Journal of Molecular Modeling最新文献

Context

The modulation of autophagy – inhibition or induction – has emerged as a promising strategy in cancer treatment, offering significant advantages over conventional chemotherapy. Previously, we demonstrated that the vanadium complex [VO(oda)(phen)] inhibits autophagy by activating the phosphoinositide 3-kinase gamma (PI3Kγ) protein. Given the therapeutic potential of autophagy modulation, we proposed structural modifications to this complex to achieve the opposite effect: autophagy activation by preventing PI3Kγ activation. In this context, this study aimed to perform structural modifications on the vanadium complex to elucidate and discuss new conformational implications and its role in the autophagic machinery. The AMBER force field (FF) was adapted for the modified vanadium complex (mVC), yielding excellent results in molecular dynamics (MD) simulations in vacuum, protein, and aqueous environments. The structural modifications successfully disrupted the interaction between [VO(oda)(phen)] and PI3Kγ, previously identified as a key factor in PI3Kγ activation. Consequently, PI3Kγ deactivation leads to a shift in the autophagy signaling pathway, promoting autophagy activation. Additionally, NMR calculations were performed to explore a novel role for mVC, broadening its potential applications.

Methods

MD simulations were conducted at 800 ns using the AMBER program, while Molegro Virtual Docker (MVD) was employed for docking simulations. Optimization calculations (B3LYP/def2-TZVP and LANL2DZ ECP for V) and NMR calculations (PBE/IGLO-II and Wachters + f for V) were performed using Gaussian 09. The key frames from the MD simulations were selected using the OWSCA algorithm. Ligand and protein performance were evaluated through RMSD, RMSF, and hydrogen bond analyses, applying cutoff distances of 3.5 Å and 30°.

Context

The accurate prediction of the standard enthalpy of formation (ΔHf°) is crucial for understanding molecular stability and reaction energetics, yet reliable experimental data are often unavailable for unstable or novel compounds. This work benchmarks three Minnesota density functionals (M06-2X, MN12-SX, and MN15) to evaluate their performance in predicting ΔHf° values for a diverse set of hydrocarbons via the atom equivalent method. Our results identify MN15 as the most accurate functional, particularly when zero-point energy (ZPE) corrections are included, achieving a mean absolute error of 1.70 kcal/mol. In contrast, MN12-SX exhibits significant sensitivity to ZPE corrections, limiting its reliability. To enhance predictive robustness, a machine learning model was developed, which demonstrated strong performance on acyclic systems but highlighted challenges in predicting strained cyclic molecules. This hybrid quantum-chemical and data-driven framework provides a validated pathway for improving the accuracy of thermochemical predictions.

Methods

All quantum chemical calculations were performed using the Gaussian 16 software package. The density functionals M06-2X, MN12-SX, and MN15 were employed in conjunction with the correlation-consistent polarized valence triple-zeta (cc-pVTZ) basis set. Single-point electronic energies and vibrational frequencies for ZPE corrections were computed at the same level of theory. Enthalpies of formation were derived using the atom equivalent method, where carbon and hydrogen energy equivalents were obtained via least-squares fitting to experimental data. Also, a machine learning workflow was implemented in Python using the scikit-learn library, wherein a random forest regressor was trained on molecular descriptors and experimental ΔHf° values, with model performance assessed via fivefold cross-validation.

Graphical Abstract

Context

The development of ordered structures upon immediately quenching from 473 K to different crystallization temperatures (Tc = 300 K, 320 K, 340 K, and 360 K) of three n-alkanes (n-eicosane (C₂₀H₄₂), n-tetracontane (C₄₀H₈₂) and n-octacontane (C₈₀H₁₆₂) to accommodate the formation of bilayer, monolayer and the folded-chain configurations, respectively), was quantitatively analyzed by evaluating chain/bond order parameters, interaction energies, conformational statistics, local dynamics, structural pair correlation function, and X-ray scattering profiles. The formation of ordered structures seems to be best at Tc = 340 K. Generally, systems that tend to form the monolayer and folded-chain configurations exhibit the most and the least ordered structures, respectively. Chains in monolayer structures tend to have a larger fraction of trans state, higher anisotropy of bond orientation, slower monomer dynamics, and more densely packed structures than chains in bilayer structures, while longer alkanes with chain-folded structures exhibit the least characteristics of these properties. The nucleation temperature (Tn) can be affected by their structural configuration, with the highest Tn for the monolayer structure. Nevertheless, the melting temperature (Tm) tends to depend solely on the molecular weights of these alkanes, not on their structural configuration.

Methods

Monte Carlo (MC) simulation of the coarse-grained (CG) models of three n-alkanes (one CG bead equivalent to an ethylene unit) on the second nearest neighbor diamond (2nnd) lattice with the same periodic box dimension of 5 nm in each size. The energetics of CG models were composed of the Rotational Isomeric State (RIS) model and the Lennard–Jones (LJ) potential energies to represent their intra- and intermolecular interactions, respectively. Structure developments within 100 million Monte Carlo steps (MCS) trajectories were monitored, and data analysis was based on snapshots collected at intervals of 10,000 MCS. All simulations and data analysis were performed using in-house FORTRAN codes with the g77 compiler.

