Journal of Molecular Modeling最新文献

Context and results: The structure, electronic and optical properties of single-layer transition metallic chalcogenides ZrX₃ (X = S, Se, Te) have been studied by density functional theory. The electron energy dispersion curve shows that ZrX₃ has semiconductor properties, in which the conduction band is mainly contributed by the correlated states of the Zr-d orbital, and the valence band is mainly contributed by the correlated states of the X-p orbital. It is found that b-axis and biaxial strain have great influence on the bandgap and the shift of density of states is also large. At the same time, the peak value of density of states increases greatly when biaxial strain is applied. It is of guiding significance for selecting suitable substrates to prepare two-dimensional ZrX₃ materials to study their electronic properties. The calculation of optical constants confirms that ZrX₃ has strong optical anisotropy. In the visible range, the light absorption efficiency of ZrX₃ in the direction of electric field polarization [100] is higher than that in the direction of [010]. The reflectance spectral results show that ZrS₃ and ZrSe₃ in the [100] directions have the highest reflectance, and ZrTe₃ in the [010] direction has the highest reflectance, even in the long electromagnetic radiation range (up to 10 eV), which is of great significance for the construction of visible optical devices.

Computational method: All computations have been carried out based on density functional theory (DFT) as implemented in the CASTEP code. The pseudo-potential is adopted by the norm conserving, and the exchange correlation functional is adopted by the Perdew-Burke-Ernzerhof in local generalized gradient approximation (GGA).

Context: Direct DFT evaluation of negatively charged or highly π-delocalized systems is intrinsically problematic. Single ionized (anionic) forms of β-diketones combine both these issues. In this article, we have summarized and analyzed the experimental and theoretical spectral dataset for anionic forms of different substituted perfluorinated β-diketones that were obtained by our team during the past few years. Using previously collected experimental data, spectra of anion of diketones containing phenol, 2-furoyl, 2-thiophen, 2-selenophen, 2-tellorphe, 2-pyridin, 2-naphthyl, and N-methyl-pyrrole substituted rings were considered and chosen for the simulation. The X3LYP density functional demonstrates good results in both ultraviolet and visible parts of the diketones spectra. Minnesota family show predictable ability within the reasonable errors. The linear correlation between the Hartree-Fock exchange and the errors of estimation has been observed. Density functionals with a low contribution of HF weight (0-30%) provide better prediction accuracy.

Methods: Quantum chemistry calculations were performed under eighteen density functionals (Slater, Becke, OPTX, LYP, PW91C, BPE0, B3LYP, CAM-B3LYP, X3LYP, TPSS, revTPSS, TPSSh, M06-L, M06, M06-2X, M06-HF, M11-L, MN15-L), paired with the SMD solvation model implemented in GAMESS US program package. Def2-SVP basis set functions were applied to light atoms, and CRENBL effective core potential was used to Tellurium.

Context: The structural, electronic, and nonlinear optical properties of Verdoocridone A (Ver A) and B (Ver B) are examined theoretically in this study. The results showed that Ver A and B exhibit good electronic properties and can be used as new materials in NLO applications. According to their maximum absorption wavelength, Ver A (λ_max = 313 nm) enables production of vitamin D, while Ver B (λ_max = 319.55 nm) can help skin pigmentation.

Methods: All calculations were performed at the DFT/B3LYP-D3/6-311 + G(d,p) level of theory using the Gaussian 16 software package. Excited states were simulated using the TD-DFT method at the CAM-B3LYP combined with 6-311 + (d,p) basis set. Also, the solvent effect was studied in water and benzene phases by the solvation model based on density (SMD) method.

Context: This work analyzes the isomerization effects and solvent contributions to the stability, electronic excitations, reactivity, and non-linear optical properties (NLO) of resveratrol molecules within the formalism of the Density Functional Theory. The findings suggest that resveratrol solvatochromism is significantly influenced by solvent polarization. The electronic and free energies (E and G) indicate that trans is the most stable conformer. The system is classified as a strong nucleophile. However, the analysis of the Fukui functions and the Mulliken charges indicate that cis-trans isomerization jointly affects the reactive indices of the carbon and hydrogen atoms. The results also suggest that solvent is relevant to solvatochromism and the NLO response. Both cis and trans conformers present strong $\pi -{\pi }^{\ast }$ excitations that undergo a visible hypsochromic change when the polarity of the solvent increases. Once the absorption spectra are connected to the first hyperpolarization ( $\beta$ ) by the Oudar and Chemla relation, the hypsochromism of resveratrol is the reason for the drop in the generation of the second harmonic when the ambient polarity decreases. The CAM-B3LYP DFT results suggest that resveratrol is interesting for NLO applications. Depending on the choice of solvent, values $\sim$ 50 times those observed for urea ( $\beta =0.34\times {10}^{-34}$ esu), which is a standard NLO material.

