Journal of Molecular Modeling最新文献

Context

This research investigates two critical areas, providing valuable insights into the properties and interactions of boron nitride nanotubes (BNNTs). Initially, a variety of BNNT structures (BNNT(m,n)_x, where m = 3, 5, 7; n = 0, 3, 5, 7; x = 3–9) with different lengths and diameters are explored to understand their electronic properties. The study then examines the interactions between these nanotubes and several gases (CO, CO₂, CSO, H₂O, N₂O, NO, NO₂, O₂, ONH, and SO₂) to identify the most stable molecular configurations using the bee colony algorithm for global optimization. The primary findings highlight the impact of nanotube diameter on these properties. It was observed that smaller diameters result in a larger energy gap due to increased quantum confinement. Significant charge transfer, especially with CO, was detected, affecting the electronic structure of the nanotubes. The study highlighted that BNNTs exhibit the strongest adsorption tendencies for NO₂, O₂, and SO₂. These findings underscore the critical roles of nanotube diameter and charge transfer in sensor applications and demonstrate the comprehensive utility of various analytical methods in understanding BNNT-gas interaction mechanisms.

Methods

The research employs a comprehensive computational framework based on density functional theory (DFT). Various DFT methods, such as PBE0, B3LYP(GD3BJ), CAM-B3LYP, HSE06i, M06-2X, and ωB97XD functionals, are utilized along with the Def2tzvp basis set for the calculations. Structural optimizations are performed to ensure accuracy, and modifications to the energy gaps are analyzed using conceptual DFT. Additionally, Total Density of States (TDOS) analyses are conducted. Charge transfer mechanisms are investigated through Natural Bond Orbital (NBO) analysis. The interactions between gases and nanotubes are characterized at critical points using the Quantum Theory of Atoms in Molecules (QTAIM) framework.

Context

Isatin-Schiff bases have wide applications in chemistry. The π conjugated electronic system and heterocylic structure of these materials make them valuable for use as photosensitized materials. The delocalization of π-electrons throughout the structure causes the UV–vis absorption spectra to shift to longer wavelengths. In this study, the isatin manganese carbonyl complex shifted the UV–vis absorption wavelength to a longer wavelength (vis. 400–700 nm) compared with our previous studies. The isatin derivatives (ISE (3[4-ethyl(phenyl)imino][indoline-2-one]), ISB (3[4-butly(phenyl)imino][indoline-2-one])) and their Mn carbonyl complexes MnISE ((ISE)Mn(CO)₃), and, MnISB ((ISB)Mn(CO)₃) were investigated via density functional theory (DFT) in different solvent media. The most stable complexes were found in medium polarity THF. The calculated HOMO–LUMO energy gap shows that the charge transfer occurs within the molecule. The HOMO–LUMO energy gap was increased with increasing solvent polarity for all investigated compounds. The smaller energy gap indicates that charge transfer occurs within the Mn(II) complex, in contrast to ISE and ISB, which exhibit larger energy gaps. As a result, the maximum absorption of Mn complexes shifts to the visible region. MnISB has the smallest HOMO–LUMO energy gap in THF. Additionally, the global reactivity parameters indicated that the MnISE complex has the highest electrophilicity index. DFT calculations have also been performed to investigate polarizability and first-order hyperpolarizability of these compounds. In water, the ISE had higher NLO values than the other structures did. These results indicate that all the studied molecules in different solvents could be good candidates for use in photosensitized and nonlinear optical materials.

Methods

Geometries were determined at the DFT level via the LANL2DZ basis set for Mn and cc-PVTZ for other atoms in the molecules with the B3LYP functional. The UV–vis absorption spectra and HOMO–LUMO energies of ISE, ISB, and their Mn complexes were calculated by Time-dependent DFT (TDDFT) with CAM-B3LYP using the same basis sets. The UV–vis absorption spectra of ISE were also measured in acetonitrile and compared with the calculated spectra, which were consistent with the experimental results. All calculations were repeated in different solvents with the polarizable continuum model (PCM).

