Hardness, softness, and the fukui function in the electronic theory of metals and catalysis

Unravelling the effect of successive electron injection into the smallest cyclic boron cluster, B3n (n = +2, +1, 0, -1, -2, -3) through electronic structure analysis

With an aim to study the effect of successive electron injection or abstraction on the electronic structure of the cyclic boron clusters; B3n (where n = +2, +1, 0, -1, -2, -3) have been explored using DFT methodology. A total of nine clusters have been studied including the minimum energy ground states and a few closely lying ground states. Through real space functions like electron density, Electron Localization Function (ELF), Localized Orbital Locator (LOL), and Phase-space-defined Fisher Information Density (PS-FID) an in-depth study has been carried out to understand how the electronic character evolves with the successive electron injection into the cluster. Based on Atoms in Molecules (AIM) theory evolution of electron density at critical points and basins has also been studied. Global indices have also been calculated using Conceptual Density Functional Theory (CDFT) to understand cluster's reactivity and stability. IR spectrum has been computed for future experimental verification. B3 clusters fall into two main symmetry classes: six of them have D3h symmetry (B3+2, both the singlet and triplet states of B3+1, B30, B3-1 and the triplet state of B3-3) and three have C2v symmetry (B3-2 and two singlet states of B3-3). It has been found that the B3-1 cluster has the minimum energy among all the structures with the most electron delocalization in the centre.

Chalcones derived from Croton anisodontus as potential anticancer agents against human cancer cell lines SNB-19 (glioblastoma), HCT-116 (colon), and PC3 (prostate)

Chalcones are a class of natural or synthetic compounds with an α, β-unsaturated carbonyl system. From a pharmacological standpoint, they are highly promising substances, particularly due to their diverse pharmacological properties, among them anticancer activity. The present study aims to evaluate through in vitro and in silico studies the cytotoxicity of chalcones derived of the natural product 2-hydroxy-3,4,6-trimethoxyacetophenone isolated from Croton anisodontus, in order to identify compounds with greater antitumor activity. Regarding the cytotoxic activity, it was observed that these chalcones exhibited activity in human cancer cells of colon (HCT-116), prostate (PC3) and glioblastoma brain (SNB-19). The results demonstrated that chalcone containing a fluorine atom at the para position in the B-ring displayed more significant activity against tumor cell lines PC-3 (IC50 = 4.79 ± 0.72 μM), HCT-116 (IC50 = 3.94 ± 0.4 μM) and SNB-19 (IC50 = 3.64 ± 0.69 μM). Molecular docking study confirmed that the synthesized chalcones interacted in the same region of the binding site of the AQ4 inhibitor against HCT-116 and the 6VN inhibitor against SNB19, indicating which have a similar action to the co-crystallized inhibitors, in addition to competing with testosterone against PC-3, since they interact with residues of the Ligand Binding Domain (LBD). In silico study of absorption, distribution, metabolism, and excretion (ADME) showed that chalcones have high cellular permeability, are slightly soluble in water and moderately bound to plasma proteins, which are essential characteristics of compounds that present antitumor activity. Thus, the chalcones derived from Croton anisodontus could be promising prototypes for development new anticancer drugs.

Electronic properties and adjuvant effect of riparins I-IV: Inhibition of β-lactamase and QacC efflux pump in Staphylococcus aureus K4100

Staphylococcus aureus is a leading cause of nosocomial infections, posing a significant health threat due to its resistance mechanisms, particularly involving β-lactamase enzymes and efflux pumps. Targeting these mechanisms is crucial to restore the efficacy of antibiotics. This study characterized the electronic properties of riparins I, II, III, and IV and evaluated their effects on the β-lactamase enzyme and the QacC efflux pump in the S. aureus K4100 strain. The electronic properties of the riparins revealed distinct electrophilic characteristics, but similar nucleophilic behavior, as indicated by the HOMO (Highest Occupied Molecular Orbital) and LUMO (Lowest Unoccupied Molecular Orbital) orbital energy values. Microbiological testing showed that riparins I, II, III, and IV did not display direct antibacterial activity against S. aureus K4100. However, riparin III significantly reduced the MIC of oxacillin, suggesting it potentiates the antibiotic's effect, likely by targeting the β-lactamase enzyme. Furthermore, riparins II and III lowered the MIC of ethidium bromide, indicating their potential as inhibitors of the QacC efflux pump. These findings highlight the potential of riparins II and III as adjuvants to enhance the effectiveness of antibiotics against multidrug-resistant strains of S. aureus.

Prediction of Activation Energies of Organic Molecules With at Most Seven Non-Hydrogen Atoms Using Quantum-Chemically Assisted ML

In this study, a hybrid machine learning (ML) approach is presented for accurately predicting activation energies (Ea) of gas-phase elementary reactions involving organic compounds with up to seven non-hydrogen atoms. Given the importance of activation energies in reaction studies and modeling, ML composite models were created that effectively integrate molecular descriptors with semi-empirical and single energy density functional theory (DFT) calculations. The dataset, containing 300 randomly selected elementary gas-phase reactions, was assembled using accurate DFT (ωB97X-D3/def2-TZVP) values for activation energies Ea from a database alongside semi-empirical computations. For accurate predictions, this approach required the inclusion of both physical organic and geometric/empirical descriptors in the training procedure. The best two ML models demonstrated efficient Ea prediction capability, achieving a mean absolute error (MAE) of 1.314 kcal mol-1 and R2 of 0.992 (Model 3) and (MAE) of 1.949 kcal mol-1 and R2 of 0.979 (Model 2) in validation tests. Notably, this performance approaches the threshold of "chemical accuracy" of 1 kcal mol-1. Model's 3 robustness was tested across the reaction types present in the dataset, demonstrating its ability in properly predicting activation energies, which is critical for the study and optimization of chemical processes.

Advanced enzyme-assembled hydrogels for the remediation of contaminated water

Enzyme-catalyzed biodegradation is an emerging green strategy for environmental remediation, although challenged by high cost and poor robustness. Herein, natural biopolymer (cellulose)-derived hydrogels concurrently doped with β-cyclodextrin and montmorillonite nanosheets that are synthesized in one-step demonstrate exceptional pollutant affinity and mechanical strength. Laccase is then stably and effectively assembled onto the hydrogels by a facile strategy based on charge-assisted H-bonding, which can be extended to other enzymes. The advanced laccase-assembled hydrogels display excellent stability and increased degradation activity achieved by strong substrate capture and rapid electron transfer. The laccase-assembled hydrogels exhibit significantly improved removal (62-fold) and degradation (52-fold) performance compared to free laccase for diverse organic pollutants (e.g., polycyclic aromatic hydrocarbons) in real wastewater. This enhanced performance is maintained despite the presence of heavy metals, other organic chemicals or dissolved organic matter. This work provides a practical strategy for designing an advanced and sustainable biodegradation tool for environmental remediation.

Insights into the Halogen Effects on Regioselectivities of Nucleophilic Haloalkylation of α,β-Enones

The halogen effects, specifically the replacement of chlorine with fluorine, on the shift in regioselectivity from 1,4- to 1,2-addition in the nucleophilic haloalkylation of α,β-enones have been investigated using density functional theory (DFT) calculations. Computational analysis revealed that the difluorocarbanion PhSO2CF2 -, being a hard nucleophile with lower energy of the highest occupied molecular orbital (HOMO), selectively undergoes 1,2-addition of chalcone, primarily dominated by Coulombic interactions. In contrast, the nucleophilic 1,4-addition of chalcone by a soft dichlorocarbanion PhSO2CCl2 - is controlled by frontier molecular orbital interactions. This work provides a deep understanding of the regioselective control in nucleophilic haloalkylation reactions.

