In the present report, the structural stability order and electronic properties of the transition metal M@Ge12 (M = Co, Pd, Tc, and Zr) doped germanium cage has been carried out at B3LYP/LANL2DZ ECP level by using spin polarized density functional theory. Initially, we selected five lowest energy structure of neutral TM doped Ge12 cluster with high symmetry point like D6h-symmetric hexagonal prism (HP), the D6d-symmetric hexagonal anti-prism (HAP), D2d-symmetric bi-capped pentagonal prism (BPP), perfect icosahedrons (Ih) and Fullerene type structures. Further, we discussed the electronic origin of stability as well as electronic properties by calculating binding energy, HOMO-LUMO gap, charge transfer mechanism and density of states. We indentified that the Pd, Tc, and Zr encapsulated Ge12 cage with hexagonal prism [HP] structures are minimum energy structures while Co@Ge12 cage prefer HAP structure. The magnitudes of binding energy of the clusters indicate that the doping of 4d transition metal gives most stable structure rather than 3d transition metal Co atom. The large HOMO-LUMO gap and natural bond orbital analysis explain the stability of these clusters using closed shell electronic configuration and the contribution of π and σ bond. Charge transfer mechanism shows that the Tc, Pd and Zr atoms play role as an electron donor in the system whereas Co inclined to accept the electrons. The importances of “d” orbital in localized electrons near the Fermi level are also explained through partial density of states.
Ab initio and DFT calculations were performed to investigate the structure, stability, and nature of chemical bonding of the F-Rg-BR2 (R = F, OH, CN and CCH; Rg = Ar, Kr, Xe and Rn) molecules. The geometries are optimized for ground as well as transition states using the B3LYP-D3 and MP2 methods. It has been found that the F-Rg-B portion of F-Rg-BR2 species is linear in the ground state but curved in the transition state. The NBO, AIM, ELF and EDA analyses suggest that the molecules can be expressed as F-(Rg-BR2)+ due to the covalent Rg-B bond and the ionic interaction between F and Rg. Calculations assert the metastable behavior of the F-Rg-BR2 molecules, thermodynamic data shows that F-Rg-BR2 can spontaneously dissociates into BFR2 + Rg, the considerable energy barrier of this two-body dissociation channel calculated by the B3LYP-D3, MP2 and CCSD(T) methods affirms the kinetic stability of the F-Rg-BR2 molecules. Thus F-Rg-BR2 molecules are kinetically protected against the decomposition reaction and may be identified under cryogenic conditions in solid rare gas matrices or in the gas phase.
Structural, electronic, topological, vibrational and molecular docking studies have been performed for both enantiomeric S(-) and R(+) forms of potential antiviral to COVID-19 chloroquine (CQ) combining DFT calculations with SQMFF methodology. Hybrid B3LYP/6-311++G** calculations in gas phase and aqueous solution predict few energy differences between both forms. Solvation energies of S(-) and R(+) form are predicted in -55.07 and 59.91 kJ/mol, respectively. Low solvation energies of both forms are justified by the presence of only four donor and acceptor H bonds groups, as compared with other antiviral agents. MK charges on the Cl1, N2, N3 and N4 atoms and AIM calculations could support the high stability of R(+) form in solution according to the higher reactivity predicted for the S(-) form in this medium. Antiviral to COVID-19 niclosamide shows higher reactivity than both forms of CQ. Complete vibrational assignments of 153 vibration modes for both forms and scaled force constants have been reported here. Reasonable concordances were found between predicted and available 1H-NMR, 13C-NMR and UV-Vis spectra. Additionally, NMR and UV-visible spectra suggest the presence of two forms of CQ in solution. A molecular docking study was performed to identify the potency of inhibition of Chloroquine molecule against COVID-19 virus
