Journal of Molecular Modeling最新文献

Context: The key factor in designing heat-resistant energetic materials is their thermal sensitivity. Further research and prediction of thermal sensitivity remains a great challenge for us. This study is based on first-principles calculations and establishes a theoretical model, which comprehensively considers band gap, density of states, and Young's modulus to obtain a empirical parameter Ψ. A quantitative relationship was established between the new parameter and the thermal decomposition temperature. The value of Ψ is calculated for 10 energetic materials and is found to have a strong correlation with the experimental thermal decomposition temperature. This further proves the reliability of our model. Specifically, the larger the value of Ψ, the higher the thermal decomposition temperature, and the more stable the energetic material will be. Therefore, to some extent, we can use the new parameter Ψ calculated by the model to predict thermal sensitivity.

Methods: Based on first-principles, this paper used the Cambridge Serial Total Energy Package (CASTEP) module of Materials Studio (MS) for calculations. The Perdew-Burke-Ernzerhof (PBE) functionals in Generalized Gradient Approximation (GGA) method as well as the Grimme dispersion correction was used in this paper.

Context: Quantum computing is an exciting area, which has grown at an astonishing rate in the last decade. It is especially promising for the computational and theoretical chemistry area. One algorithm has received a lot of attention lately, the variational quantum eigensolver (VQE). It is used to solve electronic structure problems and it is suitable to the noisy intermediate-scale quantum (NISQ) hardware. VQE calculations require ansatze and one of the most known is the unitary coupled cluster (UCC). It uses the chosen basis set to generate a quantum computing circuit which will be iteratively minimized. The present work investigates the circuit depth and the number of gates as a function of basis sets and molecular size. It has been shown that for the current quantum devices, only the smallest molecules and basis sets are tractable. The H ${}_2$ molecule with the cc-pVTZ and aug-cc-pVTZ basis sets have circuit depths in the order of 10 ${}^6$ to 10 ${}^7$ gates and the C ${}_2$ H ${}_6$ molecule with 3-21G basis set has a circuit depth of $2.2\times {10}^8$ gates. At the same time the analysis demonstrates that the H ${}_2$ molecule with STO-3G basis set, requires at least 500 shots to reduce the error and that, although error mitigation schemes can diminish the error, they were not able to completely negate it.

Methods: The quantum computing and electronic structure calculations were performed using the Qiskit package from IBM and the PySCF package, respectively. The ansatze were generated using the UCCSD method as implemented in Qiskit, using the basis sets STO-3G, 3-21G, 6-311G(d,p), def2-TZVP, cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ. The operators and the Hamiltonian were mapped using the Jordan-Wigner scheme. The classical optimizer chosen was the simultaneous perturbation stochastic approximation (SPSA). The quantum computers used were the Nairobi and Osaka, with 7 and 127 qubits respectively.

CONTEXT AND RESULTS : In this paper, the crystal structure, electronic, optical, and mechanical properties of SrVO₃ have been systematically studied by first-principles calculation. The results show that the calculated lattice parameters are in good agreement with the experimental values of X-ray diffraction. The density of states is described in detail in this paper. By analyzing the crystal structure and electronic properties of SrVO₃, the magnetic properties of SrVO₃ are obtained from the one unpaired electrons of V and the exchange interaction between two V ions. At the same time, a detailed analysis of the optical properties of SrVO₃ was conducted, and it was found that it is transparent in the visible light range. Finally, the mechanical properties of SrVO₃ are calculated, which can provide some references for future research. COMPUTATIONAL METHOD: In this paper, a first-principles method based on density functional theory (DFT) is reported for PBE-GGA analysis using the plane wave-pseudo potential method in a quantum concentrate packet, U value of 7 eV to V-d and a U value of 2 eV to O-p, Grimme correction by DFT-D method. The k points in the Brillouin region are set to 4 × 4 × 4. The energy convergence criterion for self-consistent field calculation is set at 5.0 × 10^-6 eV/atom, and the cutoff energy is 1170 eV. In this paper, the force acting on each atom is not more than 0.01 eV/Å, the maximum stress is not more than 0.02GPa, and the maximum atomic displacement is 5 × 10^-4 Å.

