DensToolKit: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields

Solano-Altamirano, J. Manuel; Hernández-Pérez, Julio M.

doi:10.1016/j.cpc.2015.07.005

Cited by 23 publications

(15 citation statements)

References 18 publications

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“…All calculations were carried out using Gaussian 09 [ 40 ]. The topological analysis of the electron density was carried out using DensToolKit program [ 41 ].…”

Section: Methodsmentioning

confidence: 99%

Looking Inside the Intramolecular C−H∙∙∙O Hydrogen Bond in Lactams Derived from α-Methylbenzylamine

et al. 2017

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Recently, strong evidence that supports the presence of an intramolecular C−H···O hydrogen bond in amides derived from the chiral auxiliary α-methylbenzylamine was disclosed. Due to the high importance of this chiral auxiliary in asymmetric synthesis, the inadvertent presence of this C−H···O interaction may lead to new interpretations upon stereochemical models in which this chiral auxiliary is present. Therefore, a series of lactams containing the chiral auxiliary α-methylbenzylamine (from three to eight-membered ring) were theoretically studied at the MP2/cc-pVDZ level of theory with the purpose of studying the origin and nature of the C−Hα···O interaction. NBO analysis revealed that rehybridization at C atom of the C−Hα bond (s-character at C is ~23%) and the subsequent bond polarization are the dominant effect over the orbital interaction energy n(O)→σ*C−Hα (E(2) < 2 kcal/mol), causing an important shortening of the C−Hα bond distance and an increment in the positive charge in the Hα atom.

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“…All calculations were carried out using Gaussian 09 [ 40 ]. The topological analysis of the electron density was carried out using DensToolKit program [ 41 ].…”

Section: Methodsmentioning

confidence: 99%

Looking Inside the Intramolecular C−H∙∙∙O Hydrogen Bond in Lactams Derived from α-Methylbenzylamine

et al. 2017

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“…In our laboratory, we have developed the Graphics Processing Units for Atoms and Molecules (GPUAM) code to evaluate several scalar and vector quantum chemistry fields coupled with the Atoms in Molecules (AIM) analysis . It is worth to mention that there are several codes with some of these capabilities . However, GPUAM has been designed to use heterogeneous computational resources.…”

Section: Evaluation Of Quantum Chemistry Fields By Using Gpusmentioning

confidence: 99%

GPUs as boosters to analyze scalar and vector fields in quantum chemistry

Hernández‐Esparza

Vázquez‐Mayagoitia

Soriano-Agueda

et al. 2018

Int J of Quantum Chemistry

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The analysis of scalar and vector fields in quantum chemistry is an essential task for the computational chemistry community, where such quantities must be evaluated rapidly to perform a particular study. For example, the atoms in molecules approach proposed by Bader has become popular; however, this method demands significant computational resources to compute the involved tasks in short times. In this article, we discuss the importance of graphics processing units (GPU) to analyze electron density, and related fields, implementing several scalar, and vector fields within the graphics processing units for atoms and molecules (GPUAM) code developed by a group of the Universidad Autónoma Metropolitana in México City. With this application, the quantum chemistry community can perform demanding computational tasks on a desktop, where CPUs and GPUs are used to their maximum capabilities. The performance of GPUAM is tested in several systems and over different GPUs, where a GPU installed in a workstation converts it to a robust high‐performance computing system.

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“…in which b i and b tot are the hyperpolarizability along ith direction and total hyperpolarizability,r espectively.C hemical bonding analysis was carried out by using the adaptive natural density partitioning (AdNDP) [56,57] method, which is an atural bonding orbital (NBO) [58,59] method extension. To further verify the AdNDP analysis results, we performed calculations of electron localization function (ELF) [60] and Laplacian topology by using the Denstoolkit [61] and AIMALL [62] packages, respectively.V ertical electron detachment energies were calculated by using the time-dependent density functional theory (TD-DFT) method, [63] CCSD(T)/aug-cc-pVTZ, and outer valence green function (OVGF) method. [64][65][66]…”

Section: Computationalmethodsmentioning

confidence: 99%

Inorganic Molecular Electride Mg₄O₃: Structure, Bonding, and Nonlinear Optical Properties

Kulichenko

Fedik

Bozhenko

et al. 2019

Chemistry A European J

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Growing demands of material science and, in particular, in the field of nonlinear optics (NLO) encourage us to look for stable highly polarizable molecules with excess diffuse electrons. An unusual class of compounds called electrides comply with these requirements. Many attempts have been made, yet only few electrides have been synthesized as solids and none of them as molecular species. In this paper, a new theoretically designed molecular species with electride characteristics is reported. The idea of this molecular electride comes from the formation of electride‐like features in the MgO crystal with defect F‐centers. The geometry of the investigated molecule can be described as a Mg4O4 cube with one oxygen atom removed. In Mg4O3, two 3s electrons are pushed out from the inner area of the molecule forming a diffuse electride multicentered bond. Our calculations show that this electride‐like cluster possesses a noticeably large first hyperpolarizability β=5733 au. At the same time, a complete cube Mg4O4 and Mg4O32+ without electride electron pair have much smaller β: 0 au and 741 au, respectively. This fact indicates the decisive role of the electride electron pair in NLO properties. Additionally, vertical detachment energies of isomers (VDE), excitation energies ΔE, polarizabilities α, and IR spectra were calculated. These properties, including β, are supposed to be observable experimentally and can serve as indirect evidence of the stable molecular electride formation.

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DensToolKit: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields

Cited by 23 publications

References 18 publications

Looking Inside the Intramolecular C−H∙∙∙O Hydrogen Bond in Lactams Derived from α-Methylbenzylamine

Looking Inside the Intramolecular C−H∙∙∙O Hydrogen Bond in Lactams Derived from α-Methylbenzylamine

GPUs as boosters to analyze scalar and vector fields in quantum chemistry

Inorganic Molecular Electride Mg₄O₃: Structure, Bonding, and Nonlinear Optical Properties

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DensToolKit: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields

Cited by 23 publications

References 18 publications

Looking Inside the Intramolecular C−H∙∙∙O Hydrogen Bond in Lactams Derived from α-Methylbenzylamine

Looking Inside the Intramolecular C−H∙∙∙O Hydrogen Bond in Lactams Derived from α-Methylbenzylamine

GPUs as boosters to analyze scalar and vector fields in quantum chemistry

Inorganic Molecular Electride Mg4O3: Structure, Bonding, and Nonlinear Optical Properties

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Inorganic Molecular Electride Mg₄O₃: Structure, Bonding, and Nonlinear Optical Properties