Experimentally (G. Mlostoń et al., J. Fluor. Chem. 190 (2016) 56–60), it has been found that the type of the obtained cycloadduct of the [3+2] cycloaddition (32CA) reaction of thiocarbonyl S-methanides with α,β-unsaturated ketones depends strongly on the location of the trifluoromethyl group. In the case of enones containing the CF3CH=CH moiety, the 32CA reaction occurs chemo- and regioselectively onto the C=C double bond giving trifluoromethylated tetrahydrothiophene derivatives. On the other hand, enones containing the CF3–C=O fragment react as carbonyl heteroethylenes leading to trifluoromethylated 1,3-oxathiolanes also in a chemo- and regioselective manner. Our aim in the present work is to perform a theoretical study of the all chemo-, regio-, and stereo-isomeric reaction paths of these 32CA reactions within the Molecular Electron Density Theory. Activation Gibbs free energies, calculated at the B3LYP/6-311G(d,p) level in tetrahydrofurane at -40°C, show that the ortho/endo reaction path giving the trifluoromethylated tetrahydrothiophene is more favoured, while the meta/endo reaction path leading to trifluoromethylated 1,3-oxathiolanes is more preferred in total agreement with experimental findings. The low activation barriers in combination of the Electron Localization Function topological analysis of the most relevant points along the Intrinsic Reaction Coordinate reveals the pseudomonoradical character of the studied 32CA reactions.
In order to explore the influence of isotope effect and ligand modification on the quantum yield of OLED, three classes Pt(II) complexes with 2,2’-bipyridine ligand have been investigated by using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The explored Pt(II) complexes, class 1 included Pt(RC≡CBpyC≡CR)(C≡CBpy)2, (R = trimethylsilyl，1a or H, 1b, C≡CBpyC≡C = 5,5-bis(ethynyl)-2,2-bipyridine, C≡CBpy corresponds to bipyridineacetylene) and Pt(Bpy)(C≡CBpy)2 (Bpy = bipyridine, 1c); class 2, Pt(Bpy)(C≡CPy)2 (C≡CPy = pyridineacetylene, 2a) , Pt(Bpy)(C≡CPh)2 (C≡CPh =phenylethynyl, 2b), Pt(dbBpy)(C≡CPh)2(dbBpy = 4,4’-di-tert-butyl-2,2’-bipyridine, 2c); and class 3, Pt(Bpy)(Tda) (Tda = tolan-2,2’-diacetylide, 3a), Pt(dbBpy)(Tda) (3b), Pt(3,3’,4,4’-OH-Bpy)(Tda) (3c). The calculation results reveal that the heavy isotope effect effectively reduces the overall vibration frequency of these complexes, and in turn decreases the non-radiative decay rate κnr, which lead to the promotion of phosphorescent quantum yield ϕem. Theoretical studies also reveal the influence of ligand modification on the phosphorescence quantum yields of OLED, and a new Pt(II) complex 3c was designed based on the theoretical study.
Ferroptosis is a recently characterized form of regulated necrosis with the iron-dependent accumulation of (phospho)lipid hydroperoxides (LOOH). It has attracted considerable attention for its putative involvement in diverse pathophysiological processes, such as cardiovascular disease and neurodegeneration. Here we describe the discovery of tetrahydroquinoxaline, a novel scaffold of ferroptosis inhibitors based on quantum chemistry methods. Tetrahydroquinoxaline deviates showed very good inhibition of ferroptosis, while being non cytotoxic for human cancer cells. And, the advantage of them is their small molecular weight (MW. = 148 Da) that can be coupled with other drugs to form multi-target drugs to better meet the treatment of complicated diseases.