Methods: The optimized geometries of cis and trans isomers of resveratrol in vacuum were obtained using Density Functional Theory (DFT) with the hybrid exchange-correlation function (CAM-B3LYP) and Pople basis set functions, specifically 6-311++G(d,p). The solvent effect on the geometries of both isomers was included using the polarizable continuum model (PCM) with the same level of QM calculation. Vibrational analysis was conducted to confirm that all optimized geometries correspond to the minimum energy. Various electronic properties, including dipole moments, molecular orbitals, transition energy, dipole polarizabilities, and global reactivity parameters, were calculated using both continuum and discrete solvation models based on the sequential QM/MM methodology. All QM calculations were performed with the Gaussian 09 program and the MC simulations with the DICE program. All NLO analysis was carried out using the Multiwfn code.

Context: Milk has nutrient-rich but thermal sensitive matrix that undergoes varying degrees of Maillard reaction (MR) at heating conditions. The MR mainly occurs between lysine residues (Lys) and lactose composed of glucose (Glc) and galactose (Gal), which are abundantly sourced from dairy products. In the present study, the MRs of Glc and Gal with Lys at the initial and intermediate stages have been investigated theoretically using density functional theory (DFT) to simulate the gaseous and aqueous phases. Reaction mechanisms have been proposed, and relative energy changes of different steps were calculated according to the total mass balance. The calculations reveal that both N^α- and N^ε-amine groups of Lys can react with the carbonyl functional group of Glc and Gal with the similar potential energy profiles, and Gal is more reactive than Glc. However, the barrier in N^ε-channel is lower than in N^α-channel, indicating a faster reaction rate through the former channel compared with the latter. The 5-hydroxymethyl-2-furfural (HMF) and derivative are formed under 3-deoxysone route in the intermediate stage. The calculation results are helpful for proposing a reasonable MR mechanism and suggesting possible control methods of the MRs.

Methods: In this study, different levels of DFT calculations have been conducted to investigate the mechanisms and favorability of generating MR products in Glc-Lys and Gal-Lys models at initial and intermediate stages in the gaseous and aqueous conditions. In order to elucidate the molecular models from the perspectives of chemistry and geometry, DFT calculations were performed by the mean of B3LYP functional at basis sets of 6-311 +  + G (d, p) and 6-311 +  + G (2df, 2p) with optional solvation settings. To examine the solvation effect, the study further constructed models with solvent H₂O and calculated in wB97XD functional with 6-31 + G (d) basis set. All computations were carried out Gaussian 09 suite of quantum chemistry software.

Context: Myocardial infarction is one of the major health challenges. It is of great significance to develop potential delivery carriers for new anti-myocardial infarction drugs. In this paper, based on first-principles calculations, monolayer WS₂ with excellent photoelectric properties was verified as a carrier for the anti-myocardial infarction drug amiodarone (AMD). Studies have shown that the WS₂-adsorbed AMD system (WS₂@AMD) maintains structural stability and produces an adsorption energy of-2.12 eV. Mulliken charge analysis shows that electrons are transferred from WS₂ atoms to AMD atoms. Among them, C, N and O obtained the maximum values of 0.51,0.37 and 0.56 e electrons, respectively, while H and I lost the maximum values of 0.32 and 0.24 e electrons, respectively. The optical response of WS₂ adsorbed AMD system is similar to that of WS₂. The light absorption coefficients of the two materials in the near ultraviolet region and the visible region can reach the order of 10⁵ cm^-1 and 10⁴ cm^-1, and the strain makes the light absorption peak red-shifted. The feasibility of temperature-controlled release mechanism of WS₂ as AMD carrier was discussed. This theoretical work helps to improve the performance of two-dimensional nanomaterials and make them better as drug delivery carriers to improve the therapeutic effect of myocardial infarction. These results indicate that the WS₂ monolayer has potential applications in the development of drug delivery carriers.

Methods: In this study, based on first-principles calculations, the CASTEP simulation software package was used to study the structure and properties of materials. The interaction between electrons and ions is considered by using Ultrasoft pseudopotentials. In order to eliminate the spurious interaction between adjacent structures caused by periodic calculations, a vacuum space no less than 18 Å is placed in the vertical direction if necessary. Different functions may produce different density functional calculation results. Due to the low sensitivity of the crystal structure to the calculation details, the PBE functional under the generalized gradient approximation (GGA) was initially used for structural optimization, and the energy cutoff value was set to 500 eV. Grimme 's dispersion correction was used to make the results more accurate. The Brillouin zone (BZ) is sampled by a 7 × 7 × 1 K-point grid to ensure the reliability of the original lattice calculation. The lattice vector and atomic coordinates are relaxed, and the tolerance of each atom is less than 0.01 eV/Å. The energy tolerance at the atomic position is less than 10^-7 eV/atom. When calculating the band gap, the HSE06 hybrid functional is used to modify the optimized structure of the PBE functional to obtain more accurate results. Spin-polarized

