scholarly journals Optimized Atomic Partial Charges and Radii Defined by Radical Voronoi Tessellation of Bulk Phase Simulations

Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 1875
Author(s):  
Martin Brehm ◽  
Martin Thomas
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Voronoi Tessellation ◽  
Software Tool ◽  
Bulk Phase ◽  
Basis Set ◽  
Total Electron Density ◽  
Total Electron ◽  
Partial Charges ◽  
Atomic Radii

We present a novel method for the computation of well-defined optimized atomic partial charges and radii from the total electron density. Our method is based on a two-step radical Voronoi tessellation of the (possibly periodic) system and subsequent integration of the total electron density within each Voronoi cell. First, the total electron density is partitioned into the contributions of each molecule, and subsequently the electron density within each molecule is assigned to the individual atoms using a second set of atomic radii for the radical Voronoi tessellation. The radii are optimized on-the-fly to minimize the fluctuation (variance) of molecular and atomic charges. Therefore, our method is completely free of empirical parameters. As a by-product, two sets of optimized atomic radii are produced in each run, which take into account many specific properties of the system investigated. The application of an on-the-fly interpolation scheme reduces discretization noise in the Voronoi integration. The approach is particularly well suited for the calculation of partial charges in periodic bulk phase systems. We apply the method to five exemplary liquid phase simulations and show how the optimized charges can help to understand the interactions in the systems. Well-known effects such as reduced ion charges below unity in ionic liquid systems are correctly predicted without any tuning, empiricism, or rescaling. We show that the basis set dependence of our method is very small. Only the total electron density is evaluated, and thus, the approach can be combined with any electronic structure method that provides volumetric total electron densities—it is not limited to Hartree–Fock or density functional theory (DFT). We have implemented the method into our open-source software tool TRAVIS.

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study

2014 ◽  
Vol 70 (3) ◽  
pp. 568-579 ◽  
Author(s):  
Gnanasekaran Rajalakshmi ◽  
Venkatesha R. Hathwar ◽  
Poomani Kumaradhas
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Direct Methods ◽  
Hirshfeld Surface ◽  
Basis Set ◽  
Total Electron Density ◽  
Total Electron

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max= 1.1 Å−1] measured at 100 (2) K. The structure was solved by direct methods usingSHELXS97 and refined bySHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen–Coppens multipole formalism implemented in theXDsoftware. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained fromCRYSTAL09at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N—H...N and N—H...O hydrogen bonds, in which the N3—H3B...N1 and N3—H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.

scholarly journals Estimation of the Efficiency of Corrosion Inhibition by Zn-Dithiocarbamate Complexes: a Theoretical Study

2021 ◽  
pp. 3323-3335
Author(s):  
Mustafa M. Kadhim ◽  
Layla A. Al. Juber ◽  
Ahmed S. M. Al-Janabi
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Room Temperature ◽  
Theoretical Study ◽  
Energy Gap ◽  
Basis Set ◽  
Total Electron Density ◽  
Functional Theory ◽  
Total Electron ◽  
Homo Lumo

    Seven Zn-dithiocarbamate complexes were suggested as corrosion inhibitors. Density functional theory (DFT) was used to predict the ability of inhibition. Room temperature conditions were applied to suggest the optimization of complexes, physical properties, and corrosion parameters. In addition, the HOMO, LUMO, dipole moment, energy gap, and other parameters were used to compare the inhibitors efficiency. Gaussian 09 software with LanL2DZ basis set was used. Total electron density (TED) and electrostatic surface potential (ESP) were utilized to show the sites of adsorption according to electron density.

