Continuous effort is dedicated to the discovery of potential drugs for the novel coronavirus-2 both clinically and computationally. Computer-Aided Drug Design CADD is the backbone of drug discovery, and shifting to computational approaches has become a need. Quantitative Structure-Activity Relationship QSAR is a widely used approach in predicting the activity of potential molecules and is an early step in drug discovery. 3CLpro is a highly conserved enzyme in the coronaviruses characterized by its role in the viral replication cycle. Despite the existence of various vaccines, the development of a new drug for SARS-CoV-2 is a necessity to provide cures to patients. In the pursuit of exploring new potential 3CLpro SARS-CoV-2 inhibitors and contributing to the existing literature, this work opted to build and compare three models of QSAR to correlate between the molecules’ structure and their activity: IC50, through the application of MLR, SVR, and SVR-PSO algorithms. The database was selected based on its novelty and proven activity, and its representative descriptors were obtained by the GA algorithm. The built models were plotted and compared following various internal and external validation criteria, and applicability domains for each model were determined. The results demonstrated that the SVR-PSO model performed best in terms of predictive ability and robustness, followed by SVR, and finally MLR. These outcomes prove that the SVR-PSO model is robust and concrete and paves the way for its prediction abilities for future screening of larger inhibitors’ datasets.
On pure and metal, non-metal, co-doped rutile TiO2, DFT simula- tions are performed. For the stability study of doped materials, the defect formation energies of non-metal (S), metal (Fe), and metal and non-metal (Fe/S) co-doped materials are determined. A Ti- rich environment is preferable over an O-rich environment. With values of 2.98 eV, 2.18 eV, 1.58 eV, and 1.40 eV, the bandgap for pristine, S-doped, Fe-doped, and Fe/S co-doped materials is found to be direct. The effective masses (m*) and ratios (R) of charge carriers are also examined, and it is discovered that Fe/S co-doped material has the lowest charge carrier recombination rate. The maximum static dielectric constant is found in the Fe/S co-doped material. Doped material’s absorption spectra shifted into the vis- ible region. Additionally, using SCAPS-1D simulation software, a complete solar cell device study using these materials as ETL is performed for the first time. The absorber layer and the ETL settings have been tweaked to perfection. Current-voltage (IV) characteristics, quantum efficiency (QE), capacitance-voltage (CV) characteristics, and capacitance-frequency (Cf) character- istics are provided for optimize solar cells.When the smallest degree of defect for each layer is taken into account, the solar cell with Fe/S co-doped ETL has the highest efficiency of 34.27%.
Here we show that substituting the ten protons in the dianion of a bispentalene derivative (C18H102-) by six Si2+ dications produces a minimum energy structure with two planar tetracoordinate carbons (ptC). In Si6C18, the ptCs are embedded in the terminal C5 pentagonal rings and participate in a three-center, two-electron (3c-2e) Si-ptC-Si σ-bond. Our exploration of the potential energy surface identifies a triphenylene derivative as the putative global minimum. But robustness to Born-Oppenheimer molecular dynamics (BOMD) simulations at 900 and 1500 K supports bispentalene derivative kinetic stability. Chemical bonding analysis reveals ten delocalized π-bonds, which, according to Hückel’s 4n+2 π-electron rule, would classify it as an aromatic system. Magnetically induced current density analysis reveals the presence of intense local paratropic currents and a weakly global diatropic current, the latter agreeing with the possible global aromatic character of this specie.
The oxygen electroreduction mechanism on the V- and Nb-doped nitrogen-codoped (6,6)armchair carbon nanotube with incorporated MN4 fragment has been studied using the ωB97XD and PBE density functional theory approaches. The metal center in MN4 fragment and the adjacent NC=CN double bond (C2 site) of the support have been revealed as active centers. The metal active centers turned out to be irreversibly oxidized at the first step of ORR affording stable O*, 2O*, or O*HO* adsorbates depending on the applied electrode potential U, that makes them no longer active in ORR. Therefore, the C2 site comes at the forefront in ORR catalysis. Among the metal oxidized forms M(O)N4–, M(O)(O)N4– and M(O)(OH)N4–CNT, the C2 site of the latter turned out to be most active for 4e dissociative ORR. For both metals the last protonation/electron transfer step, HO* + H* = H2O, is the rate-limiting step. The alternative hydrogen peroxide formation is not only thermodynamically less favorable but also kinetically slower than the 4e dissociative ORR route on the C2 site of model M(O)(OH)N4–CNT catalyst.
