atomic charges
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2022 ◽  
Author(s):  
Zhaoxi Sun ◽  
Mao Wang ◽  
Qiaole He ◽  
Zhirong Liu

Molecular simulations are becoming a common tool for the investigation of dynamic and thermodynamic properties of novel solvents such as ionic liquids and the more recent deep eutectic solvents. As the electrostatics derived from ab initio calculations often fail to reproduce the experimental behaviors of these functionalized solvents, a common treatment is scaling the atomic charges to improve the accord between experimental and computational results for some selected properties, e.g., the density of the liquids. Although there are many computational benchmarks on structural properties of bulk ionic liquids, the choice of the best scaling parameter remains an open question. As these liquids are designed to solvate solutes, whether the solvation thermodynamics could be correctly described is of utmost importance in practical situations. Therefore, in the current work, we provide a thermodynamic perspective of this charge scaling issue directly from solute-solvent interactions. We present a comprehensive large-scale calculation of solvation free energies via nonequilibrium fast-switching simulations for a spectrum of molecules in ionic liquids, the atomic charges of which derived from ab initio calculations are scaled to find the best scaling factor that maximizes the prediction-experiment correlation. The density-derived choice of the scaling parameter as the estimate from bulk properties is compared with the solvation-free-energy-derived one. We observed that when the scaling factor is decreased from 1.0 to 0.5, the mass density exhibits a monotonically decreasing behavior, which is caused by weaker inter-molecular interactions produced by the scaled atomic charges. However, the solvation free energies of external agents do not show consistent monotonic behaviors like the bulk property, the underlying physics of which are elucidated to be the competing electrostatic and vdW responses to the scaling-parameter variation. More intriguingly, although the recommended value for charge scaling from bulk properties falls in the neighborhood of 0.6~0.7, solvation free energies calculated at this value are not in good agreement with the experimental reference. By modestly increasing the scaling parameter (e.g., by 0.1) to avoid over-scaling of atomic charges, the solute-solvent interaction free energy approaches the reference value and the quality of calculated solvation thermodynamics approaches the hydration case. According to this phenomenon, we propose a feasible way to obtain the best scaling parameter that produces balanced solute-solvent and solvent-solvent interactions, i.e., first scanning the density-scaling-factor profile and then adding ~0.1 to that solution. We further calculate the partition coefficient or transfer free energy of solutes from water to ionic liquids to provide another thermodynamic perspective of the charge scaling benchmark. Another central result of the current work is about the widely used force fields to describe bonded and vdW terms for ionic liquids derivatives. These pre-fitted transferable parameters are evaluated and refitted in a system-specific manner to provide a detailed assessment of the reliability and accuracy of these commonly used parameters. Component-specific refitting procedures unveil that the bond-stretching term is the most problematic part of the GAFF derivatives and the angle-bending term in some cases is also not accurate enough. Astonishingly, the torsional potential defined in these pre-fitted force fields performs extremely well.


Author(s):  
Frank Jensen

We review different models for introducing electrical polarization in force fields, with special focus on methods where polarization is modelled at the atomic charge level. While electric polarization has been...


Author(s):  
Istvan Hargittai

AbstractThere 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.


2021 ◽  
Author(s):  
Andrew S. Rosen ◽  
Victor Fung ◽  
Patrick Huck ◽  
Cody T. O'Donnell ◽  
Matthew K. Horton ◽  
...  

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.


Nano Letters ◽  
2021 ◽  
Author(s):  
Seongjoon Lim ◽  
Shangke Pan ◽  
Kefeng Wang ◽  
Alexey V. Ushakov ◽  
Ekaterina V. Sukhanova ◽  
...  

2021 ◽  
pp. 131990
Author(s):  
Naokazu Yoshikawa ◽  
Shoko Yamazaki ◽  
Ayaka Nishiyama ◽  
Yuki Yamashita ◽  
Nobuko Kanehisa ◽  
...  

Molecules ◽  
2021 ◽  
Vol 26 (20) ◽  
pp. 6314
Author(s):  
Mohamed Yacine Ameur Ameur Messaoud ◽  
Ghenia Bentabed-Ababsa ◽  
Ziad Fajloun ◽  
Monzer Hamze ◽  
Yury S. Halauko ◽  
...  

Five protocols were first compared for the copper-catalyzed C-N bond formation between 7-azaindole and aryl/heteroaryl iodides/bromides. The 1-arylated 7-azaindoles thus obtained were subjected to deprotometalation-iodolysis sequences using lithium 2,2,6,6-tetramethylpiperidide as the base and the corresponding zinc diamide as an in situ trap. The reactivity of the substrate was discussed in light of the calculated atomic charges and the pKa values. The behavior of the 1-arylated 7-azaindoles in direct iodination was then studied, and the results explained by considering the HOMO orbital coefficients and the atomic charges. Finally, some of the iodides generated, generally original, were involved in the N-arylation of indole. While crystallographic data were collected for fifteen of the synthesized compounds, biological properties (antimicrobial, antifungal and antioxidant activity) were evaluated for others.


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