Journal of Molecular Modeling最新文献

Context: In order to synthesize InN nanoparticles (NPs), we have simulated the co-implantation of indium (In) and nitrogen (N) ions on silicon (Si) and silicon oxide (SiO₂) substrates with flat-top profiles. The choice of flat-top profile is to increase the possibility of creating homogeneous zone with well-distributed InN nanoparticles over the entire implanted layer. In this view and to obtain these flat-top profiles, we must do several implantations with different doses and energies optimized by our program. The simulation results performed on a silicon substrate < 111 > , give an average dose of 4.30 × 10¹⁶ at./cm² and the implantation energies were In (10, 46, and 180 keV) and N (13 and 35 keV). But for the SiO₂ substrate, the total mean dose is about 5.20 × 10¹⁶at./cm² for each Indium and nitrogen ion. The respective implantation energies were In (23, 63, and 120 keV) and N (12 and 28 keV) in an average depth of approximately 100 nm. The implantations were performed in a 206-nm-thick (SiO₂) layer thermally grown on < 100 > silicon. Subsequent thermal treatments (500-900 °C) lead to the formation of nanoparticles precipitates of the compound semiconductor (InN) and to cure the oxide defects during different periods of time. To verify that indium (In) and nitrogen (N) ions were located according to flat curves, we used RBS technical and study the formation (InN) stoichiometric compound several techniques, were used such as X-ray diffraction, UV-visible-IR, and photoluminescence (PL) spectroscopy.

Methods: The simulated profiles have been chosen with the aim that the implanted element not exceeding 5-10 at %maximum concentration for each species. We have elaborated our program to simulate these profiles using data as input values from SRIM2008 code taking into account the sputtering factor. The optimal conditions are determined, which are the expected depth impact energies (R_p), the standard deviation (ΔR_p) and the sputtering corrosion factor (F_s). Through these results, a simulation program has been created which allows building flat "distribution" curves for ion implantation for each element (In and N), so that each curve is obtained from three Gaussian functions whose values are carefully chosen in relation to the optimal experimental conditions.

Context: Due to advances in synthesizing lower-dimensional materials, there is the challenge of finding the wave equation that effectively describes quantum particles moving on 1D and 2D domains. Jensen and Koppe and Da Costa independently introduced a confining potential formalism showing that the effective constrained dynamics is subjected to a scalar geometry-induced potential; for the confinement to a curve, the potential depends on the curve's curvature function.

Method: To characterize the $\pi$ electrons in polyenes, we follow two approaches. First, we utilize a weakened Coulomb potential associated with a spiral curve. The solution to the Schrödinger equation with Dirichlet boundary conditions yields Bessel functions, and the spectrum is obtained analytically. We employ the particle-in-a-box model in the second approach, incorporating effective mass corrections. The $\pi$ - ${\pi }^{\ast }$ transitions of polyenes were calculated in good experimental agreement with both approaches, although with different wave functions.

Context and results: A nanocomposite photocatalyst consisting of polyaniline (PANI) and copper oxide (CuO) was successfully synthesized through an in-situ polymerization approach using aniline as the precursor. The synthesized nanocomposite was characterized using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), UV-visible spectroscopy (UV-Vis), determination of the point of zero charge (pHPZC), and scanning electron microscopy (SEM). The photocatalytic efficiency of the PANI-CuO nanocomposite was evaluated in the context of photodegrading Malachite Green (MG) dye under visible light. Malachite Green, a synthetic dye commonly used in the textile and aquaculture industries, is a significant contaminant due to its toxic, mutagenic, and carcinogenic properties, making its removal from water resources crucial for environmental and human health. Distilled water artificially contaminated with MG dye was used as the medium for testing. The parameters influencing the photodegradation efficiency were comprehensively investigated. These parameters included catalyst dosage, reaction time, initial dye concentration, and pH. The results of this study indicate that the degradation efficiency of MG dye displayed an upward trend with time, catalyst dosage, and pH while exhibiting a converse relationship with the initial dye concentration. A degradation rate of 97% was achieved with an initial concentration of 20 mg L^-1, employing a catalyst dose of 1.6 g L^-1 at pH 6 for a reaction time of 180 min. Furthermore, the reusability of the catalyst was assessed, revealing consistent performance over five consecutive cycles.

Computational and theoretical techniques: Density functional theory (DFT) was employed to optimize the structures of PANI, PANI-CuO, and their respective complexes formed through dye interaction, employing Gaussian software. These calculations employed the B3LYP/6-311G +  + (d,p) basis set in an aqueous environment with water serving as the solvent. The kinetics of Malachite Green degradation were analyzed using both first and second-order kinetic models.

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.