Unveiling the Reaction Mechanism of Diels-Alder Cycloadditions between 2,5-Dimethylfuran and Ethylene Derivatives Using Topological Tools

The [4+2] Diels-Alder cycloaddition reaction between 2,5-DMF (1) and ethylene derivatives (2 a-h) activated by electron-withdrawing groups has been studied at the density functional theory level using a panoply of tools to unravel the reaction mechanisms. From the analysis of the reactivity indices, 2 a-h behave as electrophiles while 1 as nucleophile, and the activation of the double bond of ethylene increases its electrophilicity, which is accompanied by an enhancement of the polarity of the reaction. The activation Gibbs free energy decreases linearly as a function of this increase of polarity, as estimated by the electrophilicity difference between the reactants. The difference of electrophilicity drives also the global electron density transfer at the transition state and the asynchronicity of the reaction, as evaluated by the difference of carbon-carbon bond lengths in the transition state. Then, Bonding Evolution Theory shows that the activation of the double bond of ethylene by an electron-withdrawing group changes the reaction mechanism from a one-step synchronous process to a one-step asynchronous process. Generally, the endo pathway is kinetically favored but, thermodynamically, it is the exo pathway. Finally, using the Distortion/Interaction-Activation Strain, it is shown that the endo/exo selectivity is mostly driven by the differences of interaction energies.

Charge Transfer Is Promoted by Electronic Heat Exchange in Atoms and Molecules

This work compiles almost a decade of theoretical progress in temperature-dependent chemical reactivity theory to introduce the first finite-temperature charge transfer model, predicting fractional electron transfers during chemical interactions. The key insight is that electronic heat drives charge transfer. By analyzing thermodynamic parameters like electronic heat capacity, softness, and chemical potential, the framework explains how species transition from inert to reactive states, where electrons are decorrelated enough to enable charge transfer. A crucial aspect of this model is the role of thermal fluctuations, which governs molecular response functions and facilitates the simultaneous exchange of energy and charge. This model is reduced to a simple linear equation in the chemical potential of the reservoir. When extrapolated, it supports the electrophilicity index, adding a correction term and providing a working formula more influenced by electron affinity. These findings offer new pathways to analyze and predict chemical interactions under the finite temperature regime.

Substituent structure variances alter degradation pathways of sulfonamides in UV/PAA system: Insights from intermediates, ROS, and DFT calculations

Sulfonamides (SAs) are one of the major emerging contaminants of concern, but comparative studies on the degradation of different types of SAs are still limited. This work comprehensively compared the degradation of sulfadiazine (SDZ), sulfamethoxazole (SMX) and sulfathiazole (STZ) under UV light in peracetic acid (PAA) from both experimental and theoretical aspects, as they represent two structural classes based on substituent differences. The two SAs with five-membered heterocyclic substituents (SMX, STZ) generally decomposed at faster rates, with SMX degrading up to 10 times faster than SDZ (pH = 3; PAA dosage = 80 mg/L). For all three SAs, the degradation efficiency stayed high across pH levels, peaking at pH 9 for SDZ and STZ, and at pH 3 for SMX. Free radical scavenging experiments and EPR tests proved that the degradation of SAs involved various free radicals, among which 3SA*s and •OH played a major role. Fukui functions indicated N(7) in aniline groups of SDZ and SMX had the highest reactivity, while in STZ, S(23) in the thiazole moiety was the most active site. The degradation pathways were proposed and compared and the cleavage of S-C bond was observed in all three SAs and hydroxylation was the most common reaction. This study elucidated the impacts of different substituent structures on the degradation of three sulfonamide drugs in the UV/PAA system, contributing to a better understanding of the degradation behavior of various types of sulfonamide drugs in water treatment.

Exploring Intrinsic Bond Properties with the Fukui Matrix from Conceptual Density Matrix Functional Theory

We extend the traditional conceptual density functional theory (CDFT) to conceptual density matrix functional theory (CDMFT) by replacing the external potential v(r) by the one-electron integral hrs in the energy functional. This approach provides a new path for investigating intrinsic bond properties such as bond reactivity. The derivation of the Fukui matrix, i.e., derivative of the density matrix P with respect to the number of electrons N, is elucidated, and the result is illustrated in a case study on H2O. The matrix is shown to play a crucial role in quantifying changes of bond strength for electron removal or addition processes via the bond order derivative ( ∂ B ∂ N ) - . Using the Mayer bond order and different atoms-in-molecules partitioning methods, we show that as a first-order response quantity, the bond order derivative agrees well with the finite difference bond order changes. The bond order derivative (bond Fukui function) is a bond reactivity descriptor. We demonstrate this by predicting the regioselectivity of a classical electrophilic addition reaction (the bromination of alkenes) and predicting the initial electron-driven bond cleavage in mass spectrometry. Specifically, the bond order derivative captures all of the major signals from the experimental mass spectra for a series of small molecules with a variety of functional groups.

An efficient and flexible approach for local distortion: distortion distribution analysis enabled by fragmentation

Distortion can play crucial roles in influencing structures and properties, as well as enhancing reactivity or selectivity in many chemical and biological systems. The distortion/interaction or activation-strain model is a popular and powerful method for deciphering the origins of activation energies, in which distortion and interaction energies dictate an activation energy. However, decomposition of local distortion energy at the atomic scale remains less clear and straightforward. Knowing such information should deepen our understanding of reaction processes and improve reaction design. Herein, an efficient, general and flexible fragmentation-based approach was proposed to evaluate local distortion energies for various chemical and biological molecules, which can be obtained computationally and/or experimentally. Moreover, our distortion analysis is readily applicable to multiple structures from molecular dynamics (or the minimum energy path) as well as can be evaluated by different computational chemistry methods. Our systematic analysis shows that our approach not only aids computational and experimental chemists in visualizing (relative) distortion distributions within molecules (distortion map) and identifies the key distorted pieces, but also offers deeper understanding and insights into structures, reaction mechanisms and dynamics in various chemical and biological systems. Furthermore, our analysis offers indices of local distortion energy, which can potentially serve as a new descriptor for multi-linear regression (MLR) or machine learning (ML) modelling.

Unconventional Near-Equilibrium Nucleation of Graphene on Si-Terminated SiC(0001) Surface

The transfer-free character of graphene growth on Silicon Carbide (SiC) makes it compatible with state-of-the-art Si semiconductor technologies for directly fabricating high-end electronics. Although significant progress has been achieved in epitaxial growth of graphene on SiC recently, the underlying nucleation mechanism remains elusive. Here, we present a theoretical study to elucidate graphene near-equilibrium nucleation on Si-terminated hexagonal-SiC(0001) surface. It is found that the ultra-large lattice mismatch between SiC(0001) surface and graphene and the highly localized electron distribution on SiC(0001) surface lead to a distinctive nucleation process: (i) Most of the magic carbon clusters on SiC(0001) show only C1 symmetry and are mainly composed of pentagonal rings; (ii) Two possible nucleation pathways are revealed, i.e., longitudinal and circular modes; (iii) Carbon clusters are more stable on flat terraces than near atomic step edges. Based on above findings, a graphene nucleation diagram on SiC(0001) is established and experimentally observed contradictories for graphene growth on SiC(0001) are answered. Our in-depth understanding on graphene nucleation on SiC(0001) extends nucleation mechanisms of 2D crystals and will benefit high-quality graphene growth on SiC(0001).