Reactivity of thymine peroxy radical in DNA and its fate under hypoxia or oxygen-less conditions are studied at the M06-2X/6-31+G(d,p) level. The spaciously most accessible H2’ can be abstracted by C6-peroxy radical in an intranucleotidyl manner with the estimated barriers of 18.8 ~ 21.1 kcal/mol. The calculations show that C6-peroxy radical has a highly more reactivity towards C(sp3)-H abstraction reactions than its relative C6-yl, which is a counter-intuitive case. The formed hydroperoxide with the C6-OaObH2’ constituent can fast transfer ObH2’ group to C2’ radical in an intranucleotidyl manner with a low barrier (ca. 13.2 kcal/mol) and very strong heat release. The results show that the formed hydroperoxide product is unstable so that it could be quickly transformed into other species and thus is very hard to be experimentally observed. Afterwards, H2’ can be again abstracted by C6-oxyl radical to result in formation of thymine glycol which is the main products. The parallel C5-C6 bond scission reaction leads to formation of the precursor for 5-hydroxy-5-methylhydantion. The two competitive reactions have very low barriers. Based on our present calculations, the new radical reaction paths to formation of the DNA oxidation products are suggested under hypoxia or oxygen-less conditions, which is different from the previously suggested paths under high oxygen concentration surroundings.
With the aim of describing bound and continuum states for diatomic molecules, we develop and implement a spectral method that makes use of Generalized Sturmian Functions (GSF) in prolate spheroidal coordinates. In order to master all computational issues, we apply here the method to one-electron molecular ions and compare it with benchmark data for both ground and excited states. We actually propose two different computational schemes to solve the two coupled differential equations. The first one is an iterative 1d procedure in which one solves alternately the angular and the radial equations, the latter yielding the state energy. The second, named direct $2d$ method, consists in representing the Hamiltonian matrix in a two–dimensional GSF basis set, and its further diagonalization. Both spectral schemes are timewise computationally efficient since the basis elements are such that no derivatives have to be calculated numerically. Moreover, very accurate results are obtained with minimal basis sets. This is related on one side to the use of the natural coordinate system and, on the other, to the intrinsic good property of all GSF basis elements that are constructed as to obey appropriate physical boundary conditions. The present implementation for bound states paves the way for the study of continuum states involved in ionization of one or two-electron diatomic targets.
In this study, we performed density functional theory calculations using the B3LYP, M052X, M062X, and APFD functionals to investigate substituent effects on the mechanism of 1,3-dipolar cycloaddition, a classical and effective method for the synthesis of heterocyclic compounds. The results showed that changing the substituents on the chloroxime compounds affects the energy level of the highest occupied molecular orbital and consequently, the progress of the reaction. Finally, it provided an effective idea for this kind of reaction in the design of organic synthesis and the necessary theoretical basis for revealing the course of this reaction.
The pattern of cyclic conjugation was thoroughly studied in the series of N- and P-acenaphthylene derivatives using several different aromaticity indices: the energy effect (ef), multicenter delocalization index (MCI), harmonic oscillator model of aromaticity (HOMA) index and nucleus independent chemical shifts (NICS). The Kekulé-structure-based reasoning predicts that there would be no cyclic conjugation in the “empty” five-membered heteroatom-containing rings in the studied molecules. It was found that, according to the ef, MCI and HOMA values, the extent of cyclic conjugation in the pentagonal rings is strongly influenced by the number and mutual arrangement of the hexagonal rings. In addition, it was revealed that in some of the examined molecules the intensity of cyclic conjugation in the “empty” pentagons is even stronger than that of some hexagonal rings within the same molecule. The obtained results refute what one would expect based on ”chemical intuition”, which is usually strongly rooted to the Kekulé structures.
The performance of a series of density functionals has been tested for the insertions of ethylene, methyl acrylate (MA), and vinyl bromide (VB) catalyzed by α-diimine palladium complexes. Sixty-seven density functionals are screened, and the results are compared with available experimental data. Eleven hybrid functionals (M06, BHandH, mPW1PW91, HSEh1PBE, mPW3PBE, LC-ωPBE, mPW1PBE, PBE0, M06-HF, M06-2X, M05-2X) showed better performance in the insertions of both ethylene and MA, and could be therefore suitable for ethylene-MA copolymerization. Meanwhile, three GGA (PW91PW91, HCTH, HCTH407), two meta-GGA (TPSSTPSS, tHCTH), and ten hybrid functionals (M06, BHandH, TPSSh, B971, B98, B1B95, PBE0, M06-2X, tHCTHhyb, M05-2X) perform well in the ethylene-VB copolymerization. Besides, nine D3 or D3BJ augmented functionals are found to be suitable for both copolymerization systems. The D2 dispersion correction overestimated insertion energy barriers of these monomers and is unsuitable for such copolymerization. In addition, the double-zeta basis set is found to be sufficient for solvation single-point calculation of these systems.
