Chirp-wave Expansion of the Electron Wavefunctions in Atoms

The description of the electron wavefunctions in atoms is generalized to the fractional Fourier series. This method introduces a continuous and infinite number of chirp basis sets with linear variation of the frequency to expand the wavefunctions, in which plane-waves are a special case. The chirp characteristics of each basis set can be adjusted through a single parameter. Thus, the basis set cutoff can be optimized variationally. The approach is tested with the expansion of the electron wavefunctions in atoms, and it is shown that chirp basis sets substantially improve the convergence in the description of the electron density. We have found that the natural oscillations of the electron core states are efficiently described in chirp-waves

Extension of the B3LYP - Dispersion-Correcting Potential Approach to the Accurate Treatment of both Inter- and Intramolecular Interactions

We recently showed that dispersion-correcting potentials (DCPs), atom-centered Gaussian-type functions developed for use with B3LYP (J. Phys. Chem. Lett. 2012, 3, 1738-1744) greatly improved the ability of the underlying functional to predict non-covalent interactions. However, the application of B3LYP-DCP for the {\beta}-scission of the cumyloxyl radical led a calculated barrier height that was over-estimated by ca. 8 kcal/mol. We show in the present work that the source of this error arises from the previously developed carbon atom DCPs, which erroneously alters the electron density in the C-C covalent-bonding region. In this work, we present a new C-DCP with a form that was expected to influence the electron density farther from the nucleus. Tests of the new C-DCP, with previously published H-, N- and O-DCPs, with B3LYP-DCP/6-31+G(2d,2p) on the S66, S22B, HSG-A, and HC12 databases of non-covalently interacting dimers showed that it is one of the most accurate methods available for treating intermolecular interactions, giving mean absolute errors (MAEs) of 0.19, 0.27, 0.16, and 0.18 kcal/mol, respectively. Additional testing on the S12L database of complexation systems gave an MAE of 2.6 kcal/mol, showing that the B3LYP-DCP/6-31+G(2d,2p) approach is one of the best-performing and feasible methods for treating large systems dominated by non-covalent interactions. Finally, we showed that C-C making/breaking chemistry is well-predicted using the newly developed DCPs. In addition to predicting a barrier height for the {\beta}-scission of the cumyloxyl radical that is within 1.7 kcal/mol of the high-level value, application of B3LYP-DCP/6-31+G(2d,2p) to 10 databases that include reaction barrier heights and energies, isomerization energies and relative conformation energies gives performance that is amongst the best of all available dispersion-corrected density-functional theory approaches

DFT study of alkanethiol self-assembled monolayers on gold(111) surfaces

Selbstorganisierte Monoschichten (self-assembled monolayers, SAMs) von Alkanthiolen auf Goldoberflächen sind in der Nanotechnologie von großem Interesse. Auf der Au(111) Oberfläche bilden Alkanthiole hoch geordnete Strukturen mit ($\surd$3$\times$$\surd$3)R30° Gitter oder c(4$\times$2) Überstrukturmodulation. Fragen wie die Orientierung der Moleküle, die Oberflächenrekonstruktion und die Rolle der Kettenlänge werden jedoch noch erforscht. In dieser Studie von Alkanthiol SAMs werden sterische Effekte der Alkanketten in den ($\surd$3$\times$$\surd$3)R30° Strukturen und Rekonstruktionen für die c(4$\times$2) SAM von Ethanthiol untersucht. Die energetisch günstigste Struktur beruht auf einer Rekonstruktion durch Adatome, die von der Goldoberflache kommen und Leerstellen erzeugen. Ein plausibler Mechanismus für die Bildung von Gold Ätzgrübchen (etch pits, vacancy islands), folgt aus dem schrittweisen Auffüllen der Leerstellen, das die SAM weiter stabilisiert. Diese Struktur stimmt mit vielen experimentellen Daten überein

Fractional Fourier analysis of random signals and the notion of \u3b1 -Stationarity of the Wigner-Ville distribution