A detailed TD-DFT and intermolecular interaction study of vitamin K in soluble, poorly soluble and insoluble solvents, as well as an ADME and molecular docking study

Vitamin K is one of the most important fat-soluble vitamins and while there are two main types of vitamin K in nature, known as K1 (phylloquinone) and K2 (menaquinones), there is also a synthetic type of vitamin K known as K3 (menadione). Recent studies have shown that it is crucial to know the non-covalent interactions, ADME and molecular docking of molecules in different solvent media. Therefore, we have performed some quantum chemical calculations, ADME and intra-and intermolecular interaction calculations of a number of K1, K2 and K3 such as K1-water (K1 + W), K1-methanol (K1 + M), K1-triacetin (K1 + T), K2-water (K2 + W), K2-methanol (K2 + M), K2-triacetin (K2 + T), K3-water (K3 + W), K3-methanol (K3 + M), K3-triacetin (K3 + T) performed by Density Functional Theory (DFT) and Multiwfn: A multifunctional wavefunction analyzer. Molecular structures, HOMO-LUMO energies, MEP and electronic properties have been calculated and described using DFT at the level of B3LYP/6-311G (d,p) level. The nature of the molecular interactions between vitamin K and solvents such as water, methanol and triacetin were also investigated using topological analyses such as atoms in molecule (AIM), non-covalent interaction index (NCI), reduced density gradient (RDG), Localized orbital locator (LOL) and electron localization function (ELF). In addition, FMO for electronic transitions, MEP for electrophilic and nucleophilic attack, ADME to investigate how a chemical is processed by a living organism, and Fukui functions to determine electron density are explained. Finally, molecular docking was used to determine the biological activity of the vitamin K.

Exploring the role of Chrysanthemum coronarium leaves distillation waste as a green inhibitor for carbon steel in acidic environment: an integrated study

In this study, the assessment of the Chrysanthemum coronarium leaves' co-product resulting from the hydrodistillation process was conducted to evaluate its anticorrosive potential for carbon steel in the hydrochloric acid medium. Phytochemical analysis of this biomass revealed its abundance in terms of polyphenols and flavonoids; hence the determination of total polyphenol content recorded a value of 75.4 mg GAE per g extract. This was corroborated by FTIR spectroscopy, which revealed the presence of various functional groups, thereby providing positive indications regarding the anticorrosive properties of this plant material. Electrochemical impedance spectroscopy and Tafel extrapolation analysis of polarization curves indicated that the extract from Chrysanthemum coronarium leaves reduced the corrosion rate of steel in 1 M HCl medium, reaching 78% in corrosion inhibition efficiency while following an adsorption process governed by the Langmuir isotherm. Furthermore, temperature effect investigations at a range between 293-313 K on the corrosion rate of carbon steel in the acidic medium in the presence and absence of CCLE revealed that the latter undergoes chemisorption-type adsorption on the active metal surface, thereby minimizing its degradation rate at elevated temperatures. The synergistic effect between the Chrysanthemum coronarium leaf extract and potassium iodide was examined using both electrochemical techniques, thus reflecting the cooperative abilities of the two compounds in inhibiting carbon steel corrosion. Additionally, scanning electron microscopy images of the surface state confirmed these findings, thereby providing significant insight into the anticorrosive properties of this plant material in corrosive environments. Similarly, a theoretical study using DFT and MD for the major compounds of CCLE confirmed the obtained results, concluding that the plant material derived from the hydrodistillation process of Chrysanthemum coronarium leaves exhibits remarkable corrosion inhibition capacity for carbon steel in acidic environments.

DFT studies on N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl)

In this work, molecular descriptors of N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl) halogenated benzamides (1a-h) have been computed using a quantum chemical technique through DFT. Prior work involved the synthesis of compounds (1a-h) and the assessment of their anticancer activity on breast, colon, and liver tumors: MCF-7, HCT-116, and HepG-2 cell lines respectively. Since 1a, 1b, and 1d showed the most potential anticancer impact, their ability to inhibit EGFRWT was investigated. Based on the biological data, 1b inhibited EGFRWT the most. According to the docking evaluation, an H-bond with the threonine residue was one of the main non-covalent contacts between 1b and the EGFRWT active site residues. PES, MESP, HOMOs, LUMOs, energy band gap, global reactivity indices [electron affinity (A), ionization energies (I), electrophilicity index (ω), nucleophilicity index (ε), chemical potential (μ), electronegativity (χ), hardness (η), and softness (S)], condensed Fukui functions, NBO, and NCIs are the molecular descriptors of 1a-h that were computed using DFT technique. According to the theoretical investigation results, compounds (1a-h) might have anticancer effects; these findings are consistent with the biological findings from our previous research. Compound 1b had the lowest binding energy, according to an assessment of the binding energies between the threonine and the three most active compounds (1a, 1b, and 1d). This is consistent with the outcomes of the docking study and the biological examination of the influence of 1a, 1b, and 1d on EGFRWT.

Slope of the Delocalization Function Is Proportional to Analytical Hardness

Conceptual Density Functional Theory (CDFT) has been extended beyond its traditional role in elucidating chemical reactivity to the development of density functional theory methods, e.g., the investigation of the delocalization error. This delocalization error causes the dependence of the energy on the number of electrons (N) to deviate from its exact piecewise linear behavior, an error which is the basis of many well-known limitations of commonly used density-functional approximations (DFAs). Following our previous work on the analytical hardness η± for pure functionals, we extend its application to hybrid and range-separated functionals. A comparison is made between the analytical hardness and the slope of the delocalization function introduced by Hait and Head-Gordon. Our results show that there is a linear relationship between its slope and the analytical hardness. An approximate scheme is presented to construct the energy vs N curve without fractional occupation number calculations. The extension to densities is discussed.

Harnessing high potential benzothiazole chalcones against dengue virus NS5 protein: A multi-faceted theoretical study through molecular docking, ADME, and DFT

Chalcones bearing tetralone, indanone and benzothiazole cores were synthesized successfully using a general Claisen-Schmidt condensation protocol. The prepared compounds were purified and structurally analyzed by 1H, 13C NMR, and FT-IR techniques. A multi-faceted theoretical approach, combining Density Functional Theory (DFT), molecular docking, and ADME predictions, was employed to evaluate their therapeutic potential. DFT calculations at the B3LYP/def2-TZVP level revealed key electronic properties, with TD3 compound demonstrating the highest chemical reactivity. Molecular Electrostatic Potential (MEP) and Reduced Density Gradient (RDG) analyses provided insights into the compounds' non-covalent interactions and charge distributions. Molecular docking studies against the NS5 protein (PDB: 6KR2) showed superior binding affinities for all three compounds compared to the control ligand SAH, with TD3 exhibiting the lowest binding energy (-8.41 kcal/mol) and theoretical inhibition constant (689.31 nM). ADME predictions indicated favorable drug-like properties with concerns regarding aqueous solubility and potential P-glycoprotein interactions. Toxicity evaluations highlighted challenges, particularly in hepatotoxicity and carcinogenicity. The study identified TD3 as a promising lead compound for Dengue Virus NS5 inhibition, while also emphasizing the need for targeted modifications to address toxicity concerns. This research not only contributes to anti-dengue drug discovery efforts but also provides a robust methodological framework for the theoretical evaluation of similar small compounds in future investigations.

Fluorophore-quencher complexes (Cu2+/Al3+) of coumarin Schiff bases as chemosensors for the detection of L-glutamic acid and L-arginine: in vitro and in vivo studies

This study reports the development of new probes RR1 ((1E)-1-(1-(6-bromo-2-oxo-2H-chromen-3-yl)ethylidene)ethyl thiosemicarbazone) and RR2 ((1E)-1-(1-(6-bromo-2-oxo-2H-chromen-3-yl)ethylidene)phenyl thiosemicarbazone), which selectively showed fluorescence turn 'OFF' response towards Cu2+ and Al3+. Further, complexes of RR1-Cu2+ and RR2-Al3+ acted as chemosensors for the detection of L-amino acids. RR1-Cu2+ selectively detected L-arginine (fluorescence turn 'ON'), and RR2-Al3+ selectively detected L-glutamic acid (fluorescence turn 'ON'). The existence of the fluorophore-quencher complexes RR1-Cu2+ and RR2-Al3+ was confirmed by theoretical studies. Further, the chemosensors RR1-Cu2+ and RR2-Al3+ have three possible structural isomers (RR1-Cu2+-L-arginine - A, B and C) and (R2-Al3+-L-glutamic acid - D, E and F), as confirmed by theoretical studies. In vitro bio-imaging of the probes (RR1 and RR2), complexes (RR1-Cu2+ and RR2-Al3+) and complexes associated with L-arginine (RR1-Cu2+-L-arginine) and L-glutamic acid (R2-Al3+-L-glutamic acid) was performed in the MDA-MB-231 cell line using their IC50 concentrations. In addition, in vivo live cell imaging studies were conducted using C. elegans as the model organism.

