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.

The significance of the anthracene moiety on nonlinear optical (NLO) characteristics is thoroughly examined. The presence of strong electron donor and acceptor groups, large and prolonged conjugation transfer axis, amplifies the push–pull action and increases NLO responses. The values of χ3 obtained for AC derivatives are considerably larger (10−3 esu), indicating that they accurately reflect NLO reactions. According to the optical limiting (OL) investigation, AC has a strong limiting behavior with action beginning at 1.6 KW/cm2. The relationship between transmittance and intensity has demonstrated their potential use in OL applications. Nonlinear optical studies show that all conjugated anthracene chalcones are potential materials for OL devices.

(CF3)2CFCN with excellent insulation performance has been proposed to replace the traditional SF6 as a new insulating medium in power equipment. In the present study, the molecular structure and radiative efficiency (RE) of (CF3)2CFCN are calculated and compared with SF6 based on density-functional theory (DFT) calculation. The decomposition of pure (CF3)2CFCN and the basic interactions between (CF3)2CFCN and hydroxyl radical in the constructed co-crystal of (CF3)2CFCN-H2O have been simulated by applying Monte-Carlo calculation and Car–Parrinello molecular dynamics method, in order to obtain reasonable and full-scale atmospheric dissociation processes. Then the detailed decomposition pathways are learned with DFT method of M06-2X. The rate constants of different pathways are further applied for calculating the atmosphere lifetime of (CF3)2CFCN, to evaluate the possibility of applying it as an alternative gas of SF6 in power equipment. All the atmospheric chemical behaviors are determined by electronic structure and reflected by the decomposition pathways of (CF3)2CFCN with interacting with hydroxyl radicals. Rather than traditional hypothesizing reaction models given by the chemical intuitions, this study provides a new view angle to understand the dissociation pathways based on first-principle molecular dynamic method, and to evaluate the atmospheric chemical behaviors of other protective gas of power equipment.

Thionyl fluoride (SOF2) is the dominant decomposition by-product in SF6 under electrical discharges and a novel fluorinating reagent for organic synthesis to replace sulfuryl fluoride (SO2F2). Since both SF6 and SO2F2 are strong green-house gases, for the sake of environmental concern, tropospheric oxidation of SOF2 by OH radicals in the presence of O2 has been investigated using various computational methods including density functional M06-2X, coupled-cluster (CCSD), the explicitly correlated RCCSD(T)-F12, Gaussian-4, ROCBS-QB3, and Weizmann-1 theories. The SO bond association between SOF2 and OH proceeds via the barriers of 1–3 kcal/mol to form various shallow wells HOSOF2 (−3 to −8 kcal/mol) linked by Berry pseudorotations and followed by HF-elimination. Interception of the HOSOF2 adducts by O2 produce HO2 and SO2F2 predominantly via the concerted SO bond association/dissociation and proton-transfer. The atmospheric lifetime and radiative efficiency for SOF2 were calculated to be 1.2–1.5 years and 0.223 W/m2/ppb, respectively. The global warming potential of SOF2 was estimated to be 169–211, as indicative of an eco-friendly gas. However, the environmental impact of SOF2 should take into account the production of SO2F2 and HO2 due to oxidation.

The electronic and structural properties of the armchair and zigzag single-walled GaN nanotubes (GaNNTs) are studied by using density functional theory. The effects of tube diameter on the GaN bond lengths, the axial lattice constant, the Fermi energy, the buckling separation, and the bandgap of the tube are investigated. It is revealed that there is a correlation between the bandgap and the buckling; the smaller the bandgap, the higher the buckling. The results show that by increasing diameter of tubes the buckling separation decreases. The 4p-orbitals of Ga atoms and 2p-orbitals of N have the main role to the valence band maximum and the conduction band minimum, respectively. All armchair and zigzag GaNNTs are semiconductors having indirect and direct bandgap, respectively. It is also found that by increasing the diameter of nanotubes the bandgap increases, for both armchair and zigzag GaNNTs. The consequences of this study can undoubtedly be useful in future experimental works on optoelectronic devices.