Context

Boron-dipyrromethene (BODIPY) compounds have unique photophysical properties and have been applied in fluorescence imaging, sensing, optoelectronics, and beyond. In order to design effective BODIPY compounds, it is crucial to acquire a comprehensive understanding of the relationships between the structures of BODIPY and the corresponding photoproperties. Fifteen molecular descriptors were identified to be strongly correlated with the maximum absorption wavelength. The developed ML/QSPR model exhibited good predictive performance, with coefficients of determination (R²) of 0.945 for the training set and 0.734 for the test set, demonstrating robustness and reliability. A posterior analysis of some of the selected descriptors in the model provided insights into the structural features that influence BODIPY compound properties; meanwhile, it also emphasizes the importance of molecular branching, size, and specific functional groups. This work shows that applied combined cheminformatics and machine learning approach is robust to screen the BODIPY compounds and design novel structures with enhanced performance.

Methods

In the present study, all the BODIPY models studied were fully optimized, and the corresponding absorption spectrum was obtained at DFT/TDDFT//B3LYP/6-311G(d,p) level. All the above calculations were executed by the Gaussian 16 program. Based upon the theoretical computational results, the machine learning-based quantitative structure–property relationship (ML/QSPR) model was employed for predicting the maximum absorption wavelength (λ) of BODIPY compounds by combining hand-crafted molecular descriptors (MD) and explainable machine learning (EML) techniques using Scikit-learn python library. A dataset of 131 BODIPY compounds with their experimental photophysical properties was used to generate a diverse set of molecular descriptors capturing information about the size, shape, connectivity, and other structural features of these compounds using Chemaxon and Alvadesc software. A genetic algorithm (GA) variable selection together with the multi-linear regression (MLR) method were applied to develop the best predictive model using the Genetic Selection python library.

Context

Heparan sulfate (HS) linear polysaccharide glycosaminoglycan compound is linked to components from the cell surface and the extracellular matrix. HS mediates SARS-CoV-2 infection through spike protein binding to cell surface receptors and is required to bind ACE2, prompting the need for electronic structure and molecular docking evaluation of this core system to exploit this attachment in developing new derivatives. Therefore, we have studied five molecules based on HS using molecular docking and electronic structure analysis. Non-covalent interaction analysis shows hydrogen bonding and van der Waals interactions in the binding to RBD-ACE2 interface and 3CL^pro. SDM3 and SDM1 molecules present the lowest gap, including solvent effect under 154.6 kcal/mol, and exhibit the most reactivity behavior in this group, potentially leading to enhanced interaction in docking studies.

Methods

Heparan sulfate and four derivatives were optimized using B3LYP functional with two basis sets 6–31 + G(d,p) and def2SVP. Electronic structure was used to explore the main interactions and the reactivity of these molecules, and these optimized structures were used in the molecular docking study against 3CL^pro, RBD, and ACE2.

Context

Nickel-catalyzed hydroamination of dienes with phenylmethanamines was studied theoretically to investigate reaction mechanism. These calculated results revealed that Ni-catalyzed hydroamination began with the O − H bond activation of trifluoroethanol, including three important elementary steps: the ligand-to-ligand hydrogen migration, the nucleophilic attack of phenylmethanamine, and hydrogen migration. The nucleophilic attack of phenylmethanamine was the rate-determining step, and the branched product of 3,4-addition with (S)-chirality was the most dominant. The N − H bond activation of phenylmethanamine occurred more difficultly than the O − H bond of trifluoroethanol, because of high ΔG and ΔG^≠. In addition, the origin of regioselectivity and enantioselectivity, and prediction of the ligand were also discussed in this text.

Methods

All computations were performed with Gaussian09 program. All geometries were optimized at the ωB97XD/6-31G(d,p) level (SDD for Ni), and to obtain more accurate potential energy, single-point calculation was carried out at the ωB97XD/cc-pVDZ level (SDD for Ni). The Cramer-Truhlar continuum solvation model (SMD) was used to evaluate solvation effect of mesitylene, and a correction of the translational entropy was made with the procedure of Whitesides group. 

Graphical abstract

Context

High-energy density materials (HEDMs) are integral to modern society and are in high demand. Consequently, the design and synthesis of energetic material molecules have garnered significant research interest. This study focuses on the furazan ring system as a core for developing superior HEDMs. We employed density functional theory (DFT) to assess the properties of 27 novel energetic compounds, including their geometries, densities, enthalpies of formation, detonation velocities, detonation pressures, and molecular orbital energies (HOMO–LUMO). The computation of detonation velocity and detonation pressure was based on theoretical density and enthalpy of formation. The findings revealed that incorporating energetic groups into the furazan framework, linked by sec-ammonia bridge (-NH-), enhances both the detonation performance and oxygen content of the materials. This enhancement guides the future synthetic endeavors aimed at creating advanced HEDMs.