Context: We have computationally elucidated the mechanism for formation of H₂O, N₂O and CO₃ from the reactions of CH₂OO with H₂, N₂ and CO₂, respectively, by the direct attack of the terminal O atom of CH₂OO. This unique mechanism, which is characteristically "bee-sting-like" in nature, was found to be closely parallel to their reactions with the O(¹D) atom. Reactions with H₂ and CO₂ take place by side-on attack, while the N₂ reaction occurs by end-on attack with predicted barriers, 19.4, 13.1 and 25.3 kcal.mol^-1, respectively. The CO₂ reaction with CH₂OO was found to occur by producing the C_2v CO₃, O = C < (O)O, instead of its D_3h conformer, essentially similar to the O(¹D) + CO₂ reaction. The rate constants for the three reactions have been computed by the transition state theory (TST) based on the predicted potential energy profiles. We have also utilized the isodesmic nature of the dative bond exchange in the N₂ reaction, CH₂O → O + N₂ = CH₂O + N₂ → O, to estimate the heat of the formation of CH₂OO. Based on the heat of reaction computed at the highest level of theory employed, we obtained Δ_fH^o₀ (CH₂OO) = 27.5 kcal.mol^-1; the value agrees with the recent results within ± 1 kcal.mol^-1.

Methods: All calculations were performed using Gaussian 16 software. Geometry, frequency, and IRC analysis calculations were conducted at the M06-2X/aug-cc-pVTZ level of theory. The heats of reaction have been evaluated at the highest level, CCSD(T)/CBS(T,Q,5)//M06-2x/aug-cc-pvTz.

Context: The cyclopropane skeleton plays a significant role in bioactive  molecules due to its distinctive structural properties. This has sparked keen interest and in-depth exploration in the field of stereoselective synthesis of cyclopropane derivatives. In the present study, the mechanism and the origin of stereoselectivity of diastereodivergent synthesis of cyclopropane derivatives via the catalyst-free [2 + 1]-cyclopropanation reactions of 3-diazo-N-methylindole (R1) with two types of electron-deficient olefins (R2 and R3) in both aqueous and toluene media have been studied using the DFT calculations. The findings indicate that these [2 + 1] cycloaddition reactions proceed in two stages, where the first step is not only the rate-determining step but also critically dictates the stereoselectivity of the product. The calculated diastereomeric ratios are in agreement with the experimental results. Furthermore, by utilizing non-covalent interaction (NCI) analysis and energy decomposition analysis based on molecular force fields (EDA-FF), we elucidated that the electrostatic interactions between reactant fragments in the transition state TS1s for the first step are the predominant factors determining the stereoselectivity, as opposed to the experimentally hypothesized steric hindrance and π-π stacking interactions.

Methods: The geometrical structures of all minima and transition states on the potential energy surface (PES) in solvents water and toluene were fully optimized using the DFT method at the M06-2X(D3)/SMD/6-31 + G(d,p) level of theory. Single-point energy calculations were carried out based on the optimized geometries in the solution at the M06-2X(D3)/6-311 + G(d,p) level. All the DFT calculations were performed using the Gaussian 09 software. The optimized molecular structures were visualized using CYLview software. NCI analysis was performed using the Multiwfn and VMD softwares. The Multiwfn program was also used for CDFT and EDA-FF analyses.

Context: Poly(butylene adipate-co-terephthalate) (PBAT) is a biodegradable plastic. It was introduced to the plastics market in 1998 and since then has been widely used around the world. The main idea of this research is to perform quantum chemical calculations to study the potential toxicity of PBAT and its degradation products. We analyzed the electron transfer capacity to determine its potential toxicity. We found that biodegradable products formed with benzene rings are as good electron acceptors as PBAT and OOH^•. Our results indicate that the biodegradation products are potentially as toxic as PBAT. This might explain why biodegradation products alter the photosynthetic system of plants and inhibit their growth. From this and other previous investigations, we can think that biodegradable plastics could represent a potential environmental risk.

Methods: All DFT computations were performed using the Gaussian16 at M062x/6-311 + g(2d,p) level of theory without symmetry constraints. Electro-donating (ω-) and electro-accepting (ω +) powers were used as response functions.

Context: Density functional theory (DFT) calculations on the ground and the first excited state are performed on the modified and unmodified 4-(methoxyphenyl acetonitrile) monomer (referred to as MPA). The modified monomer named MFA is obtained by Knoevenagel condensation of MPA with dimethylformamide dimethyl acetal (DMF-DMA). DFT computations show that the chemical grafting of the dimethylamino group onto the MPA unit induces a great change in the geometric, electronic, and optical properties. Going from MPA to MFA monomer, a great change in the frontier orbitals of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) in the ground and the first excited state is observed. Consequently, a reduction in the energy gap HOMO-LUMO and an enhancement in the absorption and emission properties are observed under the chemical modification. The observed modifications in the electronics and optical properties are the result of the charge transfer appearing between the cyano (C≡N) acceptor group and the dimethylamino (DMF-DMA)-grafted group donor ring.