Context: Existing researches confirmed that β amyloid (Aβ) has a high affinity for the α7 nicotinic acetylcholine receptor (α7nAChR), associating closely to Alzheimer's disease. The majority of related studies focused on the experimental reports on the neuroprotective role of Aβ fragment (Aβ_x), however, with a lack of investigation into the most suitable binding region and mechanism of action between Aβ fragment and α7nAChR. In the study, we employed four Aβ_1-42 fragments Aβ_x, Aβ_1-16, Aβ_10-16, Aβ_12-28, and Aβ_30-42, of which the first three were confirmed to play neuroprotective roles upon directly binding, to interact with α7nAChR.

Methods: The protein-ligand docking server of CABS-DOCK was employed to obtain the α7nAChR-Aβ_x complexes. Only the top α7nAChR-Aβ_x complexes were used to perform all-atom GROMACS dynamics simulation in combination with Charmm36 force field, by which α7nAChR-Aβ_x interactions' dynamic behavior and specific locations of these different Aβ_x fragments were identified. MM-PBSA calculations were also done to estimate the binding free energies and the different contributions from the residues in the Aβ_x. Two distinct results for the first three and fourth Aβ_x fragments in binding site, strength, key residue, and orientation, account for why the fourth fails to play a neuroprotective role at the molecular level.

Context: In this study, we delve into the physical characteristics of six hydride perovskites of ABH₃-type materials (CsCaH₃, CsSrH₃, KMgH₃, LiBaH₃, NaBeH₃, and RbCaH₃). Our investigation primarily focuses on assessing their structural stability by determining the enthalpy of formation and examining the dispersion of phonons. Using band structure calculations, we discern the characteristics of semiconductors, observing a direct bandgap in all four perovskites except NaBeH₃ and KMgH₃, which exhibit indirect gaps. Among these, NaBeH₃ possesses the narrowest gap at 1.91 eV, while the widest gap is observed in the perovskite RbCaH₃, measuring 4.56 eV. Furthermore, we conduct a thorough analysis of their optical properties, including parameters such as the real and imaginary dielectric function, absorption coefficient, and refractive index within an energy range of 0 to 14 eV. The results of our study are highly encouraging, suggesting that these materials hold significant promise for utilization in photovoltaic cells. This is primarily attributed to their remarkable ability to absorb light across both the ultraviolet (UV) and visible spectra. Additionally, we conducted an assessment of the thermoelectric properties of the six perovskite materials. RbMgH₃ exhibits a maximum Seebeck coefficient (S_max) of 1.5 mV/K, whereas KMgH₃ achieves a figure of merit reaching unity. These findings present promising opportunities for utilizing these compounds in thermoelectric devices.

Methods: In this study, all self-consistent field (SCF) calculations were performed using density functional theory (DFT), employing the FP-LAPW + lo method as implemented in the Wien2k code. The Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation, the modified Becke-Johnson (mBJ) methods, and the HSE06 hybrid functional were employed to characterize the exchange-correlation interactions. Thermoelectric parameters were extracted using the BoltzTraP software.

Context: The conversion of carbon dioxide (CO₂) to formic acid (FA) through hydrogenation using 1-ethyl-2,3- dimethyl imidazolium nitrite (EDIN) ionic liquid was studied to understand the catalytic roles within EDIN. CO₂ hydrogenation in various solvents has been explored, but achieving high efficiency and selectivity remains challenging due to the thermodynamic stability and kinetic inertness of CO₂. This study explored two mechanistic pathways through theoretical calculations, revealing that the nitrite (NO₂^-) group is the most active site. The oxygen site on nitrite favorably activates H2, while the nitrogen site shows a minor activation barrier of 108.90 kJ/mol. The Gibbs energy variation indicates stable FA formation via EDIN, suggesting effective hydrogen (H₂) activation and subsequent CO₂ conversion. These insights are crucial for developing improved catalytic sites and processes in ionic liquid catalysts for CO₂ hydrogenation.

Methods: Quantum chemical calculations were conducted using the ORCA software package at the Restricted Hartree-Fock (RHF) and density functional theory (DFT) levels. The RHF method, known for its predictive abilities in simpler systems, provided a baseline description of electronic structures. In contrast, DFT was employed for its effectiveness in complex interactions involving significant electron correlation. A valence triple-zeta polarization (def2-TZVPP) basis set was employed for both RHF and DFT, ensuring accurate and correlated calculations. The B3LYP functional was utilized for its rapid convergence and cost-efficiency in larger molecules. Dispersion corrected functionals (DFT-D) addressed significant dispersion forces in ionic liquids, incorporating Grimme's D2, D3, and D4 corrections. Geometry optimizations, kinetics, and thermodynamic calculations were performed in the gas phase. The Nudged Elastic Band Transition State (NEB-TS) approach, combining Climbing Image-NEB (CINEB) and Eigenvector-Following (EF) methods, was used to find the minimum energy path (MEP) between reactants and products. Thermochemical analyses based on vibrational frequency calculations evaluated properties such as Enthalpy, Entropy, and Gibbs energy using ideal gas statistical mechanics.

