Category Archives: International Journal of Quantum Chemistry

Theoretical insight on Cm(III) and Eu(III) competing with Am(III) for binding to N‐donor extractants with different dentate numbers

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Theoretical insight on Cm(III) and Eu(III) competing with Am(III) for binding to N-donor extractants with different dentate numbers

The complexation and bonding nature of Am(III), Cm(III), and Eu(III) ions with 6 N-donor ligands of different dentate numbers were theoretically investigated. The NBO analysis and QTAIM analysis revealed that the Am metal can form more covalent with the ligands than Cm and Eu. Thermodynamic analysis demonstrated effective separation of Am from Cm and Eu, with L4 showing superior performance for Am(III)/Cm(III) separation and L6 excelling in Am(III)/Eu(III) separation.


Abstract

The separation of actinides (An) from lanthanides (Ln) is crucial for nuclear resource recovery and reducing long-term radiotoxicity. While numerous N-donor ligands have been examined for the extraction separation of An and Ln, few studies have investigated the effect of the number of ligand dentate on bonding and extraction separation. To address this issue, we designed six pyridine-based ligands with different numbers of coordination dentate. We employed density functional methods to investigate their bonding properties with Am(III), Cm(III), and Eu(III), as well as the thermodynamic differences in extracting and separating these metal ions. The NBO and QTAIM analyses indicate that the metal–ligand bonds are predominantly ionic. However, the Am-N bond exhibits higher covalency compared to the Cm-N and Eu-N bonds, and it is also stronger than the latter two. This difference in bonding can be attributed to the greater involvement of the 5f orbitals of Am in coordination with the ligands, in contrast to the involvement of the Cm 5f and Eu 4f orbitals. Thermodynamic analysis reveals that the coordination ability of the ligands with metals does increase with the number of coordination teeth. However, the extraction separation effect of the ligand for Am/Cm and Am/Eu does not show a strong correlation with the number of coordination dentate. We hope that this study can offer valuable theoretical support for the design of ligands aimed at the separation of actinide(III) and lanthanide(III) ions.

SurfinPES: Performing automated analysis of activation strain, energy decomposition, and reaction force

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SurfinPES: Performing automated analysis of activation strain, energy decomposition, and reaction force

SurfinPES is a module of the Eyringpy program, written in Python, to perform automated analysis of the activation strain, energy decomposition, and reaction force from electronic structure calculations. It has a simple input format and is user-friendly.


Abstract

Analyzing activation strain, energy decomposition, and reaction force models is crucial for studying chemical reactivity and gaining quantitative insights into the factors that control energy barriers. However, manually preparing and processing the necessary data can be challenging and prone to errors. To address this issue, we introduce SurfinPES, a Python-based module in Eyringpy that automates data extraction and processing for these analyses. SurfinPES also allows monitoring of the evolution of primitive properties (geometrical and electronic) along the reaction coordinate. The module is user-friendly with a simple input format, making it accessible to any user in the field of computational chemistry.

On energetics of proton and electron transfer of selected phenol derivatives: Theoretical investigation of radical and oxonium cations

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On energetics of proton and electron transfer of selected phenol derivatives: Theoretical investigation of radical and oxonium cations

Theoretical study of phenols in forms of cation radicals and oxonium cations. The proton-coupled electron transfer and redox properties are studied. The pKa values scaled on the experimental data are obtained. Pourbaix diagrams for water are constructed.


Abstract

In this paper, the systematic theoretical study of phenol and 36 compounds representing various ortho, meta and para-substituted (R-PhOH) phenols is presented. The hydroxyl group acidity is a characteristic feature of phenol which can be modified using substitution of phenyl ring. The proton-coupled electron transfer was investigated for parent neutral phenols, R-PhOH, their cation radicals, R-PhOH+•, and oxonium cations, R-PhOH2 +. Density functional theory calculations were combined with solvent continuum model for water and dimethyl sulfoxide environment. For aqueous solution, the Pourbaix diagrams (electrochemical potential vs. pH) were constructed from the theoretically predicted acidity constants and electrochemical standard potentials. From the thermodynamic point of view, the obtained theoretical results allow the estimation of the thermodynamically preferred process and alternative reaction pathways of phenolic derivatives in very acidic media.

Thermal isomerization of phenylazoindoles: Inversion or rotation? That is the question

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Thermal isomerization of phenylazoindoles: Inversion or rotation? That is the question

Azoheteroarenes are emerging group of photoswitches with promising properties. Transformation from the E to the Z form is performed photochemically while backreaction is usually thermal on the ground state surface. Two possible mechanisms, inversion and torsion, are modeled in this study. The gas phase calculations show the necessity of large active space and dynamical correlation for balanced description of both mechanisms, while solvent effects are clearly underestimated by continuum solvation models.