Context: The exploration of CL-20 eutectic has been a subject of fervent interest within the realm of high-energy material modification. Through the utilization of density functional and molecular dynamics methods, an investigation into the characteristics of hexanitrohexaazaisowurtzitane (CL-20)/2,4-dinitroanisole (DNAN) within the molar ratio range of 9:1-1:9 was conducted. This inquiry encompassed the scrutiny of molecular interaction pathway, attachment force, initiating molecular distance, unified energy concentration, and physical characteristics. Furthermore, EXPLO-5 was harnessed to prognosticate the explosion features and byproducts of unadulterated CL-20, DNAN, and CL-20/DNAN frameworks. The findings delineate a substantial differentiation in the electrostatic charge distribution on the surface between CL-20 and DNAN particles, signifying the preeminence of intermolecular interactions between disparate entities over those within similar entities, thus intimating the plausibility of eutectic constitution. Remarkably, the identification of maximal attachment force at a molar ratio of 4:6 suggests the heightened likelihood of eutectic formation, propelled primarily by electrostatic and van der Waals forces. The resultant eutectic explosive evinces intermediate reactivity and exemplary mechanical attributes. Moreover, the detonation achievement of the eutectic with a molar proportion of 4:6 straddles that of CL-20 and DNAN, representing a new type of insensitive high-energy material.

Methods: The testing method employs the Materials Studio software and utilizes the molecular dynamics (MD) method to predict the properties of CL-20/DNAN co-crystals with different ratios and crystal faces. The MD simulation time step is set to 1 fs, and the total MD simulation time is 2 ns. An isothermal-isobaric (NPT) ensemble is used for the 2-ns MD simulation. The COMPASS force field is employed, with the temperature set to 295 K. The prediction of detonation characteristics and products is conducted using the EXPLO-5 software.

Context: The study of platinum (Pt) clusters and nanoparticles is essential due to their extensive range of potential technological applications, particularly in catalysis. The electronic properties that yield optimal catalytic performance at the nanoscale are significantly influenced by the size and structure of Pt clusters. This research aimed to identify the lowest-energy conformers for Pt $_{18}^{}$ , Pt $_{19}^{}$ , and Pt $_{20}^{}$ species using Density Functional Theory (DFT). We discovered new low-symmetry conformers for Pt $_{19}^{}$ and Pt $_{20}^{}$ , which are 3.0 and 1.0 kcal/mol more stable, respectively, than previously reported structures. Our study highlights the importance of using density functional approximations that incorporate moderate levels of exact Hartree-Fock exchange, alongside basis sets of at least quadruple-zeta quality. The resulting structures are asymmetric with varying active sites, as evidenced by sigma hole analysis on the electrostatic potential surface. This suggests a potential correlation between electronic structure and catalytic properties, warranting further investigation.

Methods: An equivariant graph neural network interatomic potential (NequIP) within the Atomic Simulation Environment suite (ASE) was used to provide initial geometries of the aggregates under study. DFT calculations were performed with the ORCA 5 package, using functional approximations that included Generalized Gradient Approximation (PBE), meta-GGA (TPSS, M06-L), hybrid (PBE0, PBEh), meta-GGA hybrid (TPSSh), and range-separated hybrid ( $\omega$ B97x) functionals. Def2-TZVP and Def2-QZVP as well as members of the cc-pwCVXZ-PP family to check basis set convergence were used. QTAIM calculations were performed using the AIMAll suite. Structures were visualized with the AVOGADRO code.

Context: In this article, we adapt a recent proposition to use a Fermi-Dirac-type population scheme on Kohn-Sham molecular orbitals to the case of an interaction with a thermalised electrode. This allows to derive a fundamental non-linear equation linking the chemical potential of the electrode and the amount of charge transferred to the system under study, hence allows to quantify the propensity to charge transfer (philicity). This methodology is applied to a large set of common electrophiles and nucleophiles, showing decent relation with more standard philicity descriptors. Chemical hardness is also revisited by this approach.

Methods: All calculations were performed using the Gaussian 16 software package at the M062X/aug-cc-pvtz level of theory. Data analysis was then performed through a Python3 dedicated program (relying on the fsolve numerical solver from the SciPy package), using Gaussian output files, and available as supplementary material.

Context and results: In this work, we perform a systematic study on the thermoelectric properties of Zr_1-xNiSnHf_x using first-principles calculations combined with Boltzmann transport equations. The power factor of Zr_1-xNiSnHf_x increases as the temperature increases from 300 to 1200 K, because the increase in electrical conductivity is greater than the decrease in the Seebeck coefficient. The power factor of Zr_7/8NiSnHf_1/8 is larger than that of other Zr_1-xNiSnHf_x thermoelectric materials, but the thermoelectric figure of merit (ZT) is similar to that of others materials. This is due to the higher electronic thermal conductivity of Zr_7/8NiSnHf_1/8 compared to other materials. The maximum ZT of p-type (n-type) Zr_1-xNiSnHf_x is 0.98 (0.97), 0.9 (0.89), 0.83 (0.80), and 0.72 (0.73) at 300 K, 600 K, 900 K, and 1200 K, respectively, which are greater than those of the pure ZrNiSn. In conclusion, Hf-doped ZrNiSn can enhance the thermoelectric performance and are promising candidates for thermoelectric materials.

Computational method: This paper uses FP-LAPW implemented in the WIEN2K code. The thermoelectric performance is calculated based on the semi-classical Boltzmann theory implanted using the BoltzTraP code. The electronic thermal conductivity (κ_e) and the carrier concentration (n) have been calculated using the density functional theory.