunction and the nature and conditions of optimized orbital basis in terms of different electronic environments involved in different interactions was also established.

A Simple Theoretical Model to Study the Voltage Dependence of the Electronic Structure of Phenyl Ethylene Oligomers

Abstract: Although very few measurements have appeared in the open literature and there seems to be a controversy about the existence of the NDR phenomenon in molecules, the prospects of building such systems have attracted significant attention. In the work reported in this paper we used a model based on DFT calculations of the electronic structure of the 2′‐amino‐4,4′‐di(ethynylphenyl)‐5′‐nitro‐1‐benzenethiolate molecule (previously reported to exhibit NDR behavior) in a capacitor‐like electric field that mimics the potential spatial profile of the junction. Our results suggest that in these systems, there seems to be a correlation between a substantial charge density rearrangement of the neutral bridge at a threshold voltage and the NDR behavior observed in previous experiments. Our results highlight the importance of inclusion of the field in the study of electrified interfaces. We applied this model to a fluorine‐substituted conjugated diethynylphenyl molecule and found that these calculations predict similar behavior. Results based on extended system calculations, including electrode‐molecule interactions, confirm the validity of the model based on the isolated molecule and suggest the use of these simple models to rationally design molecular devices with similar switching characteristics.

Identification of Active Sites of Biomolecules. 1. Methyl-α-mannopyranoside and FeIII

Car-Parrinello molecular dynamics (CPMD) simulations, DFT chemical reactivity index calculations, and mass spectrometric measurements are combined in an integrated effort to elucidate the details of the coordination of a transition-metal ion to a carbohydrate. The impact of the interaction with the FeIII ion on the glycosidic linkage conformation of methyl-alpha-d-mannopyranoside is studied by classical molecular dynamics (MD) and CPMD simulations. This study shows that FeIII interacts with specific hydroxyl oxygen atoms of the carbohydrate, affecting the ground state carbohydrate conformation. These conformational details are discussed in terms of a set of supporting experiments involving electrospray ionization mass spectrometry, and CPMD simulations clearly indicate that the specific conformational preference is due to intramolecular hydrogen bonding. Classical MD simulations proved insensitive to these important chemical properties. Thus, we demonstrate the importance of chemical reactivity calculations and CPMD simulations in predicting the active sites of biological molecules toward metal cations.

Modeling the electrostatic potential spatial profile of molecular junctions: The influence of defects and weak links

Abstract: The spatial profile of the electrostatic potential across a molecular junction is one of the single most influential factors in determining the form of intensity‐voltage characteristics. We have modeled the influence of bridge electronic defects (site substitutions) and weak links (local weak bonds) on the potential profile. The potential is determined self‐consistently by solving Poisson and Schrödinger equations simultaneously. We have considered the simplest model of a one‐dimensional molecular wire. This system already exhibits some of the most relevant features observed in I‐V curves of real chemically modified junctions, where strong asymmetries and rectification effects have been reported.

On the equilibrium geometries of anthracene trimer and naphthalene tetramer: comparison of the exp-6-1 and HFD structure predictions with experiment

Abstract Energy minimizations using Hartree–Fock dispersion (HFD) model and exp-6-1 potentials predict very different global minima for anthracene trimer and naphthalene tetramer. Comparison of the predicted geometries with available experimental data demonstrates the clear superiority of the HFD model in structure prediction.

Identification of Active Sites of Biomolecules II: Saccharide and Transition Metal Ion in Aqueous Solution

We discuss the coordination mechanism of Fe(III) and methyl-alpha-mannopyranoside in aqueous solution using a recently presented integrated approach comprising ab initio electronic structure calculations, molecular dynamics simulations, and mass spectrometric measurements. First principles Car-Parrinello molecular dynamics (CPMD) simulations find that a single Fe(III) ion interacts with specific hydroxyl groups of the saccharide in aqueous solution. Specifically, we find that one Fe(III) ion complexed to methyl-alpha-mannopyranoside also associates with two water molecules. These simulations are in accord with electrospray ionization mass spectrometry measurements involving guided ion beam hydration measurements, which reveal an optimal coordination number of four about the Fe(III) ion. CPMD simulations identified specific intramolecular and intermolecular hydrogen bonding interactions that have an impact on the conformation of the saccharide and on the coordination with Fe(III); in contrast, classical molecular dynamics simulations were insensitive to these effects. This study illustrates the strength of ab initio molecular dynamics simulations, chemical reactivity calculations, and natural partial charge analysis coupled with mass spectrometric measurements in identifying the active sites of biomolecules toward ligands and for studying the complexation and coordination chemistry associated with substrate and ligand interactions relevant to the design of biochemical syntheses, drugs, and biomarkers in medicine.