Molecular Dynamics (MD) simulations are widely used to predict the behavior of molecular systems over time. However, one of the great challenges of MD simulations is how to treat the thousands of configurations obtained from calculations, since the number of the quantum calculations (QM) required for evaluating electronic parameters is too high and, sometimes, computationally impracticable. Thus, an efficient and accurate sampling protocol is essential for combining classical MD and QM calculations. In this article, based on the OWSCA methodology, 93 wavelet signals were analyzed in order to further refine the methodology and identify the best wavelet family for [Fe(H2O)6]2+ and [Mn(H2O)6]2+ complexes in solution. Our results point out that the bior1.3 was the best wavelet, values closest to the experimental data were obtained for both studied systems.
The chalcogen vacancy defects in various transition metal dichalcogenides (TMDCs) have been studied using density functional theory (DFT) calculation. Results reveal that (i) the dissociation energy value depends on both nature of chalcogen and transition metal, (ii) the work function depends marginally on the single or double vacancies, (iii) the defect transforms direct band gap to indirect band gap materials (i.e. the pristine materials show KVKC transition whereas defective materials show ΓVKC) and (iii) the d-orbital of the transition metal plays a vital role in the formation of impurity band.
Molecular level insights into the mechanism and thermodynamics of CO oxidation by a (TiO2)6 cluster have been obtained through density functional calculations. Thereby, we have considered as an example, two different structural isomers of (TiO2)6 with the purpose of understanding the interplay between local structure and activity for the CO oxidation reaction. Active sites in the two isomeric forms were identified on the basis of global and local reactivity descriptors. For the oxidation of CO to CO2 we considered both sequential and simultaneous adsorption of CO and O2 on (TiO2)6 cluster through the ER and LH mechanisms, respectively. Three different pathways were obtained for CO oxidation by (TiO2)6 cluster, and the mechanistic route of each pathway were identified by locating the transition-state and intermediate structures. The effects of temperature on the rate of the reaction was investigated within the harmonic approximation. The structure-dependent activity of the cluster was rationalized through reactivity descriptors and analysis of the frontier orbitals. Finally, we also considered the effects of a support, i.e., graphene, on the oxidation mechanism.
Promoting the application potential of graphenes in biomolecule adsorption and detection is of great significance in the field of nanobiotechnology. In this paper, the density functional theory calculation was used to study the adsorption and sensing of L-cysteine on graphene-based compounds, single-vacancy and double-vacancy graphenes (XSV and XDV) doped with 3p-bolck elements (Al, Si, P, and S). Along with the dopant changing from Al to S, XSV exhibits decreasing exothermical chemisorption to endothermical chemi-sorption, while XDV exhibits decreasing exothermical chemisorption to endothermical physisorption. L-cysteine adsorption on XDV is weaker than corresponding adsorption on XSV. Valence electron number, and atomic ionization potential, modulated by the 3p-block dopant, and X-C interaction, modulated by the vacancy type, contribute to adsorption mechanism of L-cysteine on XGs. The study could facilitate applications of Al, Si, P and S doped graphenes in biosensing technology, biomolecule immobilization, bioseparation and other fields.
The interactions of simple and Al, B, N, S, P and Si-doped carbon nanotubes with three sulfur-containing molecules (H2S, SO2 and thiophene) have been investigated to assess their adsorption potencies and sensor abilities. DFT calculations were used to calculate the adsorption energies and NBO parameters. Besides, Population analyses were performed to calculate the energy gaps and reactivity parameters and to obtain DOS plots. The results showed an exothermic interaction of H2S, SO2 and thiophene with simple and doped CNTs while the maximum negative adsorption energies were belonged to Al and B containing complexes. Furthermore, evaluation of second order perturbation energies (obtained from NBO calculations) confirmed that the highest energies were related to B and Al containing intramolecular interactions. The results revealed the favourability of adsorption of SO2 by nanotubes (B and Al doped carbon nanotubes, in particular), in comparing with the other examined adsorbates.
Using the ab-initio calculations based on density functional theory, we have investigated the structural, electronic and magnetic properties of Ti-substituted Zn3P2 compound. One and two Ti atom replacements in the unit cell of Zn3P2, which contain eight molecules per formula unit (40 atoms), are considered in the study. Our results show that the ferromagnetic phase is favored for the single Ti atom substitution, as the total energy corresponding to the ferromagnetic phase is lower than that of the nonmagnetic phase. A considerable value of the magnetic moment at the Ti site is obtained from our calculations.