Methods: Quantum chemical calculations were performed in the ground and the first excited state using the density functional theory (DFT), and it extends the time-dependent density functional theory (TD-DFT), implemented in the Gaussian 09 software package. The ground state is obtained by optimization of the studied molecular geometries by employing the DFT/M062X/6-31G(d,p) level of theory. The first excited state is obtained by re-optimization of the ground state geometries using the TD-DFT/M062X/6-31G(d,p) level of theory. The contour plots of the frontier orbitals and the molecular electrostatic potential (MEP) maps are obtained from the ground and the first excited state, optimized geometries, and drawn using Gaussview software.

Context: In the renewable industry, pressure-dependent CsPbBr₃ perovskite has a lot of potential due to its exceptional properties. Present work revealed the mechanical stability of CsPbBr₃ between 0 to 50 GPa. The bandgap of unstressed CsPbBr₃ is 2.90 eV, indicating a direct bandgap. Band gap values decrease by increasing external pressure. CsPbBr₃ structure showed a direct band gap from 0 to 35 GPa and in-direct from 40 to 50 GPa. The unit cell volume and lattice constants are substantially decreased. Mechanical parameters, i.e., Young's modulus, bulk modulus, anisotropy factor, shear modulus, and poison's ratio are obtained. Under ambient conditions, the mechanical properties of CsPbBr₃ showed ductile behavior and with induced pressure, their ductility has significantly improved. By applying stresses ranging from 0 to 50 GPa, the considerable fluctuation in values of dielectric function (imaginary and real), absorption, reflectivity, loss function, refractive index (imaginary and real), and conductivity (imaginary and real), was also identified. When pressure rises, the optical parameters increase and drag in the direction of high energies. Response functions are used to predict the density of states and the phonon lattice dispersion to study the phonon properties. By using the quasi-harmonic Debye model, the thermal effect on the free energy, entropy, enthalpy, and heat capacity were predicted and compared. These results would be useful for theoretical research and indicate how external pressure significantly affects the physical characteristics of CsPbBr₃ perovskites, which may open up new possibilities for use in optoelectronic, photonic, and solar cell applications.

Methods: The structural, electrical, mechanical, optical, and thermal properties of cesium lead bromide (CsPbBr₃) are investigated by applying external pressure from 0 to 50 GPa, using generalized gradient approximations (GGA) and Perdew-Burke-Ernzerhof (PBE) with CASTEP code built-in material studio by density functional theory (DFT).

Context: Cyclin-dependent kinase 9 (CDK9) plays a significant role in gene regulation and RNA polymerase II transcription under basal and stimulated conditions. The upregulation of transcriptional homeostasis by CDK9 leads to various malignant tumors and therefore acts as a valuable drug target in addressing cancer incidences. Ongoing drug development endeavors targeting CDK9 have yielded numerous clinical candidate molecules currently undergoing investigation as potential CDK9 modulators, though none have yet received Food and Drug Administration (FDA) approval.

Methods: In this study, we employ in silico approaches including the molecular docking and molecular dynamics simulations for the virtual screening over the natural compounds library to identify novel promising selective CDK9 inhibitors. The compounds derived from the initial virtual screening were subsequently employed for molecular dynamics simulations and binding free energy calculations to study the compound's stability under virtual physiological conditions. The first-generation CDK inhibitor Flavopiridol was used as a reference to compare with our novel hit compound as a CDK9 antagonist. The 500-ns molecular dynamics simulation and binding free energy calculation showed that two natural compounds showed better binding affinity and interaction mode with CDK9 receptors over the reference Flavopiridol. They also showed reasonable figures in the predicted absorption, distribution, metabolism, excretion, and toxicity (ADMET) calculations as well as in computational cytotoxicity predictions. Therefore, we anticipate that the proposed scaffolds could contribute to developing potential and selective CDK9 inhibitors subjected to further validations.

Context: Constrained methods in electronic structure methodologies add terms to the variational equations and generate solutions that represent distorted electronic distributions. In some cases, the new solutions can be used to study the chemical reactivity of parts of the molecule. Additionally, this contribution presents the use of population constraints to define pseudo atoms in a molecule. The effects of the pseudo atom on the molecular properties are analyzed. The pseudo atoms are used to simulate the inductive effect of the substituent in a group of carbonyl molecules and their effect on the stability of the complexes between these organic species and one molecule of water. A discussion on the assumptions involved in the present definition of pseudo atoms is also included.

Method: The constrained RHF computations are done in a modified Hartree-Fock code for Gaussian basis sets. The selected basis set is STO-6 G.