Context

It is essential nowadays to investigate some unique and appropriate material for the purpose of optoelectronic applications. In the current study, the structural, optoelectronic, vibrational, mechanical, magnetic, and thermodynamic properties of MLaS (M = Ag, Au) in monoclinic phase are explored. The lattice parameters (Å) for AgLaS are noted to be a = 7.28, b = 7.31, and c = 6.93, whereas for AgLaS, a = 7.61, b = 7.31, and c= 6.93 with the lattice angles of α = γ = 90 and β = 98.74 for both materials. These compounds are categorized as semiconductor due to the direct energy band gap of 1.234 eV and 0.507 eV for AgLaS and AuLaS using PBE-GGA and 1.611 eV and 0.899 eV for AgLaS and AuLaS using HSE06 functional, respectively. Interestingly, these materials unveil non-magnetic and brittleness while possessing anisotropic behavior for various magnetic and mechanical applications. Also, these chalcogenides manifest a notable rise in absorptivity and optical conductivity in the IR energy region. The existence of imaginary frequencies implies that their few vibrational modes are inherently unstable upon thermal activation. Whereas, the negative Gibbs free energy endorses thermodynamic stability. The present research is the first computational effort entrusted for MLaS (M = Ag, Au) that may offer assistance to future researchers for synthesizing these materials for optoelectronic applications.

Methods

The properties are investigated by the first principles study relying on density functional theory (DFT). These computations use norm-conserving pseudopotential approach where HSE06 functional is appraised in the framework of CASTEP code. The HSE06 functional is systematically utilized to calculate better electronic band gap and obtain correct contribution from d/f electronic states. To seek mechanical stability, Born’s stability criterion is used, and the elastic parameters are computed while using Voigt–Reuss–Hills approximation. The density functional perturbation theory (DFPT) is used to examine the vibrational properties. Finally, the Harmonic Approximation technique is employed to determine thermodynamic properties.

Context

The thermal decomposition of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX) and 4,10-dinitro-2,6,8,12-tetraoxa-4,10-diazatetracyclododecane (TEX) mixed explosives, along with pure HMX, was investigated using reactive molecular dynamics at temperatures between 2000 and 3500 K. The study aimed to evaluate the effect of the caged explosive TEX on HMX decomposition and clarify the reaction mechanism of the mixture. The results showed that the primary initial decomposition step remains cleavage of the nitro group, while decomposition of TEX increased the NO₂ concentration in the system. NO₂ released from TEX combined with H atoms from HMX to form nitrite intermediates, which subsequently decompose into NO, HNO, and OH. Meanwhile, HMX and its decomposition products further reacted with OH and nitrogen oxides such as NO and HNO to yield final products including H₂O and N₂. The addition of TEX also introduced H atoms predominantly form H₂ rather than combine with N atoms to generate NH₃, leading to higher H₂ production in the mixture compared to pure HMX. The activation energies (Eₐ) for the initial and intermediate stages of decomposition in the mixed system were determined to be 87.06 kJ/mol and 100.72 kJ/mol, respectively—significantly lower than those of pure HMX. These findings confirmed that TEX promotes the decomposition of HMX and reduces the thermal stability of the mixed system.

Methods

Molecular dynamics simulations for the HMX/TEX mixed system were performed using the ReaxFF module within the LAMMPS software package, with the ReaxFF/lg force field employed to model interatomic interactions and chemical reactivity.

Context

The double hydride Cs₂XLuH₆ (X = Ca, Sr, Ba) perovskites are explored to determine the scope of these materials in hydrogen fuel cells and related applications. The DFT-based physical properties like thermoelectric, optoelectronic, vibrational, mechanical, and thermodynamic properties are calculated by applying hybrid complex HSE06 functional. The vibrational and thermodynamic stability of these materials are verified by positive (real) modes of phonons in the dispersion curves. The electronic properties illustrate the metallic behavior of these materials that make these materials favorable for hydrogen storage applications. The mechanical properties illustrate the compatibility, reliability, stability, and easy transportation of these materials for hydrogen storage applications. The peak value of Seebeck coefficient is listed as (4.82times {10}^{-5} V/K) for Cs₂CaLuH₆. The highest value of gravimetric ratio for hydrogen energy storage is found to be 4.07 wt% for Cs₂BaLuH₆. The highest calculated tolerance factors is 0.92 for Cs₂BaLuH₆. All these novel and significant properties confirmed Cs₂BaLuH₆ double hydride perovskites as the potential candidates for future energy applications like hydrogen fuel cell.

Method

In the present article, optoelectronic and other physical properties of the materials under consideration are calculated by applying first principles DFT based in the framework of CASTEP simulation code. The electronic properties have been calculated using the HSE06.