Osmium analogue to ruthenium anticancer drug NAMI-A; (ImH)[trans-OsCl4(DMSO)(Im)] (Im=imidazole, DMSO=dimethyl sulfoxide) (Os-NAMI-A) shows a three-fold higher activity in colon carcinoma. Hydrolysis mechanism of Os-NAMI-A has been investigated using density functional theory (DFT) in combination with CPCM solvation model. Calculated activation free energy values for the first chloro ligand hydrolysis in the gaseous and aqueous medium are found to be ΔGg=31.79 and ΔGaq=28.72 kcal/mol, respectively. While, activation free energy for the second cis chloro ligand hydrolysis calculated in the gas and solvent phases are observed to be significantly lower (ΔGg=29.12 and ΔGaq=22.61 kcal/mol), suggesting enhanced feasibility of second hydrolysis. However, hydrolysis of DMSO ligand in the formation of cis-[OsCl2(H2O)3(Im)]+ (P-3cis) is found to be thermodynamically preferred in aqueous medium (19.49 kcal/mol) with rate constant value of 3.20×10-2 s-1. In addition, molecular docking simulation reveals that cis-diaquated Os-NAMI-A (P-2cis) interacts with DNA (PDB ID: 1pgc) more effectively having binding energy -5.63 kcal/mol. Therefore, results of this investigation may lead us to understand the solution behaviour of osmium azole complexes as well as their mode of interaction with biomolecules which in return helps in potential anticancer drug designing.
A special class of conjugated hydrocarbons known as phenylenes, which is composed of a special arrangement of six- and four-membered rings. In particular, any two six-membered rings (hexagons) are not adjacent, and every four-membered ring(square) is adjacent to a pair of nonadjacent hexagons. If each hexagon of phenylene is adjacent only to two squares, then the obtained chain is called the phenylene chain. The main object of this paper is to determine the expected values of the sum-connectivity, harmonic, and symmetric division indices of this class of conjugated hydrocarbons. The comparisons between the expected values of these indices with respect to the random phenylene chains have been determined explicitly. The graphical illustrations have been given in terms of the differences between the expected values of these indices.
The present study reports nonlinear optical properties such as first and second hyper polarizabilities (β and γ) of Y-shaped polymer (P1) and substituted polymers. The basic Y-shaped polymer (R=R1=H) named as P1. Upon substitution of one OCH3 group in ortho position of Oxygen becomes polymer P2 (R1=H, R=OCH3) and two OCH3 group as P3 (R1=R=OCH3). We have also reported structural parameters, vibrational and electronic absorption spectra of polymer and substituted using quantum chemical methods. The geometrical parameters such as dipole moment, bond length and angles are reported at B3LYP/6-311++g** level of theory. In addition, the vibrational, electronic absorption spectra and NLO properties are also reported at the same level of theory. There is significant change in dipole moment and energy observed whereas symmetry, bond length and angles are resembling in Y-shaped and substituted polymer. The vibrational spectra of Y-shaped polymer (P1) having the intense peak is C-H stretching mode observed at 1258 cm-1. These Theoretical vibrational modes are well matching with available experimental determinations. The method dependent and the along the X, Y and Z-direction hyperpolarizabilites also reported. This study confirms the polymer P1 and P2 showing first and second hyperpolarizability response whereas P3 do not show. The electronic absorption spectra for polymer and substituted polymers are also reported at the same level of theory using (TDDFT) approach. The wavelength of electronic transition, oscillator strength and HOMO-LUMO gap also reported.