Abstract

Azoheteroarenes represent an attractive group of photochromes exhibiting a large structural variability and tunability of photoswitching characteristics. The thermal back-isomerization can proceed via inversion or rotation mechanisms, depending on the functionalization and environment. However, the distinction between the two remains a challenge for both experiment and theory. Here, four experimentally fully characterized phenylazoindoles are studied to establish the mechanism of back-reaction in solvent using density functional theory (DFT), spin-flip time-dependent (TD-)DFT, mixed-reference TD-DFT, and restricted ensemble Kohn–Sham approaches as well as CASPT2 and CCSD(T). While the inversion is consistently described by all methods, the rotation mechanism requires multireference approaches including dynamic correlation. The balanced description of both pathways becomes even more important in solvent which apparently affects the mechanism. For the present set, the range-separated functionals combined with continuum models appear to be the most consistent with experiment in terms of the substitutional and solvent effects on thermal halftimes.

Excited states of aurocarbons: CASPT2 and CCSD(T) calculations of C2Au2 and C2Au4

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Excited states of aurocarbons: CASPT2 and CCSD(T) calculations of C2Au2 and C2Au4

Highly correlated single- and multi-reference wavefunction methods are used for calculations of excitation energies upon aurosubstitution in acetylene and ethylene. Lowering of excitation energies of diauroacetylene and tetraauroethylene compared with their parent acetylene and ethylene molecules is demonstrated.


Abstract

We present CASPT2 calculations of vertical excitation energies for low-lying singlet and triplet states of auroderivatives of acetylene and ethylene representing small model aurocarbons. Data are supplemented by CCSD(T) results for triplet states. All four considered species, namely linear C2Au2 molecule and three conformers of the C2Au4 molecule—Au2C2Au2 (tetraauroethylene, the analog of the parent ethylene molecule) and σ$$ \sigma $$– and π$$ \pi $$–adducts of the Au2 molecule with the auroacetylene exhibit considerable lowering of low-lying excitation energies when compared with their parent acetylene and ethylene molecules. Singlet and triplet excitation energies of diauroacetylene drop by 57% and 48%, respectively, and of tetraauroethylene, by 68% and 56% when compared with their respective parent molecules. Even more is lowered the singlet–triplet energy gap. We stress the importance of the dynamical correlation in CASPT2 calculations and discuss problems with selection of the appropriate active space in aurocarbons.

Advances and critical assessment of machine learning techniques for prediction of docking scores

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Advances and critical assessment of machine learning techniques for prediction of docking scores

Three machine learning (ML) approaches (TensorFlow, XGBoost, and SchNetPack) are used for prediction of inhibitory potential, expressed as docking score, towards SARS-CoV-2. ML train and test sets are based on ZINC15 database of compounds. Proposed ML models are evaluated based on their prediction accuracy, screening potential, and error estimation. Prediction errors are analyzed with respect to compound size, charge, and docking score, and their improvements towards ML prediction are discussed.


Abstract

Here we present three distinct machine learning (ML) approaches (TensorFlow, XGBoost, and SchNetPack) for docking score prediction. AutoDock Vina is used to evaluate the inhibitory potential of ZINC15 in-vivo and in-vitro-only sets towards the SARS-CoV-2 main protease. The in-vivo set (59 884 compounds) is used for ML training (max. 80%), validation (5%), and testing (15%). The in-vitro-only set (174 014 compounds) is used for the evaluation of prediction capability of the trained ML models. Contributions to the prediction error are analyzed with respect to compounds' charge, number of atoms, and expected inhibitory potential (docking score). Methods for the prediction error estimation of new compounds are considered, yet critically rejected. The ML input weighted with respect to the desired property (i.e., low docking score) in the machine learning models shows to be a promising option to improve the ML performance. Proposed models provide significant reduction in number of intriguing compounds that need to be investigated.

Limonene: A scented and versatile tropospheric free radical deactivator

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Limonene: A scented and versatile tropospheric free radical deactivator

In addition to the previously reported capability of limonene to act as •OH, •NO3, and O3 scavenger, it also reacts with •OCH3, •OBr, •SH, •OOH, and •OOCH3 radicals. Thus, it can be considered as a versatile tropospheric free radical deactivator.