Antisense technology has been developed as the next generation drug discovery methodology by which unwanted gene expression can be inhibited by targeting mRNA specifically with antisense oligonucleotides. The computational studies of antisense modifications based on phosphorothioate (PS), methoxyethyl (MOE), locked nucleic acids (LNA) may help to design better novel modifications. In the present study, five novel LNA based modifications have been proposed. The conformational search has been done to identify the most stable and alternative stable conformations. The geometry optimization followed by single point energy calculation has been done at B3LYP/6-31G(d,p) level for gas phase and B3LYP/6-311G(d,p) level for the solvent phase for all modifications at monomer as well as base pair level. The electronic properties and the quantum chemical descriptors of the antisense modifications were derived and compared. The local and global reactivity descriptors, such as hardness, chemical potential, electronegativity, electrophilicity index, Fukui function all were calculated at the DFT level for the optimized geometries. A comparison of global reactivity descriptors confirmed that LNA based modifications are the most reactive modifications. They may form a stable duplex when bound to complementary nucleotides, compared to other modifications. Therefore, we are proposing that one of our proposed antisense modifications (A3) may show strong binding to the complementary nucleotide as LNA and may also show reduced toxic effects like MOE. The base pair studies may help us to understand the extent to which our proposed modifications can form standard Watson-Crick base pairing required for oligomer duplexes. This computational approach may be very useful to propose novel modifications prior to undergoing synthesis experimentally in the area of antisense or RNAi technology.
The coherent interaction between localized surface plasmon resonance modes and excitons of a single or a collection of quantum emitters have fueled the development of novel applications in quantum optics and material science. In this work, using first-principles simulations, we analyse the modifications in absorption spectra and electric near-field enhancements in a structure consisting of an aluminum nanotriangle interacting with a varying number of pyridine molecules (placed at the nanotriangle tips) in close proximity. What’s more, we find very interesting spatial variation in induced electron density and electric near-field enhancements with a remarkable dependence on the number of interacting pyridine molecules and the direction of light illumination. Our results may help to improve our understanding of the light-matter interaction at the sub-nanometer scale.
The geometric structures, energetic and electronic properties of global minima of the AlBen (n = 1–12) clusters have been systemically studied by using the hybrid density functional theory [B3LYP] and coupled cluster [CCSD(T)] methods. It is found that the impurity Al atom is externally bound to the host Ben framework and its maximum coordination number is six. Besides, the geometries of AlBen bear close resemblance to either local or global minimum structures of Ben+1. The AlBe3 and AlBe8 clusters exhibit high relative stability among the AlBen clusters, which is reflected by the evolutions of average atomic binding energy, dissociation energy, second difference in energy, adsorption energy of Al, and HOMO-LUMO gap with cluster size. In comparison to the pure Ben+1 clusters, AlBen exhibit larger binding energy values, whereas they are more polarizable.
Ru-based catalysts show high activity and stability to produce ammonia. Herein, the two-state reaction mechanism of Ru catalyzes N2 and H2 to synthesize NH3 are theoretical studied with the density functional theory(DFT)UB3LYP methods. The spin-orbital coupling constant(Hsoc) and intersystem crossing probability(Pisc) at minimum energy crossing point(MECP) were calculated, respectively. its are: Hsoc,MECP1=508.34cm-1，P2,MECP1ISC=0.85，MECP2：Hsoc,MECP2=269.21cm-1， P2,MECP2ISC=0.27. Used energy span model to determined TOF-determining transition state(TDTS) as 3TS2-3 and TOF-determining intermediate(TDI) as 3IM9 of reaction.In addition, the charge decomposition analysis(CDA), spin population analysis and frontier molecular orbital(FMO) theory were used to analyzed reaction mechanism.
Superalkalis have lower ionization energy than that of alkali atoms and superhalogens have higher electron affinity than that of halogen atoms. This property can be exploited to improve the efficacy of redox reactions that are routinely used in the scientific and industrial laboratories. Some of these reactions are theoretically studied and their thermodynamic parameters are analyzed. Alternatives to these reactions with the use of superalkalis and superhalogens are suggested by assuming similar behavior to that of their alkali metal or halogen analogues. Consequently, these reactions are analyzed, and their properties are compared to the existing reactions. Particularly, the change in reaction enthalpy, Gibbs free energy and their electrochemical potential are compared. Quantification of the reducing property of the superalkalis is also studied in the present situation by using an ionic equation. In all the cases, the results are promising and consequently, some of their applications are contemplated.
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.