Acrylonitrile (AN)–Cu9(100) interfaces: Electron distribution and nature of bonded interactions

2003 ◽  
Vol 81 (6) ◽  
pp. 542-554 ◽  
Author(s):  
Petar M Mitrasinovic
Keyword(s):  
Electron Density ◽  
Molecular Orbital ◽  
Density Functional ◽  
Electron Distribution ◽  
Atomic Orbital ◽  
Interfacial Interactions ◽  
Total Electron Density ◽  
Total Electron ◽  
Topological Features ◽  
The One

There is a fundamental interest in the investigation of the interfacial interactions and charge migration processes between organic molecules and metallic surfaces from a theoretical standpoint. Quantum mechanical (QM) concepts of bonding are contrasted, and the vital importance of using combined QM methods to explore the nature of the interfacial interactions is established. At the one-electron level, the charge distribution and nature of bonded interactions at the AN–Cu9(100) (neutral and charged (–1)) interfaces are investigated by both the Becke (B) – Vosko (V) – Wilk (W) – Nusair (N)/DZVP density functional theory (DFT) method and the MP2/6–31+G* strategy within the conceptual framework provided by natural bond orbital (NBO) – natural atomic orbital (NAO) population analysis and Atoms-In-Molecules (AIM) theory. By this approach, the interfacial interactions are given physical definitions free of any assumptions and are visualized by using the topological features of the total electron density. A natural link between the electron density on the one side and the shapes (not energies) of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) on the other side is clarified. The question of whether the spatial extents of the HOMO and LUMO resemble the corresponding spatial maps of the negative (charge locally concentrated) and positive (charge locally depleted) Laplacian of the total electron density in [AN–Cu9(100)]–1 is addressed.Key words: AN–Cu9(100) interfaces, NBO–NAO population, electron distribution, AIM, bonded interactions.

Revisiting the charge density analysis of 2,5-dichloro-1,4-benzoquinone at 20 K

2017 ◽  
Vol 73 (4) ◽  
pp. 654-659 ◽  
Author(s):  
Zhijie Chua ◽  
Bartosz Zarychta ◽  
Christopher G. Gianopoulos ◽  
Vladimir V. Zhurov ◽  
A. Alan Pinkerton
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Topological Analysis ◽  
Diffraction Measurement ◽  
X Ray Diffraction ◽  
Total Electron Density ◽  
Total Electron ◽  
Structure Factors ◽  
Density Analysis ◽  
Experimental Charge Density

A high-resolution X-ray diffraction measurement of 2,5-dichloro-1,4-benzoquinone (DCBQ) at 20 K was carried out. The experimental charge density was modeled using the Hansen–Coppens multipolar expansion and the topology of the electron density was analyzed in terms of the quantum theory of atoms in molecules (QTAIM). Two different multipole models, predominantly differentiated by the treatment of the chlorine atom, were obtained. The experimental results have been compared to theoretical results in the form of a multipolar refinement against theoretical structure factors and through direct topological analysis of the electron density obtained from the optimized periodic wavefunction. The similarity of the properties of the total electron density in all cases demonstrates the robustness of the Hansen–Coppens formalism. All intra- and intermolecular interactions have been characterized.

scholarly journals Understanding the Dipole Moment of Liquid Water from a Self-Attractive Hartree Decomposition

2020 ◽  
Author(s):  
Tianyu Zhu ◽  
Troy Van Voorhis
Keyword(s):  
Dipole Moment ◽  
Dielectric Properties ◽  
Liquid Water ◽  
Density Functional ◽  
Bulk Water ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Design Strategies ◽  
Total Electron Density ◽  
Total Electron

<p>The dipole moment of a single water molecule in liquid water has been a critical concept for understanding water’s dielectric properties. In this work, we investigate the dipole moment of liquid water through a self-attractive Hartree (SAH) decomposition of total electron density computed by density functional theory, on water clusters sampled from ab initio molecular dynamics simulation of bulk water. By adjusting one parameter that controls the degree of density localization, we reveal two distinct pictures of water dipoles that are consistent with bulk dielectric properties: a localized picture with smaller and less polarizable monomer dipoles, and a delocalized picture with larger and more polarizable monomer dipoles. We further uncover that the collective dipole-dipole correlation is stronger in the localized picture and is key to connecting individual dipoles with bulk dielectric properties. Based on these findings, we suggest considering both individual and collective dipole behaviors when studying the dipole moment of liquid water, and propose new design strategies for developing water models.</p>

scholarly journals Understanding the Dipole Moment of Liquid Water from a Self-Attractive Hartree Decomposition