The three lowest spin states (S=0,1,2) of twelve representative Na13+ isomers have been studied using both, KS-DFT via three hybrid density functionals, and benchmark multireference CASSCF and CASPT2 methods with a couple of Dunning’s correlation consistent basis sets. CASSCF(12,12) geometry optimizations were carried out. Since 12 electrons in 12 active orbitals span the chemically-significant complete valence space, the results of the present study provide benchmarks for Na13+. The CASPT2(12,12)/cc-pVTZ* lowest energy structures are three nearly degenerate singlets (S=0): an isomer formed from two pentagonal bipyramids fused together (PBPb), a capped centered-squared antiprism [CSAP-(1,3)] and an optimum tetrahedral OPTET(II) structure, the last two lying 0.88 and 1.63 kcal/mol above the first, respectively. The lowest triplet (S=1) and quintet (S=2) states lie 4.33 and 3.77 kcal/mol above the singlet global minimum, respectively. The latter is a deformed icosahedron while the former is a CSAP-(1,3). The flatness of the potential energy surface of this cluster suggests a rather strong dynamical character at finite temperature. Prediction of the lowest energy structures and electronic properties is crucially sensitive both to non-dynamical and dynamical electron correlation treatment. The CASPT2 vertical ionization energy is 3.66 eV, in excellent agreement with the $3.6 \pm 0.1$ eV experimental figure. All the isomers are found to have a strong multireference character, thus making Kohn-Sham density functional theory fundamentally inappropriate for these systems. Only large multiconfigurational complete active space self-consistent field (CASSCF) wavefunctions provide a reliable zeroth-order description; then the dynamic correlation effects must be properly taken into account for a truly accurate account of the structural and energetic features of alkali-metal clusters.
Density functional calculations have been carried out to investigate the possibility of trapping of noble gas dimers by cyclocarbon dimer. Parallel-displaced conformation of the cyclocarbon dimer is found to be the minimum energy structure. Non-covalent interaction is found to hold the noble gas dimers. The lighter noble gases (He, Ne) posses repulsive interactions, the heavier one (Ar, Kr) are held by attractive interactions forming genuine bonds. Each of the noble gas atoms in turn forms non-covalent interaction with the cyclocarbon monomers. The bond dissociation energy of the noble gas dimers dramatically increases inside the cyclocarbon dimer. Energy decomposition analysis reveals that dispersion plays the major role towards the stabilization energy.
Interactions of antimony-oxide clusters with trypanothione have been modelled to understand their inhibitory activity against leishmaniasis. Trypanothione is essential for the survival of leishmania parasites because it is responsible for maintaining their cellular thiol-disulfide redox regulation. Density functional theory (DFT) calculations show that the SbV oxide clusters form hydrogen bonds from the oxygens to the amine and carboxyl group of the trypanothione. The reaction between trypanothione and the SbV oxide cluster does not break the S-S bond of trypanothione, whereas the reaction with antimony-oxide clusters containing at least one SbIII atom leads to dissociation of the S-S bond of both the oxidized and the reduced form of trypanothione suggesting that antimony-oxide clusters with at least one SbIII atom may destroy trypanothione that is vital for the parasite metabolism.
Spectrum graph theory not only facilitate comprehensively reflflect the topological structure and dynamic characteristics of networks, but also offer signifificant and noteworthy applications in theoretical chemistry, network science and other fifields. Let Ln (8, 4) represent a linear octagonal-quadrilateral network, consisting of n eight-member ring and n four-member ring. The M¨obius graph Qn(8, 4) is constructed by reverse identifying the opposite edges, whereas cylinder graph Q’n (8, 4) identififies the opposite edges by order. In this paper, the explicit formulas of Kirchhoffff indices and complexity of Qn(8, 4) and Q‘n (8, 4) are demonstrated by Laplacian characteristic polynomials according to decomposition theorem and Vieta’s theorem. In surprise, the Kirchhoffff index of Qn(8, 4)(Q’n (8, 4)) is approximately one-third half of its Wiener index as n → ∞.