Adsorption grand potential of OH on metal oxide surfaces

CONTEXT

Describing chemical processes at solid-liquid interfaces as a function of a fixed electron chemical potential presents a challenge for electronic structure calculations and is essential for understanding electrochemical phenomena. Grand Canonical Density Functional Theory (GCDFT) allows treating solid-liquid interfaces in such a way that studying the influence of a fixed electron potential arises naturally. In this work, GCDFT is used to compute the adsorption grand potential (AGP), a key parameter for understanding and predicting the behavior of adsorbates on surfaces. We focused on the adsorption of an OH molecule on three metallic surfaces commonly used in electrochemical processes, such as the oxygen evolution reaction (OER). Our study aims to offer insights into how AGP can be used to compare adsorption strengths under different fixed electron chemical potentials, which is crucial for designing efficient electrode materials. By determining the average number of electrons self-consistently under varying chemical potentials, we showed how one can distinguish between electron acquisition and depletion during the adsorption process, offering a deeper understanding of the adsorbate-surface interactions.

METHODS

The approach used in this work employs the Kohn-Sham-Mermin formulation of the Grand Canonical Density Functional Theory. The computations were performed using the periodic open-source density functional theory software, JDFTx, with the Garrity-Bennett-Rabe-Vanderbilt library of ultrasoft pseudopotentials. Calculations were made using truncated Coulomb potentials and the auxiliary Hamiltonian method with the PBE exchange-correlation functional, along with DFT-D2 long-range dispersion corrections. The implicit solvation model CANDLE was used to describe the electrolyte with a 1 M concentration.

Why are information-theoretic descriptors powerful predictors of atomic and molecular polarizabilities

CONTEXT

We rationalize the excellent performance of information-theoretic descriptors for predicting atomic and molecular polarizabilities. It seems that descriptors which capture information about the change in valence-shell structure, especially the relative Fisher information measures, are particularly useful. Using this, we can rationalize why the G3 form of the relative Fisher information, which measures the deviation of effective nuclear charge between an atom-in-a-molecule and the reference pro-atom, is especially effective as a predictor of molecular polarizability.

METHODS

There are no methods used in this paper, which relies on mathematical derivation and analysis.

Hyperhardness and hypersoftness of atoms and their ions

CONTEXT

The theory of reactivity based on cDFT has been supplemented with the new method of calculating the atomic and local indices. With the use of previously derived relationship of the electron density gradient to the softness kernel and to the linear response function, we deliver theoretical analysis to obtain significant reactivity indices-the electron density derivatives: local softness and local hypersoftness together with the global hyperhardness index and the derivative of the global softness with respect to the number of electrons. The local derivatives have been applied in the calculation of responses of atoms to perturbation by an external potential by the alchemical approach. The vital role of the local softness has been confirmed; the potential role of the hypersoftness has been indicated.

METHOD

Our original theoretical scheme has been numerically illustrated with the results obtained with electron density calculations with B3LYP method implemented in Gaussian 16 package. The aug-cc-pvqz basis set has been routinely applied, except for the Ca atom (cc-pvqz). Using the pVTZ basis set recommended by Sadlej was necessary for the potassium atom.

Information-theoretic quantities as effective descriptors of electrophilicity and nucleophilicity in density functional theory

CONTEXT

Electrophilicity and nucleophilicity are two vastly important chemical concepts gauging the capability of atoms in molecules to accept and donate the maximal number of electrons. In our earlier studies, we proposed to simultaneously quantify them using the Kullback-Leibler divergence from the information-theoretic approach in density functional theory. However, several issues with this scheme remain to be clarified such as its general validity, predictability, and relationship with other information-theoretic quantities. In this work, we revisit the matter with bigger datasets and deeper theoretical insights. Five information-theoretic quantities including Kullback-Leibler divergence, Hirshfeld charge, Ghost-Berkowitz-Parr entropy, and second and third orders of relative Onicescu information energy are found to be reliable and robust descriptors of electrophilicity and nucleophilicity propensities. Employing these five descriptors, we design a list of new compounds and predict their electrophilicity and nucleophilicity scales. This work should markedly improve our confidence and capability in applying information-theoretic quantities to evaluate electrophilicity and nucleophilicity propensities and henceforth pave the route for more applications of these quantities from information-theoretic approach in density functional theory in the future.

METHODS

All structures were fully optimized at the M06-2X/6-311 + G(d) level of DFT functional using the Gaussian 16 package (version C01) with integration grids and tight self-consistent-field convergence. The solvent effect was taken into account by using the implicit solvent model (CPCM) in the CH2Cl2 solvent, and all 3D contour surfaces of Fukui function, local temperature, and ITA (information-theoretic approach) quantities were generated by GaussView. The Multiwfn 3.8 program was used to calculate the ITA indexes and atomic charges.

On the link between the reaction force constant and conceptual DFT

CONTEXT

The reaction force constant ( κ ), introduced by Professor Alejandro Toro-Labbé, plays a pivotal role in characterizing the reaction pathway by assessing the curvature of the potential energy profile along the intrinsic reaction coordinate. This study establishes a novel link between κ and the reactivity descriptors of conceptual density functional theory (c-DFT). Specifically, we derive expressions that relate the reaction force constant to nuclear softness and variations in chemical potential. Our findings indicate that regions of the reaction pathway where κ is negative match with significant electronic structure rearrangements, while positive κ regions match mostly with geometric rearrangements. This correlation between κ and c-DFT reactivity descriptors enhances our understanding of the underlying forces driving chemical reactions and offers new perspectives for analyzing reaction mechanisms.

METHODS

The internal reaction path for the proton transfer in SNOH, chemical potential, and nuclear softness were computed using DFT with B3LYP exchange-correlation functional and 6-311++G(d,2p) basis set.

Density-based quantification of steric effects: validation by Taft steric parameters from acid-catalyzed hydrolysis of esters

The steric effect is one of the most widely used concepts for chemical understanding in publications and textbooks, yet a well-accepted formulation of this effect is still elusive. Experimentally, this concept was quantified by the acid-catalyzed hydrolysis of esters, yielding the so-called Taft steric parameter. Theoretically, we recently proposed a density-based scheme to quantify the effect from density functional theory. In this work, we directly compare these two schemes, one from theory and the other from experiment. To this end, we first establish the ester hydrolysis mechanism with multiple water molecules explicitly considered and then apply the energetic span model to represent the hydrolysis barrier height between the two schemes. Our results show that the barrier height of the reaction series is strongly correlated with both Taft steric parameters from experiment and steric quantification from theory. We also obtained strong correlations with steric potential, steric force, and steric charge from our theoretical scheme. Strong correlations with a few information-theoretic quantities are additionally unveiled. To the best of our knowledge, this is the first time in the literature that such a direct comparison between theoretical and experimental results is made. These results also suggest that our proposed two-water three-step mechanism for ester hydrolysis is effective, and our theoretical quantification of the steric effect is valid, robust, and experimentally comparable. In our view, this work should have satisfactorily addressed the issue of how the steric effect can be formulated and quantified, and thus it lays the groundwork for future applications.