Context: This research aims to offer a deeper understanding of the bonding interactions between M-Se and M-CO and how these interactions change across the group 6 transition metal series: [Se₂M₃(CO)₁₀]^2- (M = Cr, Mo, W). It also seeks to explore the impact of carbonyl groups on M-M interactions within the clusters. Seven criteria, which are based on QTAIM properties, have been considered and compared with the corresponding criteria in other transition metal clusters. The results confirm that no such bond critical points or bond baths occur between transition metals, which instead have 5c-7e bonding interactions delocalized over their five-membered M₃(μ-Se)₂ ring, as evidenced by the non-negligible nonbonding delocalization indices. The topological properties of three bond clusters, Cr-Se, Mo-Se, and W-Se, resemble those of "intermediate closed shell characters," which combine covalent and electrostatic properties. Source function calculations indicated that the bonded Se atom contributed the most to each Cr-Se and Mo-Se bcp. The O_CO atoms and nonbonded Se atoms also contributed to some extent. However, metal atoms act as sinks rather than as sources of electron density. In contrast, the majority of the metal atoms, both bonded and nonbonded, contribute to Cr-W bcps. Analysis of the delocalization indices δ(M…O) in the three clusters indicates that CO significantly contributes to Cr π-back donation in cluster 1. In contrast, no π-back donation occurs from CO to Mo or W in clusters 2 or 3, respectively.

Methods: The B3P86 hybrid functional was used for computations in the Gaussian 09 software. The LanL2DZ basis set was employed for Cr, Mo, and W, while the 6-31G (d, p) basis set was used for C, O, and Se atoms. We performed QTAIM analysis using the AIM2000 and Multiwfn packages, incorporating B3P86/WTBS for Cr, Mo, and W atoms. The 6-311++G(3df,3pd) basis set was used for C, O, and Se atoms. Additionally, we utilized the ELF and SF.

Context: Conformation generation, also known as molecular unfolding (MU), is a crucial step in structure-based drug design, remaining a challenging combinatorial optimization problem. Quantum annealing (QA) has shown great potential for solving certain combinatorial optimization problems over traditional classical methods such as simulated annealing (SA). However, a recent study showed that a 2000-qubit QA hardware was still unable to outperform SA for the MU problem. Here, we propose the use of quantum-inspired algorithm to solve the MU problem, in order to go beyond traditional SA. We introduce a highly compact phase encoding method which can exponentially reduce the representation space, compared with the previous one-hot encoding method. For benchmarking, we tested this new approach on the public QM9 dataset generated by density functional theory (DFT). The root-mean-square deviation between the conformation determined by our approach and DFT is negligible (less than about 0.5Å), which underpins the validity of our approach. Furthermore, the median time-to-target metric can be reduced by a factor of five compared to SA. Additionally, we demonstrate a simulation experiment by MindQuantum using quantum approximate optimization algorithm (QAOA) to reach optimal results. These results indicate that quantum-inspired algorithms can be applied to solve practical problems even before quantum hardware becomes mature.

Methods: The objective function of MU is defined as the sum of all internal distances between atoms in the molecule, which is a high-order unconstrained binary optimization (HUBO) problem. The degree of freedom of variables is discretized and encoded with binary variables by the phase encoding method. We employ the quantum-inspired simulated bifurcation algorithm for optimization. The public QM9 dataset is generated by DFT. The simulation experiment of quantum computation is implemented by MindQuantum using QAOA.

Context: The addition of central metal atoms to hydrogen clathrate structures is thought to provide a certain amount of "internal chemical pressure" to offset some of the external physical pressure required for compound stability. The size and valence of the central atoms significantly affect the minimum pressure required for the stabilization of hydrogen-rich compounds and their superconducting transition temperature. In recent years, many studies have calculated the minimum stable pressure and superconducting transition temperature of compounds with H₂₄, H₂₉, and H₃₂ hydrogen clathrates, with centrally occupied metal atoms. In order to investigate the stability and physical properties of compounds with H cages in which the central atoms change in the same third group B, herein, based on first-principles calculations, we systematically investigated the lattice parameters, crystal volume, band structures, density of states, Mulliken analysis, charge density, charge density difference, and electronic localization function in $Im\overline{3}m$ -MH₆ and P6₃/mmc-MH₉ systems with different centered rare earth atoms M (M = Sc, Y, La) under a series of pressures. We find that for MH₉, the pressure mainly changes the crystal lattice parameters along the c-axis, and the contributions of the different H atoms in MH₉ to the Fermi level are H3 > H1 > H2. The density of states at the Fermi level of MH₆ is mainly provided by H 1 s. Moreover, the size of the central atom M is particularly important for the stability of the crystal. By observing a series of properties of the structures with H₂₄ and H₂₉ cages wrapping the same family of central atoms under a series of pressures, our theoretical study is helpful for further understanding the formation mechanism of high-temperature superconductors and provides a reference for future research and design of high-temperature superconductors.

Methods: The first principles based on the density functional theory and density functional perturbation theory were employed to execute all calculations by using the CASTEP code in this work.