The effects of shear deformation on the electronic structure and optical properties of intrinsic arsenene and arsenene adsorbed Li are investigated using a first-principles approach. Shear deformation can transform the band gap of intrinsic arsenene from indirect-direct-indirect. After the adsorption of Li atoms by arsenene, it transforms from semiconductor to metal with a very obvious hybridization between the 2s orbital of Li and the 4p orbital of As. With the increase of shear deformation, the charge transfer increases and has a good modulation of the absorption coefficient and reflectivity. The adsorption of multiple Li atoms makes the dielectric constant of arsenene more sensitive to low energy spectra and increases the imaginary part of the photoconductivity, which increases the refractive index and decreases the extinction coefficient to some extent.

Employing Fourier-transform technique, this work derives the molecular multicenter integrals for the modified Slater-type orbitals (STOs) with arbitrary principal and angular quantum numbers, in which the spherical harmonics parts are the homogeneous solutions of original STOs. The integrands include spherical Bessel functions and associated Legendre functions. One-electron three-center nuclear attraction integral and two-electron four-center Coulomb repulsion integral are presented as numerical integrations in two dimensions and three dimensions, respectively. A simple Python script is provided to run the formulas. The correctness and computational efficiency of the script have been verified.

The development of kinetic energy (KE) functionals is one of the current challenges in density functional theory (DFT). The Yukawa non-local KE functionals [Phys. Rev. B 103, 155127 (2021)] have been shown to describe accurately the Lindhard response of the homogeneous electron gas (HEG) directly in the real space, without any step in the reciprocal space. However, the Yukawa kernel employs an exponential function which cannot be efficiently represented in conventional Gaussian-based quantum chemistry codes. Here, we present an expansion of the Yukawa kernel in Gaussian functions. We show that for the HEG this expansion is independent of the electronic density, and that for general finite systems the accuracy can be easily tuned. Finally, we present results for atomistic sodium clusters of different sizes, showing that simple Yukawa functionals can give superior accuracy as compared to semilocal functionals.

Developing 2D materials with intrinsic magnetism is an essential issue owing to their wide potential applications in spintronics. Here, a type of transition metal tetraborides, TMB4, (TM = TiCo) monolayers were systematically investigated by employing first principles calculations. Our results showed that the predicted structures hold buckled motif, ultrahigh stability and large magnetic anisotropy energy. It is revealed that CrB4, MnB4, and FeB4 monolayers are robust ferromagnetism, differently, TiB4, VB4, and CoB4 monolayers are stable anti-ferromagnetism. Based on the Monte Carlo simulation, the critical temperatures of these magnetic systems are around 177–755 K. Most importantly, CoB4 monolayer is confirmed to be an antiferromagnetic semiconductor with out-of-plane magnetic easy axis and out-of-plane piezoelectricity with large piezoelectric stress coefficients. Our study suggests that the 2D TMB4s hold promising applications for spintronic devices and piezoelectric devices.

A detailed mechanistic study of ring-opening polymerization (ROP) of l-lactide by a lanthanum aryloxide complex, La(OTMP)3 (−OTMP = 2,4,6-trimethylphenolate), is carried out using DFT theoretical calculations. Both initiation and propagation steps were considered. The calculations reveal the two-step coordination-insertion mechanism, proceeding via an unprecedented lanthanum π-arene intermediate, with the selective acyl-oxygen bond scission of the monomer. The first step of phenolate insertion into the La − O bond of the initiator is rate-limiting, and the bulkiness of the aryloxide ligand initiates the ROP slowly with the activation energy of 19.3 kcal mol−1, in consistent with the activation energy (15 kcal mol−1) obtained with previous kinetic experiment. Furthermore, a rationale for the broadening of molecular weight distribution reported in this initiating system is also provided.

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.

The equilibrium geometries, and electronic and magnetic properties of phosphorus, cobalt-phosphorus, and nickel-phosphorus (Pn+1, CoPn, and NiPn, n = 1–24) clusters have been investigated by using first principle calculations. The doping with cobalt or nickel atom favors the endohedral structures in which the metal atom is encapsulated inside the phosphorus framework, while geometrical structures are metal-dependent. The growth pattern behaviors and stabilities are examined from the binding energies, the second-order energy differences, and the HOMO–LUMO gaps. The doping with Co or Ni atom contributes to strengthening the stability of the phosphorus frame with a marked improvement in the case of Ni atom. The total spin magnetic moment is enhanced with doping with Co atom. In contrast, the magnetic moment is quenched in the case of NiPn. Vertical electron affinities and ionization potentials are also reported and discussed.