Method

DFT has been employed to investigate the detonation performance and stability of energetic materials. Molecular optimization and performance metrics were all calculated using the DFT-B3LYP method with a 6–311 + G* basis set. The optimization and volume calculations were performed using the Gaussian 09 package. The electrostatic potential energy was computed using Multiwfn software. The impact sensitivity of the designed molecules was calculated using the heat of detonation model.

Context

Ammonium dinitramide (ADN) is highly hygroscopic, which poses significant challenges in its practical applications. Consequently, mitigating this hygroscopic nature has been a primary focus in the research and development of ADN. This study investigated the properties of the ADN/3-amino-4-nitrofurazan (ANF) cocrystal using density functional theory, molecular dynamics, and Monte Carlo methods. The research involved analyzing binding energies, radial distribution functions, and molecular interaction energies; predicting crystallographic properties of the cocrystal; and ADN theoretically assessing its hygroscopic and detonation properties. The results indicated that the cocrystal achieved relative stability at a 1:1 molar ratio of ADN to ANF, driven by favorable conditions for cocrystal formation. The primary forces facilitating this cocrystal formation were electrostatic and van der Waals interactions. The predicted space group for the cocrystal was P21-C, with a calculated crystal density of 1.8836 g·cm⁻³. Additionally, the cocrystal demonstrated a calculated saturated moisture absorption rate of 9.07%, which contrasted significantly with the 18.12% absorption rate observed for pure ADN. Theoretical calculations indicated that the detonation performance of the cocrystal surpassed that of the pure components ADN and ANF, suggesting that the ADN/ANF cocrystal was a new type of high-energy material with low hygroscopicity.

Methods

For the whole molecular dynamics simulation, the simulation was done in Materials Studio 2020 software, under NPT ensemble, with a set temperature of 298 K, a pressure of 0.0001 GPa, a temperature control of Andersen, and a pressure control of Berendsen. The total simulation time was 1 ns. The first 0.5 ns was used for the thermodynamic equilibrium, and the second 0.5 ns was used for statistical calculations and analysis. It was used for statistical calculations and analysis. Samples were recorded every 10 fs during the calculation. All systems were simulated similarly. Surface electrostatic potentials were calculated using Gaussian and Multiwfn programs with B3LYP, 6-31G +  + basis sets, and levels. Hygroscopicity calculations utilized the Sorption module to simulate pure ADN and ADN/ANF cocrystals. Water was chosen as the adsorbate, with a pressure of 2.813 kPa, temperature set at 308.15 K, and adsorbate coverage ranging from 0.12 to 0.8.

Context

1,2,4-Oxadiazole serves as a fundamental building block driving advancements across diverse scientific and technological arenas, contributing to the creation of innovative materials for various applications including devices, sensors, medications, agrochemicals, and biomedical instruments. Employing density functional theory (DFT) methods, we investigate the impact of different conformers of an oxadiazole substituted derivative, specifically 3,5-bis[4-(4-methylphenylcarbonyloxy)phenyl]-1,2,4-oxadiazole, in both monomeric and stacked configurations (dimeric and tetrameric). We analyze the electronic structures of various conformers, including assessment of HOMO–LUMO energy gaps, to detect the influence of diverse substituents and stacking arrangements. We have also explored the stability of stacked structure in explicit solvent environment. Additionally, we examine absorption spectra, non-linear optical properties, and electronic circular dichroism to evaluate the potential applications of these molecules in optoelectronic devices. Our calculations showed that all the conformers were thermodynamically stable within an energy difference of 2.64 kcal mol⁻¹. The study also suggests possible application of the material in optical and electronic devices.

Methods

DFT calculations were carried out using the CAM-B3LYP and wB97XD functionals with a 6–31 + G* all-electron basis set, paired with the SCRF/PCM solvation model, implemented in the Gaussian 09 package. Equilibrium structure was achieved by performing NPT and NVT simulations using the Gromacs package.