Paradigms and paradoxes: fractional electron charge

There is hardly a generic connection between the partial atomic charges, a useful concept in chemistry, and the “fractionalization” of the electron accomplished under extreme experimental conditions in solid samples. Nonetheless, there is a relationship on a philosophical level. There is no information of who first introduced the concept of partial atomic charges in chemistry. In contrast, the physicists whose experiment turned the electron into excitations carrying a partial charge and whose theory provided the interpretation received the Nobel Prize for their discoveries.

High-Throughput Predictions of Metal–Organic Framework Electronic Properties: Theoretical Challenges, Graph Neural Networks, and Data Exploration

With the goal of accelerating the design and discovery of metal–organic frameworks (MOFs) for (opto)electronic and energy storage applications, we present a new dataset of predicted electronic structure properties for thousands of MOFs carried out using multiple density functional approximations. Compared to more accurate hybrid functionals, we find that the widely used PBE generalized gradient approximation (GGA) functional severely underpredicts MOF band gaps in a largely systematic manner for semi-conductors and insulators without magnetic character. However, an even larger and less predictable disparity in the band gap prediction is present for MOFs with open-shell 3d transition metal cations. With regards to partial atomic charges, we find that different density functional approximations predict similar charges overall, although hybrid functionals tend to shift electron density away from the metal centers and onto the ligand environments compared to the GGA point of reference. Much more significant differences in partial atomic charges are observed when comparing different charge partitioning schemes. We conclude by using the new dataset of computed MOF properties to train machine learning models that can rapidly predict MOF band gaps for all four density functional approximations considered in this work, paving the way for future high-throughput screening studies. To encourage exploration and reuse of the theoretical calculations presented in this work, the curated data is made publicly available via an interactive and user-friendly web application on the Materials Project.

Optimized SQE atomic charges for peptides accessible via a web application

Background Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity Equalization Method (EEM), Charge Equilibration method (QEq), and Extended QEq (EQeq). They all are fast, even for large molecules, but require empirical parameters. However, even these advanced methods have limitations—e.g., their application for peptides, proteins, and other macromolecules is problematic. An empirical charge calculation method that is promising for peptides and other macromolecular systems is the Split-charge Equilibration method (SQE) and its extension SQE+q0. Unfortunately, only one parameter set is available for these methods, and their implementation is not easily accessible. Results In this article, we present for the first time an optimized guided minimization method (optGM) for the fast parameterization of empirical charge calculation methods and compare it with the currently available guided minimization (GDMIN) method. Then, we introduce a further extension to SQE, SQE+qp, adapted for peptide datasets, and compare it with the common approaches EEM, QEq EQeq, SQE, and SQE+q0. Finally, we integrate SQE and SQE+qp into the web application Atomic Charge Calculator II (ACC II), including several parameter sets. Conclusion The main contribution of the article is that it makes SQE methods with their parameters accessible to the users via the ACC II web application (https://acc2.ncbr.muni.cz) and also via a command-line application. Furthermore, our improvement, SQE+qp, provides an excellent solution for peptide datasets. Additionally, optGM provides comparable parameters to GDMIN in a markedly shorter time. Therefore, optGM allows us to perform parameterizations for charge calculation methods with more parameters (e.g., SQE and its extensions) using large datasets. Graphic Abstract

The Charge State of Pt in Binary Compounds and Synthetic Minerals Determined by X-ray Absorption Spectroscopy and Quantum Chemical Calculations

The binary synthetic compounds of Pt with chalcogens (O, S, Se, Te), pnictogens (As, Sb, Bi), and intermetallic compounds with Ga, In, and Sn of various stoichiometry were studied via X-ray absorption spectroscopy (XAS). The partial atomic charges of Pt in the compounds were computed using quantum chemical density functional theory (DFT) based methods: the Bader (QTAIM) method, and the density-derived electrostatic and chemical (DDEC6) approach. Strong positive correlations were established between the calculated partial atomic charges of Pt and the electronegativity (χ) of ligands. The partial charge of Pt in PtL2 compounds increases much sharply when the ligand electronegativity increases than the Pt partial charge in PtL compounds. The effect of the ligand-to-Pt atomic ratio on the calculated Pt partial charge depended on ligand electronegativity. The DDEC6 charge of Pt increases sharply with the growth of the number of ligands in PtSn (n = 1, 2; electronegativity χ(S) >> χ(Pt)), weakly depends on the phase composition in PtTen (n = 1, 2; χ(Te) is slightly lower than χ(Pt)), and decreases (becomes more negative) with increase of the ligand-to-Pt ratio in intermetallic compounds with electron donors (χ(L) < χ(Pt), L = Ga, In, Sn). According to XANES spectroscopy, the number of 5d (L2,3 absorption edges) and 6p (L1-edge) electrons at the Pt site decreased when ligand electronegativity increased in chalcogenides and pnictides groups. An increase of the ligand-to-Pt ratio resulted in the increase of the Pt L3-edge white line intensity and area in all studied compounds. In the case of chalcogenides and pnictides, this behavior was consistent with the electronegativity rule as it indicated a loss of Pt 5d electrons caused by the increase of the number of ligands, i.e., acceptors of electrons. However, in the case of ligands–electron donors (Te, Sn, Ga, In) this observation is in apparent contradiction with the electronegativity arguments as it indicates the increase of the number of Pt 5d-shell vacancies (holes) with the increase of the number of the ligands, for which the opposite trend is expected. This behavior can be explained in the framework of the charge compensation model. The loss of the Pt d-electrons in compounds with low ligand electronegativity (χ(Pt) > χ(L)) was overcompensated by the gain of the hybridized s-p electron density, which was confirmed by Pt L1 - edge spectra analysis. As a result, the total electron density at the Pt site followed the electronegativity rule, i.e., it increased with the growth of the number of the ligands-electron donors. The empirical correlations between the Pt partial atomic charges and parameters of XANES spectral features were used to identify the state of Pt in pyrite, and can be applied to determine the state of Pt in other ore minerals.

Implementação dos parâmetros da quitosana no campo de força OPLS-AA para simulações da quitosana por dinâmica molecular

In this work, the molecular dynamics of the finite biopolymer of chitosan in the force field OPLS-AA was made. DFT calculations for structural optimization were performed in the ORCA program with the B3LYP functional and 6-31G base function. The partial atomic charges of Chitosan were obtained by the RESP methodology. The molecular structure of chitosan was structurally evaluated in terms of RMSD and ring overlap. A comparison between the chitosan parameters in OPLS-AA and GROMOS53a6 force-field indicated that in OPLS-AA energy and structural stability are achieved more quickly. The results obtained are in accordance with reports in the literature for this molecule in the GROMOS53A6 force field.