In this paper, a generalized notion of wide-sense \u3b1-stationarity for random signals is presented. The notion of stationarity is fundamental in the Fourier analysis of random signals. For this purpose, a definition of the fractional correlation between two random variables is introduced. It is shown that for wide-sense \u3b1-stationary random signals, the fractional correlation and the fractional power spectral density functions form a fractional Fourier transform pair. Thus, the concept of \u3b1-stationarity plays an important role in the analysis of random signals through the fractional Fourier transform for signals nonstationary in the standard formulation, but \u3b1-stationary. Furthermore, we define the \u3b1-Wigner-Ville distribution in terms of the fractional correlation function, in which the standard Fourier analysis is the particular case for \u3b1=pi2, and it leads to the Wiener-Khinchin theorem. \ua9 1991-2012 IEEE.Peer reviewed: YesNRC publication: Ye

A (nearly) universally applicable method for modeling noncovalent interactions using B3LYP

B3LYP is the most widely used density-functional theory (DFT) approach because it is capable of accurately predicting molecular structures and other properties. However, B3LYP is not able to reliably model systems in which noncovalent interactions are important. Here we present a method that corrects this deficiency in B3LYP by using dispersion-correcting potentials (DCPs). DCPs are utilized by simple modifications to input files and can be used in any computational package that can read effective-core potentials. Therefore, the technique requires no programming. DCPs (developed for H, C, N, and O) produce the best results when used in conjunction with 6-31+G(2d,2p) basis sets. The B3LYP-DCP approach was tested on the S66, S22, and HSG-A benchmark sets of noncovalently interacting dimers and trimers and was found to, on average, significantly outperform almost all other DFT-based methods that were designed to treat van der Waals interactions. Users of B3LYP who wish to model systems in which noncovalent interactions (viz., steric repulsion, hydrogen bonding, \u3c0-stacking) are present, should consider B3LYP-DCP.Peer reviewed: YesNRC publication: Ye

A density functional theory study of the reconstruction of gold (111) surfaces

We studied (p 7 1a3) gold (111) surface reconstructions within the DFT/PW91 approximation. Our findings clearly show that the reconstruction is energetically favorable in unreconstructed surfaces equal to or larger than the unit cell of the final reconstructed surface. Reconstructions in surfaces smaller than 3c2.95 nm in the [11\u3040] direction are not more stable than the unreconstructed surface, and this may explain why (p 7 1a3) type reconstructions have not been observed in subnanometer gold particles. We found that reconstructions with (22 7 1a3) and (23 7 1a3) unit cells, usually reported in experiments, are isoenergetic.Peer reviewed: YesNRC publication: Ye

Aplicación del metodo de dinamica molecular a la implantacion de iones de nitrogeno en hierro

El método de Dinámica Molecular se aplica para hacer simulaciones de implantación de iones en hierro cristalino. Visualización de trayectorias de iones implantados permite entender la diferencia entre procesos de penetración de iones en hierros monocristalino y plicristalino. Se muestra que la distribución de los iones de nitrógeno en el hierro policristalino difiere significativamente de lo ob-tenido para el hierro monocristalino. Se encuentra que la distribución espacial de los átomos de ni-trógeno implantados en el caso policristalino coincide bien con los datos experimentale

Density-Functional Theory with Dispersion-Correcting Potentials for Methane: Bridging the Efficiency and Accuracy Gap between High-Level Wave Function and Classical Molecular Mechanics Methods

Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD­(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD­(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD­(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G­(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system

A (Nearly) Universally Applicable Method for Modeling Noncovalent Interactions Using B3LYP

B3LYP is the most widely used density-functional theory (DFT) approach because it is capable of accurately predicting molecular structures and other properties. However, B3LYP is not able to reliably model systems in which noncovalent interactions are important. Here we present a method that corrects this deficiency in B3LYP by using dispersion-correcting potentials (DCPs). DCPs are utilized by simple modifications to input files and can be used in any computational package that can read effective-core potentials. Therefore, the technique requires no programming. DCPs (developed for H, C, N, and O) produce the best results when used in conjunction with 6-31+G­(2d,2p) basis sets. The B3LYP-DCP approach was tested on the S66, S22, and HSG-A benchmark sets of noncovalently interacting dimers and trimers and was found to, on average, significantly outperform almost all other DFT-based methods that were designed to treat van der Waals interactions. Users of B3LYP who wish to model systems in which noncovalent interactions (viz., steric repulsion, hydrogen bonding, π-stacking) are present, should consider B3LYP-DCP

Density-Functional Theory with Dispersion-Correcting Potentials for Methane: Bridging the Efficiency and Accuracy Gap between High-Level Wave Function and Classical Molecular Mechanics Methods

Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD­(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD­(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD­(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G­(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system