Journal of Molecular Modeling最新文献

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.

Context

Fentanyl’s sub-nanomolar affinity and ultra-slow dissociation from the μ-opioid receptor (μOR) limit the efficacy of pharmacological antagonists like naloxone in acute overdose. We propose a non-pharmacological strategy in which structured terahertz (THz) vortex fields imprint a geometric (Berry) phase on the ligand-receptor complex to selectively bias unbinding pathways without bulk heating. This approach targets the quantum-coherent control of the dissociation coordinate through topological phase engineering.

Method

We formulated the quantum dynamics on a curved 2D reaction manifold ((r,theta )) encoding proton transfer distance and ligand torsion. The system was driven by a near-field THz vortex (topological charge ℓ ≠ 0) and evolved via the covariant time-dependent Schrödinger equation, solved with a Crank-Nicolson propagator and absorbing boundaries. Berry phases were computed on adiabatic ((theta ,Phi )) cycles, and dissociation rate enhancement was quantified through probability flux analysis incorporating solvent recapture effects. The model parameters were derived from cryo-EM and QM/MM data to ensure biochemical realism. Simulations indicate an effective torsional barrier reduction of 0.06 eV ((approx 2.3 {k}_{B}T) at 300 K) within the 1–1.5 THz band, sufficient to accelerate μOR–fentanyl escape by∼10x   at fixed temperature. A value consistent with non-thermal, frequency-addressable biasing of dissociation pathways. These findings provide a quantum-coherent, non-pharmacological strategy for disengaging potent opioid ligands, offering a new pathway for photonic control of Biochemical interactions with sub-molecular precision.

Context

Selective separation of trivalent actinides from chemically similar lanthanides remains a central challenge in advanced nuclear fuel reprocessing. To identify structural and electronic factors that govern Am(III)/Eu(III) selectivity, we investigated six 1,10-phenanthroline-based N-donor ligands bearing symmetric or asymmetric side rings. Calculations indicate metal–ligand interactions are predominantly ionic with measurable covalent contributions; Am(III) complexes exhibit shorter bonds, higher Wiberg bond indices, and larger charge transfer than Eu(III) analogues. Projected density of states and charge-decomposition analyses show stronger 5f participation in Am(III) bonding, rationalizing preferential Am binding. Electrostatic potential and thermodynamic results further indicate that symmetric pyrrole side rings yield lower surface potentials and stronger binding, and computed free-energy differences confirm complexation with Am(III) is thermodynamically more favorable. These results delineate how electrostatics and f-orbital covalency jointly determine Am/Eu discrimination and provide practical guidance for designing more effective N-donor extractants.

Methods

Density functional theory (PBE0) was used with relativistic effective core potentials (Am: ECP60MWB-SEG; Eu: ECP28MWB-SEG). Solvent effects (n-dodecane, cyclohexanone, 1-octanol) were modeled with CPCM. Bonding analyses included Wiberg bond indices, QTAIM, NBO/CDA, EDA, and PDOS. Gibbs free energies were derived from 298.15 K thermal corrections, and all optimized structures were verified as minima by frequency analysis; spin–orbit coupling was not included.

Graphical Abstract

Context

In this work, we explore a novel analogy between the classical capacitor from electrostatics and the linear response function within the framework of conceptual density functional theory (CDFT). Parallels are drawn between the electrostatic behavior of capacitors and the chemical reactivity described by the linear response function, a key descriptor in CDFT. This analogy is illustrated on molecular systems ranging from diatomics to four-atom molecules, and generalized to larger systems. We further show how this relationship extends to other chemical descriptors, offering new physical interpretations. The results demonstrate that this capacitor analogy provides fresh insights into chemical reactivity and enriches the conceptual framework of theoretical chemistry.

Methods

All calculations were performed using the ADF package. Molecules were optimized in the gas phase at the PBE0/TZP level, including scalar relativistic effects, with convergence verified by positive vibrational frequencies. Conceptual DFT descriptors, including the condensed linear response function, were obtained using the standard implementation in ADF. An in-house Python program was developed to extract and visualize condensed linear response data, perform diagonalizations, and generate graphical representations of eigenmodes.

Context

This study aims and objectives of the present research are to provide fundamental insights into their electronic properties and adsorption behavior, and predict the corrosion inhibition performance of seven nucleobase-derived organic compounds—adenine (S1), cytosine (S2), glutamine (S3), guanine (S4), purine (S5), pyrimidine (S6), and thymine (S7)—on Cu, Fe, Al, and Sn metal surfaces. Results revealed that cytosine (S2) and guanine (S4) exhibit the highest inhibition efficiency on Cu surfaces, driven by their small HOMO–LUMO energy gap (~ 5.00, ~ 5.10 eV), high softness (0.203, 0.198 eV⁻¹), and molecule-to-metal electron charge transfer (0.193, 0.237), indicating strong adsorption and electron exchange capabilities from the HOMO_donor ⟶ LUMO_acceptor. The importance of the results highlights the potential of these compounds for developing sustainable corrosion inhibitors and advanced Cu-based anticorrosive coatings and biosensors.