2020 ◽  
Author(s):  
Tianyu Zhu ◽  
Troy Van Voorhis
Keyword(s):  
Dipole Moment ◽  
Dielectric Properties ◽  
Liquid Water ◽  
Density Functional ◽  
Bulk Water ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Design Strategies ◽  
Total Electron Density ◽  
Total Electron

<p>The dipole moment of a single water molecule in liquid water has been a critical concept for understanding water’s dielectric properties. In this work, we investigate the dipole moment of liquid water through a self-attractive Hartree (SAH) decomposition of total electron density computed by density functional theory, on water clusters sampled from ab initio molecular dynamics simulation of bulk water. By adjusting one parameter that controls the degree of density localization, we reveal two distinct pictures of water dipoles that are consistent with bulk dielectric properties: a localized picture with smaller and less polarizable monomer dipoles, and a delocalized picture with larger and more polarizable monomer dipoles. We further uncover that the collective dipole-dipole correlation is stronger in the localized picture and is key to connecting individual dipoles with bulk dielectric properties. Based on these findings, we suggest considering both individual and collective dipole behaviors when studying the dipole moment of liquid water, and propose new design strategies for developing water models.</p>

Theoretical investigation of the stability, reactivity, and the interaction of methyl-substituted peridinium-based ionic liquids

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Emmanuel A. Bisong ◽  
Hitler Louis ◽  
Tomsmith O. Unimuke ◽  
Victoria M. Bassey ◽  
John A. Agwupuye ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Electron Density ◽  
Density Functional ◽  
Natural Bond Orbital ◽  
Stabilization Energy ◽  
Basis Set ◽  
Bond Critical Point ◽  
Electronic Interaction ◽  
Donor And Acceptor ◽  
The Stability

Abstract This research work focuses on the reactivity, stability, and electronic interaction of pyridinium hydrogen nitrate (PHN)-based ionic liquids and the influence of methyl substituent on this class of ionic liquids: Ortho- (O-MPHN), meta- (M-MPHN), and para- (P-MPHN) substitution. Natural bond orbital (NBO) calculations were performed at the density functional theory (DFT) with Becke’s Lee Yang and Parr functional (B3LYP) methods and DFT/B3LYP/6-311++G(d,p) as basis set using GAUSSIAN 09W and GAUSSVIEW 6.0 software and the most important interaction between donor (Filled Lewis-type NBO’s) and the acceptor (vacant non-Lewis NBOs) were observed. From our natural bond orbital (NBO) result, it could be deduced that the higher the stabilization energy value, the greater the interaction between the donor and acceptor NBOs. The stability of the studied compounds is said to follow the order from O-MPHN > PHN > P-MPHN > M-MPHN based on the hyperconjugative interaction (stabilization energy) of the most significant interaction. The result of the highest occupied molecular orbital (HOMO), shows that PHN has the highest HOMO while the substituted derivatives have similar HOMO values between −7.70 and −7.98 eV thus PHN complex is the best electron donor while the substituted derivatives act as electron acceptors due to the presence of methyl group substituent which is observed to be electron deficient as a result of its withdrawal effect from the aromatic ring. Furthermore, the electron density, real space functions such as energy density and Laplacian of electron density at bond critical point (BCP) of the hydrogen bond interaction of the studied compounds were analyzed using Multifunctional Wavefunction analyzer software version 3.7 and it was observed that the hydrogen at position 6 and oxygen at position 11 (H6–O11) of M-methyl pyridinium nitrate with bond distance of 4.59 (Å) gave binding energy with the strongest electrostatic interaction between the cation and anion of the compounds under investigation. We also observed from our results that, substitution at the ortho position enhances the stability and strengthen the extent of charge transfer. This therefore implies that substitution at ortho position is more favorable for inter- and intramolecular interactions resulting to stabilization of the studied molecules.

Sign in / Sign up

Export Citation Format

Share Document