An efficient method for computing the QTAIM topology of a scalar field: The electron density case

Rodríguez, Juan I.

doi:10.1002/jcc.23180

Cited by 93 publications

(82 citation statements)

References 19 publications

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“…Figure shows the gold cluster complex Au 4 −S−C 6 H 4 −S′−Au′ 4 , which is composed of a benzene ring linking two gold nanoclusters Au 4 through sulfur atoms . The nature of the sulfur–gold and gold–gold chemical bonds in these types of complexes was previously analyzed in detail by us using ZORA‐QTAIM . Thus, we focus here only on the new features on the QTAIM topology (chemical bonding) in these gold complex systems due to relativistic effects.…”

Section: Resultsmentioning

confidence: 99%

Molecular QTAIM Topology Is Sensitive to Relativistic Corrections

Anderson

Rodríguez

Ayers

et al. 2019

Chemistry A European J

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The topology of the molecular electron density of benzene dithiol gold cluster complex Au4−S−C6H4−S′−Au′4 changed when relativistic corrections were made and the structure was close to a minimum of the Born–Oppenheimer energy surface. Specifically, new bond paths between hydrogen atoms on the benzene ring and gold atoms appeared, indicating that there is a favorable interaction between these atoms at the relativistic level. This is consistent with the observation that gold becomes a better electron acceptor when relativistic corrections are applied. In addition to relativistic effects, here, we establish the sensitivity of molecular topology to basis sets and convergence thresholds for geometry optimization.

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Section: Resultsmentioning

confidence: 99%

Molecular QTAIM Topology Is Sensitive to Relativistic Corrections

Anderson

Rodríguez

Ayers

et al. 2019

Chemistry A European J

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“…However, this algorithm has an important issue: there are no boundaries on the NR method when it is launched over each point of the grid. This is the main reason why the Rodríguez' algorithm is not efficient, as himself discussed in his report …”

Section: Methodsmentioning

confidence: 99%

“…The critical points,

{\overset{R}{true}}_{c}

, of the electron density are those points where

\nabla ρ ({\overset{R}{true}}_{c}) = \vec{0} .

The Rodríguez’ algorithm to find critical points of the electron density, can be summarized in the following steps: The molecule to be studied is immersed in a 3D‐grid. The NR method is applied over each point of the grid. This is an iterative method, where the gradient of the electron density is expanded through a Taylor series, around

{\overset{r}{true}}_{i}

, to first order

\nabla ρ ({\overset{r}{true}}_{i + 1}) = \nabla ρ ({\overset{r}{true}}_{i}) + H |_{{\overset{r}{true}}_{i}} ({\overset{r}{true}}_{i + 1} - {\overset{r}{true}}_{i}) .

This equation yields an iterative method to obtain

{\overset{r}{true}}_{i + 1}

, because at this point

\nabla ρ ({\overset{r}{true}}_{i + 1}) = \vec{0}

.…”

Section: Methodsmentioning

confidence: 99%

“…Grid‐based methods (GBMs) alleviate part of the computational work because the gradient can be evaluated numerically and consequently, this approach offers an alternative to find critical points of any scalar field defined on a grid . In 2013, Rodríguez proposed an algorithm to find critical points, of the electron density, based on GBM . The main point of the Rodríguez' report steams on the distribution of the Newton–Raphson (NR) method, launched on each point of the grid over the servers where the application is executed.…”

Section: Introductionmentioning

confidence: 99%

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Grid‐based algorithm to search critical points, in the electron density, accelerated by graphics processing units

Hernández‐Esparza¹,

Mejía²,

Zapata–Escobar³

et al. 2014

J Comput Chem

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Using a grid-based method to search the critical points in electron density, we show how to accelerate such a method with graphics processing units (GPUs). When the GPU implementation is contrasted with that used on central processing units (CPUs), we found a large difference between the time elapsed by both implementations: the smallest time is observed when GPUs are used. We tested two GPUs, one related with video games and other used for high-performance computing (HPC). By the side of the CPUs, two processors were tested, one used in common personal computers and other used for HPC, both of last generation. Although our parallel algorithm scales quite well on CPUs, the same implementation on GPUs runs around 10× faster than 16 CPUs, with any of the tested GPUs and CPUs. We have found what one GPU dedicated for video games can be used without any problem for our application, delivering a remarkable performance, in fact; this GPU competes against one HPC GPU, in particular when single-precision is used.

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“…28 Finally, Voronoi 29 , natural bonding orbitals (NBO) 30 , quantum theory of atoms in molecules (QTAIM) 31,32 approaches were used to determine net charges to describe the possibility of charge transfer phenomena on the complexes.…”

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confidence: 99%

RELATIVISTIC-DFT STUDY OF THE ELECTRONIC STRUCTURE, BONDING AND ENERGETIC OF THE [ReF8]־ AND [UF8]2- IONS

Rabanal‐León¹,

Arratia‐Pérez²

2013

J. Chil. Chem. Soc.

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In this study we evaluated the importance of the relativistic effects (scalar and spin-orbit) on the description of the electronic structure, bonding and the energetic of the [ReF 8 ] -and [UF 8 ] 2-ions. We described the bonding interaction between ligands and metal center using the energy decomposition analysis (EDA) proposed by Morokuma and Ziegler, in which it can be appreciated a strong ionic behavior for both ions since the electrostatic interaction energy (∆E Elestat ) is greater than the orbitalic interaction energy (∆E Orb ). Furthermore, a qualitative analysis using the mapping of the electrostatic potential over the total electronic density evidence an increase of the ionic character, as well as, the polarization of the electronic density as U > Re. The electron localization function (ELF) corroborates the bonding analysis because of the lack of di-synaptic basins on the metal-ligand bonding region.

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An efficient method for computing the QTAIM topology of a scalar field: The electron density case

Cited by 93 publications

References 19 publications

Molecular QTAIM Topology Is Sensitive to Relativistic Corrections

Molecular QTAIM Topology Is Sensitive to Relativistic Corrections

Grid‐based algorithm to search critical points, in the electron density, accelerated by graphics processing units

RELATIVISTIC-DFT STUDY OF THE ELECTRONIC STRUCTURE, BONDING AND ENERGETIC OF THE [ReF8]־ AND [UF8]2- IONS

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An efficient method for computing the QTAIM topology of a scalar field: The electron density case

Cited by 93 publications

References 19 publications

Molecular QTAIM Topology Is Sensitive to Relativistic Corrections

Molecular QTAIM Topology Is Sensitive to Relativistic Corrections

Grid‐based algorithm to search critical points, in the electron density, accelerated by graphics processing units

RELATIVISTIC-DFT STUDY OF THE ELECTRONIC STRUCTURE, BONDING AND ENERGETIC OF THE [ReF8]&#1470; AND [UF8]2- IONS

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RELATIVISTIC-DFT STUDY OF THE ELECTRONIC STRUCTURE, BONDING AND ENERGETIC OF THE [ReF8]־ AND [UF8]2- IONS