Geometries and electronic properties of selfassembled (InN)12n (n=1-9) nanosheets or nanowires are investigated at the PBE1PBE level. The growth patterns of semiconductor InN nanocrystal are revealed. Relative stabilities of (InN)12n (n=1-9) are studied. The even-numbered (InN)12n (n is even) nanoclusters have stronger stabilities than the neighboring odd-numbered (InN)12n ones. The particular stable geometries are assigned as the (InN)48 nanosheet for selfassembled film nanomaterials. The calculated energy gaps exhibit even-odd oscillation and reveal that (InN)12n (n=1-9) semiconductor nanoclusters are apparently good optoelectronic or energy nanomaterials; Furthermore, (InN)12n nanoclusters with energy gaps at the visible regions have potential applications in microelectronic and optoelectronic nanodevices. The slightly varied energy gaps for (InN)12n nanowires reveals they maintain individual (InN)12 properties. The calculated charge-transfers for (InN)12n (n=1-9) reflect that their ionic bonding enhances the stabilites of nanoclusters and that ionic bonding in (InN)12n (n=1-9) nanoclusters exists with covalent.
Theoretical investigation of metastable small boron clusters nucleation in a plasma stream with helium is carried out using the non-Hermitian formalism. The electronic structure and decay time of excited states of the gas-phase clusters are considered. The formation of pure small boron stable clusters, as well as new metastable B-He systems and unstable He-He systems, is discussed.
A new class of materials was identified as Cu20Nb monolayer clusters, which hosts strong correlation electrons. Direct observation show maps of electron wave function patterns, where the symmetry, brightness and size of features was directly related to the position of a Nb atom in Cu lattice, around which the electron was bound. Using the Fourier transform (FT) of the fractal dimension of the AFM images, these clusters present quasi-particle interference (QPI), which reveals a unique picture of electron waves and the trapping of further electrons in the lattice. Furthermore, density functional theory (DFT) calculations validated electronic features of the clusters with remarkable accuracy. DFT calculations also revealed differences between the lowest unoccupied energy (LUMO) and the highest occupied energy (HOMO), and these phase gaps evolved in the ground state. These phenomena provide evidence that electron correlation stimulates electronic bands to pseudo-gap states. Indeed, our experiments pave the way for realizing unconventional superconductivity in zero-dimension materials.
Non covalent biliproteins are found in a growing number of living organisms and even in viruses, such as SARS-CoV-2. Unlike the well described covalent biliproteins, such as the phytochromes, they present a vast structural and functional diversity, and often with limited experimental information. A very important tool (and sometimes the only one available) to study these systems is the UV-Vis spectrum, which is modulated both by conformational changes of the biliverdin chromophore and specific interactions with the apoprotein. In this work we present a theoretical study of the microscopic determinants of the UV-Vis spectrum of these compounds through the use of hybrid QM(TD-DFT)/MM techniques and molecular dynamics simulations. Comparing our results with existing experimental data, we prove that it is possible to predict spectroscopic properties, such as relative position and intensity ratio of main bands, with affordable methods, and to provide a microscopic explanation of them. This systematic information can be very useful for the study of described biliproteins or for those yet unknown.
Imidazole derivatives are the foundation of different types of drugs with a wide range of biological activities. In this study, the genetic algorithm multiple linear regression (GA- MLR), and backpropagation-artificial artificial neural network (BP-ANN) were applied to design QSPR models to predict the quantum chemical properties like the entropy(S) and enthalpy of formation(∆Hf) of imidazole derivatives. In order to draw molecular structure of 84 derivative compounds Gauss View 05 program was used. These structures were optimized at DFT-B3LYP / 6-311G* level with Gaussian09W. The Dragon software was used to calculate a set of different molecular descriptors, and the genetic algorithm procedure and backward stepwise regression were applied for the selection of descriptors. The resulting quantitative GA-MLR model of ∆Hf, showed that there is good linear correlation between the selected descriptors and ∆Hf of compounds. Also the results show that the BP-ANN model appeared to be superior to GA-MLR model for prediction of entropy. Different internal and external validation metrics were adopted to verify the predictive performance of QSPR models. The predictive powers of the models were found to be acceptable. Thus, these QSPR models may be useful for designing new series of imidazole derivatives and prediction of their properties.