Developing the oxygen reduction reaction (ORR) catalysts with high catalytic activity and low cost is necessary to improve the energy conversion efficiency of hydrogen fuel cells. MXenes with oxygen-functional terminals have been extensively used as the substrate materials of single-atom electrocatalytsts. Herein, the novel sulfur-functionalized Ti3C2S2 supporting 3d, 4d, and 5d transition metal (TM) atoms (TM = Fe, Co, Ni, Cu, Ag, Au, Ir, Os, Pd, Pt, Rh, and Ru) are theoretically constructed and investigated for their ORR activity and stability by the first-principles calculations. Ni/Ti3C2S2, Pd/Ti3C2S2, and Ir/Ti3C2S2 are screened as the potential ORR catalysts based on their lower overpotentials, while the single-atom Fe, Ru, and Os with unfilled d electrons and Cu, Ag, and Pt with filled d electrons exhibit high overpotentials up to about 1 V. Compared with Ti3C2O2, Ti3C2S2-based single-atom catalysts show higher ORR activity due to the larger charge density and moderate adsorption ability to oxygen intermediates.

Perovskite solar cells (PSC) are the third-generation solar cells, which have a low production cost and have achieved similar laboratory scale efficiencies as the first-generation silicon solar cells. In the present work, we performed density functional theory calculations on the organic material, poly[3-(5-carboxypentyl) thiophene-2,5-diyl] regioregular (P3CPenT). The ground state and excited state properties of P3CPenT are calculated. The HOMO-LUMO levels and electronic bandgap obtained from the calculations are compared with the experimental values for validation of the theory. A high electron reorganization energy and low hole reorganization energy ensures that P3CPenT aids the flow of holes and hinders the flow of electrons. The optical bandgap and low exciton binding energy indicates its potential as a hole transport layer (HTL). The ease of fabrication of P3CPenT is established by showing that the oligomer is soluble in dimethyl sulfoxide (DMSO), which is the most commonly utilized solvent for the fabrication of PSCs. The hydrophobic nature of P3CPenT as established by the present work shows that it is stable with moisture and would thus protect the underlying MAPbI3 perovskite layer from decomposing and hence improve its lifetime and stability. Fill factor (FF) of 78.07% and a power conversion efficiency (PCE) of 14.88% has been obtained for PSC with P3CPenT HTL.

New conception of spin-tautomery was developed based on the results of quantum chemical investigation of the endohedral Y@C60 complex. The embedding energies of yttrium into the fullerene cavity, dipole moments, polarizabilities, and IR spectra in the doublet and quartet spin states were calculated by the density-functional theory quantum chemical methods. The degeneracy degree of the state of the complex is retained upon doublet–quartet excitation, since a twofold increase in the number of electron spin projections is compensated by a twofold decrease in the number of equivalent potential energy minima. The non-conservation of spin by an endohedral complex with a heavy atom makes it possible to interpret the interconversion of doublet and quartet states as a non-degenerate spin-tautomery.

The reaction mechanism of cytochrome P450-mediated intramolecular cyclization of 2-aminoamide compounds to imidazolinone was studied by density functional theory. The cyclization reaction involves three steps: hydrogen abstraction, dehydration of intermediates to zwitterions and final ring closure. Interestingly, high spin (HS) state P450-catalyzed dehydration exhibits a mechanism distinct from conventional processes such as in low spin state. In HS pathways, the hydroxyl group after hydrogen abstraction does not rebound but produce an intermediate, which makes the second hydrogen abstraction regioselective. Regioselectivity leads to diverse intermediates and mechanisms to zwitterion, which implies different functions of the high and low spin states P450. The alkylamine nitrogen and amide group are key groups to enables regioselectivity of in HS pathway. Small changes of molecular structure can affect the molecular transformation process, indicating the complex regulation of electronic state to reaction process. The results lay the theoretical basis for the regioselectivity determined by P450 enzyme and substrate structure together. The research establishes a foundation for the drug design, drug metabolite, and synthesis of nitrogen-containing heterocyclic drugs.