Abstract

The reactions of limonene with various free radicals (•OCH3, •OBr, •SH, •OOH, and •OOCH3) were investigated along the 273.15–312.15 K temperature range. To that purpose the density functional theory was used, at the M06-2X/6–311+g(d,p) level. Two reaction mechanisms, hydrogen atom transfer (HAT) and radical adduct formation (RAF) were considered. It was found that the relative reactivity of the studied radicals toward limonene is: •SH > •OBr > •OCH3 > •OOH > •OOCH3. HAT was identified as the dominant mechanism for •OOH and •OOCH3, while RAF contributes the most to the reactions involving •OCH3, •OBr, and •SH. The obtained Arrhenius expressions are: k(•OCH3) = 1.58 × 10−13 e−1.59/RT, k(•OBr) = 3.55 × 10−12 e+1.82/RT, k(•SH) = 3.30 × 10−11 e+0.79/RT, k(•OOH) = 1.33 × 10−15 e−5.99/RT, and k(•OOCH3) = 5.88 × 10−17 e−6.26/RT. According to them, the reactions of •OBr and •SH become slower as temperature rises from 273.15 to 312.15 K, while for the other radicals the reactions rate increases with temperature. The subsequent tropospheric fate of the most abundant •OBr adduct was also investigated in the same temperature range, considering O2 addition to this radical (step 2) and the reaction of the peroxyl radical yielded in this step 2 with NO. The latter is predicted to take place in two steps: the NO addition (3a) and the NO2 elimination (3b). The corresponding Arrhenius expression are k 2 = 3.56 × 10−15 e+1.43/RT and k 3b = 1.35 × 1014 e−31.65/RT. Step 3a was found to be barrierless. To our best knowledge, all the data provided here is reported for the first time. Thus, it would hopefully contribute to enhance the knowledge necessary for the full understanding (and accurate modeling) of the troposphere.

A theoretical adsorption study of the inner‐core and outer‐core hydrated alkali metal cation–circumcoronene complexes

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A theoretical adsorption study of the inner-core and outer-core hydrated alkali metal cation–circumcoronene complexes

The cation radius along with the microhydrated environment are the key factors for the (micro)hydrated alkali cations interacting the circumcoronene surface. It was found that balance between M+–π interactions, M+–water complexation, and the hydrogen bonding of water to the π-system govern the formation mechanism of the cation–π complexes in solution, favoring the outer-sphere solvated Li+ and Na+–πCC complexes and the inner-sphere solvated K+–πCC complexes.


Abstract

Cation-π interactions are theoretically investigated for alkali metal cation (M+)-circumcoronene (CC) complexes (M = Li, Na, K), in gas phase and in aqueous solution with consideration of micro- and global solvation models using the DFT/PBEh-3c-RI/TZVP method. The solvent effect on the M+–CC energy interaction regarding the cation size and the stability of inner- and outer-sphere [M(H2O) n ]+–CC complexes are calculated by means of geometry optimizations and potential energy (PE) curves. The PE curves, calculated as a function of perpendicular distance of M+ to the CC plane, predicted one energy minimum for each of the isolated M+–CC complexes. However, for microhydrated complexes, two minima assigned to two different surface complexations were obtained. Microhydrated Li+ and Na+ favored outer-sphere complexation while inner-sphere complexation was found more stable for microhydrated K+. These results illustrate nicely the key role, which the cation radius plays for the polarization of the water molecules and the aromatic system.

SVECV‐f12: A composite scheme for accurate and cost‐effective evaluation of reaction barriers. II. Benchmarking using Karton’s BH28 barrier heights database

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SVECV-f12: A composite scheme for accurate and cost-effective evaluation of reaction barriers. II. Benchmarking using Karton's BH28 barrier heights database

Our SVECV-f12 composite protocol is applied to several diverse reactions (proton transfer, pericyclid, dipolar cycloaddtion, and cycloreversion) and the reaction barriers obtained compared to very accurate ones. A mean absolute difference of 2.4 kJ mol−1 and a root mean square difference of 1.9 kJ mol−1 were obtained, underlying the chemical accuracy of the protocol.


Abstract

A simple composite scheme developed for the calculation of accurate reaction barriers, and benchmarked against small systems, is applied here to compute barriers in the BH28 data set published in 2019 by Karton. This set comprises more complex transition states, with up to 7 non-hydrogen and 10 hydrogen atoms, which barriers calculated at the SVECV-f12 level are compared to the accurate CCSDT(Q)/CBS values obtained by Karton. A mean absolute difference of 2.4 kJ mol−1 and a root mean square difference of 1.9 kJ mol−1 were obtained, underlying the chemical accuracy of the protocol.