Graphical Abstract

Context

Proton tunneling via hydrogen bonds is a widespread quantum phenomenon in chemistry and biochemistry. Modeling the dynamics of proton transfer is a challenging task due to the multidimensional nature of the problem. The picture becomes even more complex in tautomerisms where multiple protons are transferred simultaneously, as occurs in the base pairs of biological molecules. In this study, we investigate the dynamics of double proton tunneling by solving the Schrödinger equation using the time-dependent Fourier grid Hamiltonian method. This approach enables straightforward calculations of the tunneling probability and the dynamics of the tunneling protons in the classically forbidden region. Notably, in a semiclassical framework, the model allows the computation of the average and instantaneous tunneling velocity, the rate constant of the double transfer, the temporal variation of the Lagrangian at each barrier penetration step, and the transition state energy. The model is formulated for both symmetric and asymmetric four-well potentials. To evaluate the predictive capability of the model, a detailed investigation of double proton tunneling in the isolated formic acid dimer is performed.

Methods

The time-dependent Schrödinger equation with a two-interacting double-well potential is solved using the Fourier grid Hamiltonian method. This approach leads to an algebraic equation that can be easily solved with standard mathematical software, such as Mathematica in the Wolfram language. The solutions are expressed as discretized time-dependent wave functions, which allow for the calculation of the tunneling probability as a function of the reaction coordinates. Using semiclassical approximation we can derive the action, as well as the mean and instantaneous velocities, and determine the rate constant of double tunneling.

Context and results

The FeNiCrMn alloy gasket is vital for the sealing performance of the engine cylinder head-block interface and thus engine reliability. The transition temperature at which the plastic region disappears in the FeNiCrMn alloy gasket remains ambiguous. Molecular dynamics (MD) simulations show that lowering temperature suppresses plastic deformation under tension but improves compressive performance, while strain rate has negligible effects on elastic and strength properties. Based on MD data, a machine learning (ML) model achieved high prediction accuracy ((text {MAE} = 0.0072, R^{2} = 0.9949)). Mathematical analysis (MA) further identified critical temperatures of (T_{c} = {509},text {K}) (tension) and 526 K (compression), beyond which tensile plasticity vanishes and compressive behavior exhibits the opposite trend.

Methods

A combined MD-ML-MA framework was employed to investigate the mechanical properties and critical temperature of the FeNiCrMn alloy gasket. MD simulations assessed tensile and compressive responses across temperatures and strain rates. The resulting dataset was used to train an ML neural network with a backpropagation algorithm for predictive modeling, while MA quantified the plastic region m(T), enabling determination of critical temperature thresholds.

Context

(3 + 2) Cycloaddition reactions are foundational in the synthesis of biologically and industrially relevant heterocycles, including isoxazolidine and spirocyclic frameworks. In this work, we investigated the reactivity of C-substituted-N-phenyl nitrones with 3,5-bis-(arylidene)-1-methylpiperidine-4-one toward the synthesis of isoxazolidine derivatives. The study revealed how structural modifications of the nitrone substituents influence reaction dynamics, with emphasis on chemo-, regio-, and stereoselectivity. Two possible reaction pathways were identified: selective addition of the nitrone to the olefinic bond of the bis-arylidene piperidine and alternative addition across the carbonyl group. Energy profiles and kinetic data indicate that the second step responsible for generating the bis-products is unfavorable relative to the mono-products. Global electron density transfer (GEDT) values indicated that the processes are highly polar, and reactivity indices correlated well with the observed activation energies and selectivity trends.

Methods

All computations were performed using density functional theory at the M06-2X/6-311G(d,p) level. Solvent effect was included with the integral equation formalism polarizable continuum model (IEFPCM). Transition structures were verified by frequency analysis and intrinsic reaction coordinate (IRC) calculations. Global and local reactivity indices, together with GEDT values, were calculated to characterize electron density transfer and reactivity. All computations were carried out with Gaussian 09.

Graphical abstract

Context

This study starts from several aspects, including ionic structure and geometric parameters (bond parameters, weak interactions), electronic properties (surface electrostatic potential, frontier molecular orbitals, and energy gaps), solid-phase heat of formation, and detonation performance. The anions (2H-1,2,3-triazole-4,5-dikyl) bis(1,2,4-oxadiazole-3,5-dikyl)bis(dinitro methane) were combined with ammonium ions, hydroxyl ammonium ions, hydrazide ions, guanidine ions, triaminoguanidine ions, aminoguanidine ions, 1,2-diamidinoethane ions, 5-aminotetrazole ions, and 1,3-bis(1H-tetrazole-5-yl)propane ions to form ionic salts. The aim is to clarify the internal relationship between molecular structure and performance from a theoretical perspective and attempt to select the energetic material with the optimal performance. The following conclusions are drawn: B7 has the highest heat of formation (1302.12 kJ/mol). B6 demonstrates optimal values in the three critical performance parameters of detonation velocity, pressure, and heat, indicating its excellent detonation performance and highlighting the potential of aminoguanidinium ionic salts.

Method

All calculations in this paper are based on density functional theory and were performed using the Gaussian16 software. Initially, the structures of B1 to B9 were optimized at the B3LYP-D3/6-311G** level. Subsequently, single-point energy calculations were conducted at the def2-TZVPP level to determine the formation enthalpy, detonation velocity, and detonation pressure of the compounds. The Multiwfn and VMD programs were used to plot the energy gap diagrams, isosurface maps, scatter plots, and surface electrostatic potential maps for B1 to B9.