Journal of Computational Chemistry

doi: 10.1002/jcc.27136pmid: N/A

Mó, Otilia; Lamsabhi, Al Mokhtar; Guillemin, Jean‐Claude; Yáñez, Manuel

doi: 10.1002/jcc.27223pmid: 37698484

The structure, stability, and bonding characteristics of 1,1‐ and 1,2‐ethenediol, their radical cations, and their protonated and deprotonated species were investigated using high‐level ab initio G4 calculations. The electron density of all the neutral and charged systems investigated was analyzed using the QTAIM, ELF, and NBO approaches. The vertical ionization potential (IP) of the five stable tautomers of 1,2‐ethenediol and the two stable tautomers of 1,1‐ethenediol go from 11.81 to 12.27 eV, whereas the adiabatic ones go from 11.00 to 11.72 eV. The adiabatic ionization leads to a significant charge delocalization along the O‐C‐C‐O skeleton. The most stable protonated form of (Z)‐1,2‐ethenediol can be reached by the protonation of both the anti‐anti and the syn‐anti conformers, whereas the most stable deprotonated form arises only from the syn‐anti one. Both charged species are extra‐stabilized by the formation of an O‐H···O intramolecular hydrogen bond (IHB) which is not found in the neutral system. (Z)‐1,2‐ethenediol is predicted to be less stable, less basic, and more acidic than its cis‐glycolaldehyde isomer. The most stable protonated species of (E)‐1,2‐ethenediol comes from its syn‐syn conformer, although the anti‐anti conformer is the most basic one. Contrarily, the three conformers yield a common deprotonated species, so their acidity follows exactly their relative stability. Again, the (E)‐1,2‐ethenediol is predicted to be less stable, less basic, and more acidic than its trans‐glycolaldehyde isomer. Neither the neutral nor the protonated or the deprotonated forms of 1,1‐ethenediol show the formation of any O‐H···O IHB. The most stable protonated species is formed by the protonation of any of the two tautomers, but the most stable deprotonated form arises exclusively from the syn‐anti neutral conformer. The conformers of 1,1‐ethenediol are much less stable and significantly less basic than their isomer, acetic acid, and only slightly more acidic.

Mi, Xiao Peng; Lu, Hui; Xu, Tianlv; Früchtl, Herbert; Mourik, Tanja; Paterson, Martin J.; Kirk, Steven R.; Jenkins, Samantha

doi: 10.1002/jcc.27225pmid: 37698200

A pair of simulated left and right circularly polarized ultra‐fast laser pulses of duration 20 femtoseconds that induce a mixture of excited states are applied to ethane. The response of the electron dynamics is investigated within the next generation quantum theory of atoms in molecules (NG‐QTAIM) using third‐generation eigenvector‐trajectories which are introduced in this work. This enables an analysis of the mechanical and chiral properties of the electron dynamics of ethane without needing to subject the C‐C bond to external torsions as was the case for second‐generation eigenvector‐trajectories. The mechanical properties, in particular, the bond‐flexing and bond‐torsion were found to increase depending on the plane of the applied laser pulses. The bond‐flexing and bond‐torsion, depending on the plane of polarization, increases or decreases after the laser pulses are switched off. This is explainable in terms of directionally‐dependent effects of the long‐lasting superpositions of excited states. The chiral properties correspond to the ethane molecule being classified as formally achiral consistent with previous NG‐QTAIM investigations. Future planned investigations using ultra‐fast circularly polarized lasers are briefly discussed.

Liu, Lina; Wei, Zhihong; Chen, Qiang; Shen, Chaoren; Shen, Tonghao; Tian, Xinxin; Li, Si‐Dian

doi: 10.1002/jcc.27226pmid: 37698288

Using full configuration interaction (FCI) and multi‐reference configuration interaction methods (MRCI), reliable geometrical and energetic references for Bn (n = 1–4) clusters were established. The accuracy of the computed results was confirmed by comparison with available experimental data. Benchmark calculations indicated that B97D3, B97D, VSXC, HCTH407, BP86 and CCSD(T) methods provided reasonable results for structural parameters, with mean absolute error (MAEs) within 0.020 Å. Among the tested density functional theory (DFT) methods, the VSXC functional showed the best performance in predicting the relative energies of B1B4 with a MAE of 12.8 kJ mol−1. Besides, B1B95, B971, TPSS, B3LYP, and BLYP functionals exhibited reasonable performance with MAE values of less than 15.0 kJ mol−1. T1 diagnostic values between 0.035 and 0.109 at the CCSD(T) level revealed strong correlations in B2B4 clusters, highlighting the need for caution in using CCSD(T) as an energy reference for small boron clusters. The methods of CCSDT, CCSDT(Q) and CCSDT[Q], which incorporate three‐electron and four‐electron excitations, effectively improved the accuracy of the energy calculations.

Petrova, Vlada V.; Domnin, Anton V.; Porozov, Yuri B.; Kuliaev, Pavel O.; Solovev, Yaroslav V.

doi: 10.1002/jcc.27227pmid: 37772443

Prediction of catalytic reaction efficiency is one of the most intriguing and challenging applications of machine learning (ML) algorithms in chemistry. In this study, we demonstrated a strategy for utilizing ML protocols applied to Quantum Theory of Atoms In Molecules (QTAIM) parameters to predict the ability of the A17 L47K catalytic antibody to covalently capture organophosphate pesticides. We found that the novel “composite” DFT functional B97‐3c could be effectively employed for fast and accurate initial geometry optimization, aligning well with the input dataset creation. QTAIM descriptors proved to be well‐established in describing the examined dataset using density‐based and hierarchical clustering algorithms. The obtained clusters exhibited correlations with the chemical classes of the input compounds. The precise physical interpretation of the QTAIM properties simplifies the explanation of feature impact for both supervised and unsupervised ML protocols. It also enables acceleration in the search for entries with desired properties within large databases. Furthermore, our findings indicated that Ridge Regression with Laplacian kernel and CatBoost Regressor algorithms demonstrated suitable performance in handling small datasets with non‐trivial dependencies. They were able to predict the actual reaction barrier values with a high level of accuracy. Additionally, the CatBoost Classifier proved reliable in discriminating between “active” and “inactive” compounds.

Hirao, Kimihiko; Nakajima, Takahito; Chan, Bun; Lee, Ho‐Jin

doi: 10.1002/jcc.27228pmid: 37707426

The core ionization energies of second‐ and third‐period elements of the molecules C2H5NO2, SiF4, Si(CH3)4, PF3, POF3, PSF3, CS2, OCS, SO2, SO2F2, CH3Cl, CFCl3, SF5Cl, and Cl3PS are calculated by using Hartree‐Fock (HF), and Kohn‐Sham (KS) with BH&HLYP, B3LYP, and LC‐BOP functionals. We used ΔSCF, Slater's transition state (STS), and two previously proposed shifted STS (1) and shifted STS (2) methods, which have been developed. The errors of ΔSCF and STS come mainly from the self‐interaction errors (SIE) and can be corrected with a shifting scheme. In this study, we used the shifting parameters determined for each atom. The shifted STS (1) reproduces ΔSCF almost perfectly with mean absolute deviations (MAD) of 0.02 eV. While ΔSCF and STS vary significantly depending on the functional used, the variation of shifted STS (2) is small, and all shifted STS (2) values are close to the observed ones. The deviations of the shifted STS (2) from the experiment are 0.24 eV (BH&HLYP), 0.19 eV (B3LYP), and 0.23 eV (LC‐BOP). These results further support the use of shifted STS methods for predicting the core ionization energies.