In recent years, bis-1,2,4-triazine ligands have been widely used in actinide separation processes for their good separation ability and stability in high acidity. However, the hard stripping of BTP, kinetics sluggish of BTBP, and inexhaustive separation of BTPhen are still issues to be improved. Here, we evaluated the effects of bis-1,2,4-triazine ligands containing 6-membered aliphatic rings L1-3 and bis-1,2,4-triazine ligands containing 5-membered aliphatic rings L4-6 on selective separation of Am(III)/Eu(III) to understand the structure-effect relationship of ligands (skeleton of pyridine L1,4, bipyridine L2,5, and phenanthroline L3,6). Six bis-1,2,4-triazine ligand structures are optimized based on density function theory(DFT). Herein, complexations of L2, L3 L5 L6 with Am/Eu ions were investigated. The results show that all BTPs ligands preferentially bind to Am(III). The electronic structures of the [M(L)2(NO3)]2+ (M = Am, Eu) complex and the bonding properties between metal and ligand were investigated. The results suggest that phenanthroline containing six-membered aliphatic rings L3 shows the best affinity for Am(III) and phenanthroline containing five-membered aliphatic rings L6 show faster dynamics. The calculated thermodynamic and separation factors indicate that L6 has the best selective separation of Am(III)/Eu(III). In conclusion, the skeleton of phenanthroline has the best extraction effect on Am(III), while the kinetics and separation effect can be improved by adjusting aliphatic rings.

The efficiency of Pb substitution on the Sn site of CsSnI3 is studied theoretically utilizing DFT as employed by Wien2k code. The energetical, structural, and thermodynamic stability criteria have been fully explained for the studied compounds. Structural and mechanical properties have shown the thermodynamic stability of the studied compounds and their ability to be formed. From their electronic properties, the electronic band gap tuning is observed by systematically substituting Pb in CsSnI3. All these compounds (Pb/CsSnI3) have shown a direct band gap nature within the range 1.11–2.95 eV, a potential indication of their possible usage in fabricating solar cells. On further investigating of their optical properties, the most stable and optically active band gap for solar cell application is observed for CsSn0.75Pb0.25I3 and CsSn0.5Pb0.5I3. Furthermore, the measured minimum thermal conductivity of Pb/CsSnI3 is greatest along the [1 1 1] direction. While the direct proportion predicts that the crystal structure with Pb atoms is anharmonic. High melting temperature, thermal stability, a wide optically active region, and a low Debye temperature indicate plausible operable conditions of these compounds under wide ambient conditions. The optical properties, ductile nature, and the bond bending attributes illustrate that CsSnxPb1−xI3 has exciting potential to be used in flexible electronic devices, solar cells, and optical sensors.

MXenes have the excellent electrochemical properties as electrode of supercapacitors. Using density functional theory, we investigated the electronic properties and quantum capacitance of Zr2CO2 with atomic swap. The atomic swap results in the appearance of Frenkel-type defect and Schottky defect. The negative binding energy confirms the stability of the studied systems. The atomic swap makes ZrC1, ZrC2, ZrO1, ZrO2, CO2 systems maintain the indirect semiconductor character, and CO2 system has the direct semiconductor character. The thermionic emission performance of Zr2CO2 MXene is greatly improved by atomic swap. ZrO1 and ZrO2 systems in aqueous system are appropriate anode materials. The wide voltage has little effect on the electrode type for perfect Zr2CO2, ZrO1, ZrO2, CO1, and CO2 systems, but changes ZrC1 and ZrC2 systems from cathode material in aqueous system to anode material in ionic/organic system. The work function and effective mass are also explored.

Optomechanics is a growing field of research, studies the interaction between optical field and mechanical oscillator. In this study, we theoretically analyze a hybrid system which consists of Fabry Perot cavity containing two-level N- Number of atoms. The cavity having two mirrors one is fixed, and other is oscillating. The oscillating mirror has a position dependent mass, considered as effective mass. The mechanical resonator generates a nonlinear effect because it is position dependent. Dynamics of the system's operators, steady-state solutions, and optical response of the hybrid optomechanical system are analytically calculated. Optical response in the regime of position dependent effective mass (PDEM) are the main result in this article. We deduced that position dependent parameter of the resonator not only effect the dynamics but also the optical response of the optomechanical system.