Structural characterization and keto-enol tautomerization of 4-substituted pyrazolone derivatives with DFT approach

The synthesis of two pyrazolone derivative compounds, PYR-I(4-Acetyl-1-(4-chlorophenyl)-3-isopropyl-1H-pyrazol-5(4H)-one) and PYR-II1-(4-Chlorophenyl))-3-isopropyl-5-oxo-4,5-5-dihydro-1H-pyrazole-4-carbaldehyde, their characterization by FT-IR, NMR, UV-Vis and GC-MS techniques, and the evaluation of the keto-enol tautomerization process of the structures along with the DFT approach and spectral data were reported in this paper. Spectral findings indicated that PYR-I was stable at the keto state. The IR spectrum recorded in solid form showed that the PYR-II structure was stable in the enol state, while the NMR spectrum in the solution medium showed that it was stable in the keto state. DFT-based analyses were realized with the B3LYP hybrid functional and the 6-311++G(d,p) basis set. The modelled keto, transition and enol state molecular geometries of structures were optimized in the gas phase and different solvent media and the total energy and dipole moment values were investigated at the specified theoretical level. The possible keto-enol tautomerism mechanism of the structures was evaluated through some thermodynamic parameters such as the difference in free Gibbs energy (ΔG), enthalpy (ΔH), entropy (ΔS), and predictive tautomeric equilibrium constants (Keq), acidity constants (pKa) and percentages of tautomers at 298.15 K and 1 atm pressure. The results of these analyses based on the DFT approach indicated that the keto-enol tautomer equilibrium heavily favours the keto form for PYR-I and the enol form for PYR-II in all cases. Moreover, natural bond orbital (NBO) analysis was performed for the tautomers, and the chemical reactivity profiles of the most stable tautomers were examined with the values of frontier molecular orbital energy and some reactivity descriptors.

Inhibition of the Janus kinase protein (JAK1) by the A. Pyrethrum Root Extract for the treatment of Vitiligo pathology. Design, Molecular Docking, ADME-Tox, MD Simulation, and in-silico investigation

This study delves into the therapeutic efficacy of A. pyrethrum in addressing vitiligo, a chronic inflammatory disorder known for inducing psychological distress and elevating susceptibility to autoimmune diseases. Notably, JAK inhibitors have emerged as promising candidates for treating immune dermatoses, including vitiligo. Our investigation primarily focuses on the anti-vitiligo potential of A. pyrethrum root extract, specifically targeting N-alkyl-amides, utilizing computational methodologies. Density Functional Theory (DFT) is deployed to meticulously scrutinize molecular properties, while comprehensive evaluations of ADME-Tox properties for each molecule contribute to a nuanced understanding of their therapeutic viability, showcasing remarkable drug-like characteristics. Molecular docking analysis probes ligand interactions with pivotal site JAK1, with all compounds demonstrating significant interactions; notably, molecule 6 exhibits the most interactions with crucial inhibition residues. Molecular dynamics simulations over 500ns further validate the importance and sustainability of these interactions observed in molecular docking, favoring energetically both molecules 6 and 1; however, in terms of stability, the complex with molecule 6 outperforms others. DFT analyses elucidate the distribution of electron-rich oxygen atoms and electron-poor regions within heteroatoms-linked hydrogens. Remarkably, N-alkyl-amides extracted from A. pyrethrum roots exhibit similar compositions, yielding comparable DFT and Electrostatic Potential (ESP) results with subtle distinctions. These findings underscore the considerable potential of A. pyrethrum root extracts as a natural remedy for vitiligo.

A comprehensive electron wavefunction analysis toolbox for chemists, Multiwfn

Analysis of electron wavefunction is a key component of quantum chemistry investigations and is indispensable for the practical research of many chemical problems. After more than ten years of active development, the wavefunction analysis program Multiwfn has accumulated very rich functions, and its application scope has covered numerous aspects of theoretical chemical research, including charge distribution, chemical bond, electron localization and delocalization, aromaticity, intramolecular and intermolecular interactions, electronic excitation, and response property. This article systematically introduces the features and functions of the latest version of Multiwfn and provides many representative examples. Through this article, readers will be able to fully understand the characteristics and recognize the unique value of Multiwfn. The source code and precompiled executable files of Multiwfn, as well as the manual containing a detailed introduction to theoretical backgrounds and very rich tutorials, can all be downloaded for free from the Multiwfn website (http://sobereva.com/multiwfn).

Hydrogen, Oxygen, and Lead Adsorbates on Al13Co4(100): Accurate Potential Energy Surfaces at Low Computational Cost by Machine Learning and DFT-Based Data

Intermetallic compounds are promising materials in numerous fields, especially those involving surface interactions, such as catalysis. A key factor to investigate their surface properties lies in adsorption energy maps, typically built using first-principles approaches. However, exploring the adsorption energy landscapes of intermetallic compounds can be cumbersome, usually requiring huge computational resources. In this work, we propose an efficient method to predict adsorption energies, based on a Machine Learning (ML) scheme fed by a few Density Functional Theory (DFT) estimates performed on n sites selected through the Farthest Point Sampling (FPS) process. We detail its application on the Al13Co4(100) quasicrystalline approximant surface for several atomic adsorbates (H, O, and Pb). On this specific example, our approach is shown to outperform both simple interpolation strategies and the recent ML force field MACE [arXiv.2206.07697], especially when the number n is small, i.e., below 36 sites. The ground-truth DFT adsorption energies are much more correlated with the predicted FPS-ML estimates (Pearson R-factor of 0.71, 0.73, and 0.90 for H, O and Pb, respectively, when n = 36) than with interpolation-based or MACE-ML ones (Pearson R-factors of 0.43, 0.39, and 0.56 for H, O, and Pb, in the former case and 0.22, 0.35, and 0.63 in the latter case). The unbiased root-mean-square error (ubRMSE) is lower for FPS-ML than for interpolation-based and MACE-ML predictions (0.15, 0.17, and 0.17 eV, respectively, for hydrogen and 0.17, 0.25, and 0.22 eV for lead), except for oxygen (0.55, 0.47, and 0.46 eV) due to large surface relaxations in this case. We believe that these findings and the corresponding methodology can be extended to a wide range of systems, which will motivate the discovery of novel functional materials.

Spurious proton transfer in hydrogen bonded dimers

In some hydrogen bonded systems, the proton may translocate along the hydrogen bond (hb) upon geometry optimization with electronic structure methods like density functional theory (DFT). Such proton transfer (pt) events, however, may be spurious. In this work, spurious pt events are investigated in a set of hydrogen bonded dimers formed with molecules HXN, where X stands for C, Si, Ge and Sn. It is found that standard approximations to the electronic exchange and correlation (xc) functional either predict spurious pt events or too strong hbs in all the (HXN)2 dimers except the (HCN)2 one. The latter result is revealed by comparing DFT calculations against wave function methods. Such spurious pt events may be avoided by fine-tuning the percentage of exact exchange (ex) in hybrid xc-functionals. It is shown that the minimum amount of ex to avoid a spurious pt event ranged from 8% to 90%, depending on the system, basis set and xc-functional approximation used. However, these fine-tuned xc-functionals inadequately describe the hb in the (HXN)2 dimers. Moreover, it is determined that the spurious pt event originates from a wrong description of the isolated HXN molecules by xc-functionals that do not include ex or a small amount of it. Therefore, it is argued that one can determine if a pt event is spurious by analyzing the geometry and electronic structure of the isolated molecule.

Charge transfer interaction revisited by a Fermi-Dirac derived approach

CONTEXT

In this article, we adapt a recent proposition to use a Fermi-Dirac-type population scheme on Kohn-Sham molecular orbitals to the case of an interaction with a thermalised electrode. This allows to derive a fundamental non-linear equation linking the chemical potential of the electrode and the amount of charge transferred to the system under study, hence allows to quantify the propensity to charge transfer (philicity). This methodology is applied to a large set of common electrophiles and nucleophiles, showing decent relation with more standard philicity descriptors. Chemical hardness is also revisited by this approach.

METHODS

All calculations were performed using the Gaussian 16 software package at the M062X/aug-cc-pvtz level of theory. Data analysis was then performed through a Python3 dedicated program (relying on the fsolve numerical solver from the SciPy package), using Gaussian output files, and available as supplementary material.