Lithium-decorated (Li-decorated) C3N has been investigated as a potential material for high capacity reversible hydrogen storage. The energetic stability, dynamical stability and thermal stability were studied, indicating that C3N is energetically stable, imaginary frequencies are not found from the result of phonon spectrum calculation, and the free energy vibrates slightly around -64.63 eV during the 5000 fs period and no structure reconstruction. Electronic properties showed the band gaps are 0.39 eV and 1.12 eV, via PBE and HSE calculations, respectively. The four probable Li-adsorbed sites were calculated, indicating that the hollow site above the center of a hexagon ring HC site is the most likely site to absorb Li atom. Hydrogen molecules were added one by one to research the maximum hydrogen gravimetric density. Each Li atom can attach 10 hydrogen molecules within the range of physical adsorption processes (-0.1 ~ -0.4 eV/H2) and the hydrogen storage capacity can reach 8.81 wt%. Li-decorated C3N shows the greatest potential for on-board reversible solid-state hydrogen molecule storage application.
Sulfur hexafluoride decompositions have been studied to analyze their adsorption properties on pristine graphene (PG) and Mg-doped graphene (MgG). First of all, after calculating the formation energy of three Mg doping sites, the T doping site of Mg-doped graphene is the most stable one. Then, several characteristic structures with different orientations and positions of the gas molecules have been used to adsorb on PG and MgG, respectively. By calculating the adsorption energies and distance, the most stable adsorption structure of each gas molecule is obtained. In addition, charge transfer (Qt), the density of states (DOS) distribution, the energy of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) were used to further analyze the conductivity change and chemical stability of each adsorption system. The results indicate that the adsorption interactions of H2S, SO2, SOF2 and SO2F2 on PG are weak. H2S adsorbed on MgG presented physical adsorption, while the adsorption behaviors of SO2, SOF2 and SO2F2 on MgG are chemisorption. And the adsorption strength was SO2F2 > SOF2 > SO2. In short, MgG shows better selectivity and higher sensitivity to SO2, SOF2 and SO2F2 than PG, demonstrating that the MgG material can be used as suitable gas sensing equipment based on SF6 decomposition products detection, which provides a meaningful guide of alkaline earth metal doped graphene in the detection of partial discharge and partial overheat in gas-insulated switchgears (GIS).
Singlet and triplet spin state energies for three-dimensionalHooke atoms, i .e. electrons in a quadratic confinement, with even number of electrons (2, 4, 6, 8, 10) is discussed using Full-CI and CASSCF type wavefunctions with a variety of basis sets and considering perturbative corrections up to second order. The effect of the screening of the electron-electron interaction is also discussed by using a Yukawa-type potential with different values of the Yukawa screening parameter (λee =0.2, 0.4, 0.6, 0.8, 1.0). Our results show that the singlet state is the ground state for 2 and 8 electron Hooke atoms, whereas the triplet is the ground spin state for 4, 6 and 10 electron systems. This suggests the following Auf bau structure 1s < 1p < 1d with singlet ground spin states for systems in which the generation of the triplet implies an inter-shell one electron promotion, and triplet ground states in cases when there is a partial filling of electrons of a given shell. It is also observed that the screening of electronelectron interactions has a sizable quantitative effect on the relative energies of both spin states, specially in the case of 2 and 8 electron systems, favouring the singlet state over the triplet. However, the screening of the electron-electron interaction does not provoke a change in the nature of the ground spin state of these systems. By analyzing the different components of the energy, we have gained a deeper understanding of the effects of the kinetic, confinement and electron-electron interaction components of the energy.
We have designed Ti3AlB2 and two new layered ordered double-transition metals MAX compound Ti2ZrAlB2 based on the structure of Ti3AlC2. By first-principles calculations with density functional theory, their structure, phase stability, elastic properties, electronic properties and thermal properties have been further investigated. Results show that they are all energetic, thermodynamically and mechanically stable. The bulk modulus, shear modulus, Young's modulus, Poisson's ratio and Debye temperature were computed to discuss their elastic and thermal properties. Results show that they are all good ductile materials with high melting points. Density of states and electron localization function of these three phases were presented to research the chemical bonds and explore the reason limiting their melting points.
In thiswork,we have computed and implemented one-body integrals concerning gaussian confinement potentials over gaussian basis functions. Then, we have set an equivalence between gaussian and Hooke atoms and we have observed that, according to singlet and triplet state energies, both systems are equivalent for large confinement depth for a series of even number of electrons n = 2, 4, 6, 8 and 10. Unlike with harmonic potentials, gaussian confinement potentials are dissociative for small enough depth parameter; this feature is crucial in order to model phenomena such as ionization. In this case, in addition to corresponding Taylor series expansions, the first diagonal and sub-diagonal Padé approximant were also obtained, useful to compute the upper and lower limits for the dissociation depth. Hence, this method introduces new advantages compared to others.