Electrochemical ammonia synthesis is being actively studied as a low temperature, low pressure alternative to the Haber-Bosch process. This work studied iridium as the electrochemical catalyst, following a previous study of adsorption characteristics on platinum. The characteristics studied include bond energies, bond lengths, spin densities, and free and adsorbed vibrational frequencies for the molecules N2, N, NH, NH2, and NH3. Overall, these descriptive characteristics explore the use of dispersion-corrected Density Functional Theory methods that can model N2 adsorption – the key reactant for electrochemical ammonia synthesis via transition metal catalysis. Specifically, three methods were tested: hybrid B3LYP, a dispersion-corrected form B3LYP-D3, and semi-empirical B97-D3. The latter semi-empirical method was explored to increase the accuracy obtained in vibrational analysis as well as reduce computational time. Two lattice surfaces, (111) and (100), were compared. The adsorption energies are stronger on (100) and follow the trend EB3LYP > EB3LYP-D3 > EB97-D3 on both surfaces.
The current study investigates the correlation between biological activity and physicochemical properties of a few specific estradiol isomers. Theoretical studies on the physicochemical properties of estradiol isomers were performed using different quantum mechanical methods. The computational methods used in this study include the Density Functional Theory (DFT) method, the Hartree-Fock (HF) method and Semi-empirical (AM1) method. Some physicochemical properties such as dipole moment, molecular weight, the energy of the highest occupied molecular orbital (E HOMO), the energy of the lowest unoccupied molecular orbital (E LUMO), polarizability, the octanol-water partition coefficient (Log P), polar surface area (PSA) the number of hydrogen bond donors (HBDs) and the number of hydrogen bond acceptors (HBAs), the surface area, volume of the molecule, and ovality are calculated for the isomers. However, only dipole moment values are suitable to identify a correlation of experimental biological activity of estradiol isomers. To the best of our knowledge, this is the first report on the relationships between dipole moment and biological activities of estradiol isomers. It is observed that the active compound has a significantly higher dipole moment value compared to the inactive compound. We have also analyzed the geometrical and graphical models of these isomers and related compounds to evaluate the differences in the molecular charge distributions.
Atomically precise metallic clusters behaving as superatoms, are relevant building blocks towards new materials under the bottom-up approach. Here we discussed the plausible formation of the Cu10Ru cluster as a superatomic specie accounted its 1S2 1P6 1D10 shell order, with the aim of identification of particular clusters with enhanced stability. By stochastic structure search on Cu10Ru clusters, we found six low-lying cluster isomers with ΔE values from 0.0 to 4.7 kcal∙mol above the ground state denoting an endohedral motif with the Ru dopant inside the Cu10 cage, as the favored structures. By using molecular dynamics simulations we found a clear trend of encapsulation of the Ru atom at low temperatures, quantified by the Cu-Ru bonding distances during the annealing procedure. The 17-ve counterpart, Cu9Ru shows a large electron affinity, owing to the trend to achieve a electronic shell closing as a new superhalogen species. These results are useful for further rationalization and design of novel superatoms expanding the libraries of endohedral clusters.
Quantum-chemical “descriptors”, including atomic partial charges, orbitals, and electrostatic potentials are powerful tools for understanding chemical reactivity. Localized defects in graphene are a particular challenge for these tools, especially to model the adsorption processes and to predict the interactions of transition metals with these defects. Such defects often have little charge polarization and a combination of localized and delocalized states. Our orbital overlap distance D(r) measures the “size” of occupied orbital lobes about point r, distinguishing the hybridization state and compact vs. diffuse character of local electronic structure. Here we apply the overlap distance to graphene defects. We find that the overlap distance clearly distinguishes differential reactivities of different atoms at intrinsic defects. Combining the overlap distance and electrostatic potential provides a rich picture of extrinsic defect reactivity, including semiquantitative predictions of transition metal binding.