Expanding horizons in conceptual density functional theory: Novel ensembles and descriptors to decipher reactivity patterns

Conceptual density functional theory (CDFT) and the quantum reactivity descriptors stemming from it have proven to be valuable tools for understanding the chemical behavior of molecules. This article is presented as being intrinsically of dual character. In a first part, it briefly reviews, in a deliberately didactical way, the main ensembles in CDFT, while the second half presents two additional ensembles, where the chemical hardness acts as a natural variable, and their respective reactivity descriptors. The evaluation of these reactivity descriptors on common organic chemical reagents are presented and discussed.

Alkaloid extract of seed Citrullus colocynthis as novel green inhibitor for mild steel corrosion in one molar HCl acid solution: DFT and MC/MD approaches

The study was designed to explore the corrosion prevention capabilities of Citrullus colocynthis seeds alkaloid-rich extract (CSEA) on MS in a 1 M HCl environment by use of electrochemical and theoretical methods. Notably, Electrochemical Impedance Spectroscopy (EIS) and potentiodynamic polarization were used to probe the impact of immersion time and temperature. Energy-dispersive X-ray spectroscopy (EDX) and spanning electron microscopy (SEM) were used to confirm the presence of a protective layer on the substrate surface. Density functional theory (DFT) method was used to optimize the investigated species by use of B3LYP/6-31 + G(d, p) level of theory. The global and local quantum chemical reactivity descriptors were calculated to explore the inhibition corrosion efficiency and to identify the most favorable sites for electrophilic and nucleophilic attacks. Monte Carlo (MC) and molecular dynamics simulation (MDS) methods were used to study the interactions between corrosion inhibitor and metal surface. Noteworthy, results showed that CSEA exhibited an impressive inhibition efficiency, which reached 94.3% with a concentration of 2 g/L at 298 K. Potentiodynamic polarization revealed that the extract acted as a mixed-type inhibitor. Nyquist graphs showed that charge-transfer resistance and dæouble-layer capacitance both rised with increasing CSEA concentration, suggesting better inhibition efficiency. Notably, the Langmuir adsorption isotherm is well-aligned with the adsorption of inhibitor compounds. Importantly, all aforementioned theoretical methods were in agreement with the experimental findings. The outcome of the present work supported using Citrullus colocynthis seeds alkaloid-rich extract as ecofriendly agents to prevent corrosion.

Exploring ethylene insertion reaction mechanism in nickel complexes: a comparative study by the reaction force and reaction electronic flux in molecular and SiO2-supported catalysts

CONTEXT

This study investigates the ethylene insertion reaction mechanism for polymerization catalysis, aiming to discern differences between Ni-α-imine ketone-type catalyst and their SiO2-supported counterpart. The reaction force analysis unveils a more intricate mechanism with SiO2 support, shedding light on unexplored factors and elucidating the observed lower catalytic activity. Furthermore, reactivity indexes suggest earlier ethylene activation in the supported catalyst, potentially enhancing overall selectivity. Finally, the reaction electronic flux analysis provides detailed insights into the electronic activity at each step of the reaction mechanism. In sum, this study offers a comprehensive understanding of the ethylene insertion reaction mechanism in both molecular and supported catalysts, underscoring the pivotal role of structural and electronic factors in catalytic processes.

METHODS

Density functional theory (DFT) calculations were conducted using the ωB97XD functional and the 6-31 + G(d,p) basis sets with Gaussian16 software. Computational techniques utilized in this study encompassed the IRC method, reaction force analysis, and evaluation of electronic descriptors such as electronic chemical potential, molecular hardness, and electrophilicity reactivity indexes. Additionally, reaction electronic flux analysis was employed to investigate electronic activity along the reaction coordinate.

Investigating the effects of solvent polarity and temperature on the molecular, photophysical, and thermodynamic properties of sinapic acid using DFT and TDDFT

Sinapic acid (SA) is widely used in cosmetics, foods, and pharmaceuticals due to its antioxidant, anti-inflammatory, neuroprotective, antimicrobial, antifungal, anticancer, and cardioprotective properties. However, environmental factors such as solvent polarity and temperature can influence its biological activity. This work determined how solvent polarity and temperature affected the molecular, photophysical, and thermodynamic properties of SA in gas and various solvents using semi-empirical (MP6), Hartree-Fock (HF) with the B3LYP method and a 6-311++G(d,p) basis set, and density functional theory (DFT) with various basis sets, such as 3TO-3G*, 3-21G+, 6-31G++G(d,p), 6-311++G(d,p), aug-CC-PVDZ, LanL2DZ, SDD, and DGD2VP. The results indicated that solvent polarity influences molecular and spectroscopic properties, such as bond angles, dihedral angles, bond lengths, FTIR spectra, solvation energy, dipole moments, HOMO-LUMO band gaps, chemical reactivity, and thermodynamic properties, resulting from interactions between the drug and solvent molecules. The findings suggested that increasing the temperature within the range of 100 to 1000 Kelvin leads to an increase in heat capacity, enthalpy, and entropy due to molecular vibrations, ultimately causing degradation and instability in SA. Furthermore, the results showed that SA underwent a redshift in the absorption peak (from 320.18 to 356.26 nm) and a shift in the fluorescence peak (from 381 to 429 nm) in the solvent phase compared to those in the gas phase. Overall, this study provides background knowledge on how solvent polarity and temperature affect the properties of SA molecules.

Computational studies on a selection of phosphite esters as antioxidants for polymeric materials

CONTEXT

Phosphite esters, a class of organo-phosphorus compounds, are widely used as non-discolouring antioxidants in many polymeric products. Apart from normal radical scavenging, they prevent the splitting of hydroperoxides (ROOH), one of the initial products of autoxidation, from forming extremely reactive free radicals such as alkoxy (RO.) and hydroxy (.OH) radicals. The inherent molecular properties of antioxidants and the chemistry of their action are essential for researchers working in this field of science. Four organo-phosphorous compounds well-known for their antioxidant activity are selected here for theoretical analysis: Tri(m-methylphenyl) phosphite (m-TMPP), Tri(4-methyl-2,6-di-tert-butylphenyl) phosphite (TMdtBPP), Tri(allylphenyl) phosphite (TAPP) and Tri(mercaptobenzothiazoyl) thiophosphate (TMBTTP). The antioxidant activity exhibited by these compounds is theoretically verified, and the results are consistent with the available experimental data. Such theoretical predictions offer advantages in scientific research, particularly when researchers need to select certain molecules as antioxidants for experiments from a pool of molecular systems.

METHODS

The chemical computations presented in this report are done in Gaussian 16 program package. The procedure of density functional theory (DFT) with the model chemistry B3LYP/6-31G(d,p) is used to generate computational data. Global reactivity indices, thermochemical data, Fukui functions, molecular electrostatic potential and NMR spectra are computed for the chosen molecular systems from their optimized geometries.

Investigation on the Influence of Solvents Environment on the Optoelectronic Properties of the Fluorescent Probe 1,3,4-Oxadiazole Analogues: A Combined Theoretical and Experimental Study

This study investigates the photophysical properties of a nitrobenzene-substituted 1,3,4-oxadiazole derivative (OX-NO) using both theoretical and experimental methods. The impact of the solvent on OX-NO absorption and fluorescence spectra, as well as its fluorescence quantum yield, was initially studied. A noticeable bathochromic shift in the Stokes shift indicated a π→ π* transition within the molecules. Solute-solvent interactions were analysed using Catalan parameters, distinguishing between specific and nonspecific interactions. Excited state dipole moments were derived from Lippert's, Bakshiev's, and Chamma Viallet's equations, showing increased polarity in the excited state compared to the ground state. Ground state dipole moments were determined via solvatochromic shift methods and ab initio techniques. Additionally, detailed analyses of bond length, angles, dihedral angles, Mulliken charge distribution, and HOMO-LUMO energy gap were conducted using the DFT-B3LYP-6-311G basis set in Gaussian-09 W. The energy band gap values obtained from theoretical calculations and experimental methods (cyclic voltammetry and UV-Visible spectroscopy) exhibited excellent agreement. Reactive sites such as electrophilic and nucleophilic regions were identified through total electron density, electrostatic maps, molecular electrostatic potential, and 3D plots using DFT computational analysis. Global descriptors were employed to characterize the compounds' chemical reactivity comprehensively. The observed photophysical attributes underscore the potential of these fluorophores in various applications like organic light-emitting diodes, solar cells, and chemosensors. This study contributes crucial insights into the optoelectronic properties of nitrobenzene-substituted 1,3,4-oxadiazole derivatives, paving the way for their future integration in advanced technological domains.

Revisiting nucleophilicity: an index for chemical reactivity from a CDFT approach

CONTEXT

Understanding and predicting the nucleophilic reactivity are paramount in elucidating organic chemical reactions and designing new synthetic pathways. In this study, we propose a nucleophilicity index within the framework of Conceptual Density Functional Theory (CDFT). Through rigorous theoretical formulations, we introduce an original quantum reactivity descriptor that captures the nucleophilic propensity of molecules based on their electronic structure and chemical environment. Subsequently, this proposed index is applied to a series of nucleophiles (pyrrolidines derivatives), spanning a diverse range of chemical functionalities. Our computational assessments reveal insightful correlations between the predicted nucleophilicity index and experimental observations of nucleophilic behavior. Thereby, they offer a promising avenue for advancing the understanding of organic reactivity and guiding synthetic efforts.

METHODS

Experimentally, Mayr's experimental parameters accounting for nucleophilicity were selected for the pyrrolidines. This study used DFT calculations at the B3LYP/Aug-cc-pVTZ level of theory using the Gaussian 16 program. Geometry optimization was thus performed, and the methodology employed for the computation of quantum reactivity descriptor is presented. Solvent effect was also taken into account using IEFPCM, and empirical dispersion correction (GD3) was employed.

Theoretical Study of the Mechanism of the Formation of Azomethine Ylide from Isatine and Sarcosine and Its Reactivity in 1,3-Dipolar Cycloaddition Reaction with 7-Oxabenzonorbornadiene

The reaction mechanism of tthe formation of azomethine ylides from isatins and sarcosine is addressed in the literature in a general manner. This computational study aims to explore the mechanistic steps for this reaction in detail and to assess the reactivity of formed ylide in a 1,3-dipolar cycloaddition reaction with 7-oxabenzonorbornadiene. For this purpose, density functional theory (DFT) calculations at the M06-2X(SMD,EtOH)/6-31G(d,p) level were employed. The results indicate that CO2 elimination is the rate-determining step, the activation barrier for 1,3-dipolar cycloaddition is lower, and the formed ylide will readily react with dipolarophiles. The substitution of isatine with electron-withdrawal groups slightly decreases the activation barrier for ylide formation.

Predicting phase-I metabolism of piceatannol: an in silico study

Piceatannol is a natural compound found in plants and can be derived from resveratrol. While resveratrol has been extensively researched for its effects and how the body processes it, there are concerns about its use. These concerns include its limited absorption in the body, the need for specific dosages, potential interactions with other drugs, lack of standardization, and limited clinical evidence to support its benefits. Interestingly, Piceatannol, another compound derived from resveratrol, has received less attention from researchers but appears to offer advantages. It has better bioavailability and seems to have a more favorable therapeutic profile compared to resveratrol. Surprisingly, no previous attempts have been made to explore or predict the metabolites of piceatannol when it interacts with the enzyme cytochrome P450. This study aims to fill that gap by predicting how piceatannol is metabolized by cytochrome P450 and assessing any potential toxicity associated with its metabolites. This research is interesting because it's the first of its kind to investigate the metabolic fate of piceatannol, especially in the context of cytochrome P450. The findings have the potential to significantly contribute to the field of piceatannol research, particularly in the food industry where this compound has applications and implications.

Graphical abstract

Study on Regio- and Diastereoselectivity of the 1,3-Dipolar Cycloaddition Reaction of Azomethine Ylide with 2-(Benzo[d]thiazol-2-yl)-3-(aryl)acrylonitrile: Synthesis, Spectroscopic, and Computational Approach

An unprecedented and efficient three-component 1,3-dipolar cycloaddition reaction using (E)-2-(benzo[d]thiazol-2-yl)-3-(aryl)acrylonitriles 4a-g and an in situ generated azomethine ylide 3 from isatin and N-methylglycine is described. The reaction exhibits exclusive regioselectivity, resulting in the formation of 3'-(benzo[d]thiazol-2-yl)-1'-methyl-2-oxo-4'-(aryl)spiro[indoline-3,2'-pyrrolidine]-3'-carbonitriles regioisomers through exo/endo approaches. The diastereoselectivity of the reaction is highly dependent on the substitution pattern of the phenyl ring in dipolarophiles 4a-g, leading to the formation of exo-/endo-cycloadducts in varying ratios. To understand the stereoselectivity, the transition state structures were optimized using the TS guess geometry with the QST3-based method. The reaction mechanism and regioselectivity were elucidated by evaluating global and local electrophilicity and nucleophilicity descriptors at the B3LYP/cc-pVTZ level of theory, along with considerations based on the HSAB principle. The analysis of global electron density transfer (GEDT) showed that the reactions are polar and electron density fluxes from azomethine ylide 3 toward dipolarophile 4a-g. It was found from the molecular electrostatic potential map (MESP) that at the more favorable transition state, approach of reactants locates the oppositely charged regions over each other resulting in attractive forces between the two fragments. The computational results are consistent with the experimental observations, confirming that the reactions proceed through an asynchronous one-step mechanism.

Computational Chemistry Strategies to Investigate the Antioxidant Activity of Flavonoids-An Overview

Despite several decades of research, the beneficial effect of flavonoids on health is still enigmatic. Here, we focus on the antioxidant effect of flavonoids, which is elementary to their biological activity. A relatively new strategy for obtaining a more accurate understanding of this effect is to leverage computational chemistry. This review systematically presents various computational chemistry indicators employed over the past five years to investigate the antioxidant activity of flavonoids. We categorize these strategies into five aspects: electronic structure analysis, thermodynamic analysis, kinetic analysis, interaction analysis, and bioavailability analysis. The principles, characteristics, and limitations of these methods are discussed, along with current trends.

Tunable molecular editing of indoles with fluoroalkyl carbenes

Building molecular complexity from simple feedstocks through precise peripheral and skeletal modifications is central to modern organic synthesis. Nevertheless, a controllable strategy through which both the core skeleton and the periphery of an aromatic heterocycle can be modified with a common substrate remains elusive, despite its potential to maximize structural diversity and applications. Here we report a carbene-initiated chemodivergent molecular editing of indoles that allows both skeletal and peripheral editing by trapping an electrophilic fluoroalkyl carbene generated in situ from fluoroalkyl N-triftosylhydrazones. A variety of fluorine-containing N-heterocyclic scaffolds have been efficiently achieved through tunable chemoselective editing reactions at the skeleton or periphery of indoles, including one-carbon insertion, C3 gem-difluoroolefination, tandem cyclopropanation and N1 gem-difluoroolefination, and cyclopropanation. The power of this chemodivergent molecular editing strategy has been highlighted through the modification of the skeleton or periphery of natural products in a controllable and chemoselective manner. The reaction mechanism and origins of the chemo- and regioselectivity have been probed by both experimental and theoretical methods.

Polarizability matters in enantio-selection

The prevalence of chirality, or, handedness in biological world is a fundamental phenomenon and a characteristic hallmark of life. Thus, understanding the origin of enantio-selection, i.e., the sense and magnitude of asymmetric induction, has been a long-pursued goal in asymmetric catalysis. Herein, we demonstrated a polarizability-derived electronic effect that was shown to be capable of rationalizing a broad range of stereochemical observations made in the field of asymmetric catalysis. This effect provided a consistent enantio-control model for the prediction of major enantiomers formed in a ruthenium-catalyzed asymmetric transfer hydrogenations of ketones. Direct and quantitative linear free energy relationships between substrates' local polarizabilities and observed enantio-selectivity were also revealed in three widely known asymmetric catalytic systems covering both reductions and oxidations. This broadly applicable polarizability-based electronic effect, in conjunction with conventional wisdom mainly leveraging on steric effect considerations, should aid rational design of enantio-selective processes for better production of chiral substances.

Computational investigation of structural, electronic, and spectroscopic properties of Ni and Zn metalloporphyrins with varying anchoring groups

Porphyrins are prime candidates for a host of molecular electronics applications. Understanding the electronic structure and the role of anchoring groups on porphyrins is a prerequisite for researchers to comprehend their role in molecular devices at the molecular junction interface. Here, we use the density functional theory approach to investigate the influence of anchoring groups on Ni and Zn diphenylporphyrin molecules. The changes in geometry, electronic structure, and electronic descriptors were evaluated. There are minimal changes observed in geometry when changing the metal from Ni to Zn and the anchoring group. However, we find that the distribution of electron density changes when changing the anchoring group in the highest occupied and lowest unoccupied molecular orbitals. This has a direct effect on electronic descriptors such as global hardness, softness, and electrophilicity. Additionally, the optical spectra of both Ni and Zn diphenylporphyrin molecules exhibit either blue or red shifts when changing the anchoring group. These results indicate the importance of the anchoring group on the electronic structure and optical properties of porphyrin molecules.

Harvesting Chemical Understanding with Machine Learning and Quantum Computers

It is tenable to argue that nobody can predict the future with certainty, yet one can learn from the past and make informed projections for the years ahead. In this Perspective, we overview the status of how theory and computation can be exploited to obtain chemical understanding from wave function theory and density functional theory, and then outlook the likely impact of machine learning (ML) and quantum computers (QC) to appreciate traditional chemical concepts in decades to come. It is maintained that the development and maturation of ML and QC methods in theoretical and computational chemistry represent two paradigm shifts about how the Schrödinger equation can be solved. New chemical understanding can be harnessed in these two new paradigms by making respective use of ML features and QC qubits. Before that happens, however, we still have hurdles to face and obstacles to overcome in both ML and QC arenas. Possible pathways to tackle these challenges are proposed. We anticipate that hierarchical modeling, in contrast to multiscale modeling, will emerge and thrive, becoming the workhorse of in silico simulations in the next few decades.

Fragment-Based Deep Learning for Simultaneous Prediction of Polarizabilities and NMR Shieldings of Macromolecules and Their Aggregates

Simultaneous prediction of the molecular response properties, such as polarizability and the NMR shielding constant, at a low computational cost is an unresolved issue. We propose to combine a linear-scaling generalized energy-based fragmentation (GEBF) method and deep learning (DL) with both molecular and atomic information-theoretic approach (ITA) quantities as effective descriptors. In GEBF, the total molecular polarizability can be assembled as a linear combination of the corresponding quantities calculated from a set of small embedded subsystems in GEBF. In the new GEBF-DL(ITA) protocol, one can predict subsystem polarizabilities based on the corresponding molecular wave function (thus electron density and ITA quantities) and DL model rather than calculate them from the computationally intensive coupled-perturbed Hartree-Fock or Kohn-Sham equations and finally obtain the total molecular polarizability via a linear combination equation. As a proof-of-concept application, we predict the molecular polarizabilities of large proteins and protein aggregates. GEBF-DL(ITA) is shown to be as accurate enough as GEBF, with mean absolute percentage error <1%. For the largest protein aggregate (>4000 atoms), GEBF-DL(ITA) gains a speedup ratio of 3 compared with GEBF. It is anticipated that when more advanced electronic structure methods are used, this advantage will be more appealing. Moreover, one can also predict the NMR chemical shieldings of proteins with reasonably good accuracy. Overall, the cost-efficient GEBF-DL(ITA) protocol should be a robust theoretical tool for simultaneously predicting polarizabilities and NMR shieldings of large systems.

Flexibility of Binding Site is Essential to the Ca2+ Selectivity in EF-Hand Calcium-Binding Proteins

High binding affinity and selectivity of metal ions are essential to the function of metalloproteins. Thus, understanding the factors that determine these binding characteristics is of major interest for both fundamental mechanistic investigations and guiding of the design of novel metalloproteins. In this work, we perform QM cluster model calculations and quantum mechanics/molecular mechanics (QM/MM) free energy simulations to understand the binding selectivity of Ca2+ and Mg2+ in the wild-type carp parvalbumin and its mutant. While a nonpolarizable MM model (CHARMM36) does not lead to the correct experimental trend, treatment of the metal binding site with the DFTB3 model in a QM/MM framework leads to relative binding free energies (ΔΔGbind) comparable with experimental data. For the wild-type (WT) protein, the calculated ΔΔGbind is ∼6.6 kcal/mol in comparison with the experimental value of 5.6 kcal/mol. The good agreement highlights the value of a QM description of the metal binding site and supports the role of electronic polarization and charge transfer to metal binding selectivity. For the D51A/E101D/F102W mutant, different binding site models lead to considerable variations in computed binding affinities. With a coordination number of seven for Ca2+, which is shown by QM/MM metadynamics simulations to be the dominant coordination number for the mutant, the calculated relative binding affinity is ∼4.8 kcal/mol, in fair agreement with the experimental value of 1.6 kcal/mol. The WT protein is observed to feature a flexible binding site that accommodates a range of coordination numbers for Ca2+, which is essential to the high binding selectivity for Ca2+ over Mg2+. In the mutant, the E101D mutation reduces the flexibility of the binding site and limits the dominant coordination number of Ca2+ to be seven, thereby leading to reduced binding selectivity against Mg2+. Our results highlight that the binding selectivity of metal ions depends on both the structural and dynamical properties of the protein binding site.

Surface Chemistry of Biologically Active Reducible Oxide Nanozymes

Reducible metal oxide nanozymes (rNZs) are a subject of intense recent interest due to their catalytic nature, ease of synthesis, and complex surface character. Such materials contain surface sites which facilitate enzyme-mimetic reactions via substrate coordination and redox cycling. Further, these surface reactive sites are shown to be highly sensitive to stresses within the nanomaterial lattice, the physicochemical environment, and to processing conditions occurring as part of their syntheses. When administered in vivo, a complex protein corona binds to the surface, redefining its biological identity and subsequent interactions within the biological system. Catalytic activities of rNZs each deliver a differing impact on protein corona formation, its composition, and in turn, their recognition, and internalization by host cells. Improving the understanding of the precise principles that dominate rNZ surface-biomolecule adsorption raises the question of whether designer rNZs can be engineered to prevent corona formation, or indeed to produce "custom" protein coronas applied either in vitro, and preadministration, or formed immediately upon their exposure to body fluids. Here, fundamental surface chemistry processes and their implications in rNZ material performance are considered. In particular, material structures which inform component adsorption from the application environment, including substrates for enzyme-mimetic reactions are discussed.

Some Recent Advances in Density-Based Reactivity Theory

Establishing a chemical reactivity theory in density functional theory (DFT) language has been our intense research interest in the past two decades, exemplified by the determination of steric effect and stereoselectivity, evaluation of electrophilicity and nucleophilicity, identification of strong and weak interactions, and formulation of cooperativity, frustration, and principle of chirality hierarchy. In this Featured Article, we first overview the four density-based frameworks in DFT to appreciate chemical understanding, including conceptual DFT, use of density associated quantities, information-theoretic approach, and orbital-free DFT, and then present a few recent advances of these frameworks as well as new applications from our studies. To that end, we will introduce the relationship among these frameworks, determining the entire spectrum of interactions with Pauli energy derivatives, performing topological analyses with information-theoretic quantities, and extending the density-based frameworks to excited states. Applications to examine physiochemical properties in external electric fields and to evaluate polarizability for proteins and crystals are discussed. A few possible directions for future development are followed, with the special emphasis on its merger with machine learning.