Methods

Using density functional theory (DFT) at the B3LYP/6–311 + + G(d,p) level of theory with applying Gaussian 09, Revision D.01, to optimize the structures combined with Monte Carlo simulations applied to point out interactions surface, and evaluated adsorption energies on Fe (110), Sn (111), Cu (111), and Al (111) surfaces of S1–S7 title compounds. Topological analyses, including electron localization function (ELF), localized orbital locator (LOL), and density of states (DOS), were performed using Multiwfn software to understand electron distribution and bonding characteristics. The comprehension and knowledge gathered from these techniques can help create a prediction of nucleobase-derived capacity to suppress corrosion inhibitors that are both sustainable and effective.

Graphical Abstract

Context

Lipid oxidation degrades food quality by producing harmful aldehydes, ketones, and acids. This study integrates density functional theory (DFT) and kinetic analysis to elucidate the thermal oxidation mechanism of oleic acid using a 4-octene model. Mechanistic insights reveal distinct early- and mid-stage processes: the initial phase is dominated by low-barrier allyl-oxygen bonding (< 10.0 kcal/mol), while allyl isomerization (> 60.0 kcal/mol) is negligible. Deep oxidation involves four pathways: 1) O–O• radical attack on adjacent carbons (29.2/11.3 kcal/mol), forming aldehydes; 2) peroxy radical isomerization (rate-limiting carbon jump > 30.0 kcal/mol); 3) epoxide formation via O–O• attack on double bonds (6.8 kcal/mol); 4) hydroperoxide conversion hindered by high barriers (57.3–58.7 kcal/mol). Alkoxy radicals induce C–C bond cleavage, forming minor cyclic epoxides. Kinetic analysis (60 and 150 °C) identifies tricyclic epoxide as the dominant product, stabilized at elevated temperatures.

Methods

This article uses density functional theory (DFT) and Gaussian 16 program to complete structural optimization, frequency analysis, and single point energy calculation. B3LYP-D3/6-31G (d, p) method is used for optimization and frequency calculation, and single point energy correction is performed using the def2TZVPP basis set. The transition state has been verified by IRC, and the free energy has been corrected by Shermo program zero-point energy. The reaction rate constant is based on the transition state theory (TST) and takes into account the tunneling effect, and is calculated using the TST calculator program. Finally, the differential equation system is solved using MATLAB to obtain the time concentration curve of the oxidation product.

Context

This study investigates the thermal degradation behavior of cis-1,4-polyisoprene and its nanocomposites using a combined approach of reactive molecular dynamics simulations and experimental techniques. Pyrolysis was experimentally conducted up to 500 °C using a custom-built lab-scale-tubular reactor (20 mm diameter, 300 mm length). Samples were prepared by melt mixing, followed by compression molding into 1 mm thick sheets. Simulations were performed up to 2500 K using the ReaxFF reactive force field, selected for its ability to dynamically model bond breaking and formation in reactive systems. We constructed a simulation system containing ten polymer chains and up to two nano-silica units (576 atoms each) within a 150 Å periodic box, using the NVT ensemble with a Nosé–Hoover thermostat and a time step of 0.25 fs over a total duration of 42 ps. Experimental analyses via TGA, FTIR, and GC–MS confirmed the formation of key pyrolysis products such as isoprene (C₅H₈), ethylene (C₂H₄), and methane (CH₄). The addition of 60 wt% nano-silica extended the degradation time by approximately 100% and increased the activation energy from 121.9 to 133.8 kJ/mol—a 9.77% rise—suggesting a stabilizing role in the thermal degradation process. Mechanistic insights revealed that degradation proceeds via radical-driven scission near double bonds, with nano-silica modulating both the rate and pathway of decomposition. Overall, the results demonstrate a concentration-dependent dual role of nano-silica in thermal degradation and provide a predictive framework for designing heat-resistant rubber nanocomposites and advancing sustainable pyrolysis-based recycling technologies.

Methods

Cis-1,4-polyisoprene, a naturally derived elastomer with high flexibility and unsaturation, was used as the base polymer (Mw ≈ 38,000 g/mol, Sigma-Aldrich). Nanocomposites containing 30 wt% and 60 wt% nano-silica were prepared via magnetic stirring and compression molding. Pyrolysis experiments were conducted in a lab-scale tubular reactor under nitrogen flow, and thermal behavior was analyzed using thermogravimetric analysis (STA 504, Bahr, Germany). Volatile products and functional groups were identified via FTIR and GC–MS. Reactive molecular dynamics simulations were performed using LAMMPS with a ReaxFF force field parameterized for C/H/O/Si systems. Simulations employed the NVT ensemble with a Nosé–Hoover thermostat to model bond dissociation and reaction pathways at elevated temperatures (1500–2500 K), enabling direct comparison with experimental results.

Context

Spin-crossover (SCO) phenomena in Fe(II) complexes, especially those with octahedral coordination, are of growing interest for their potential in molecular electronics, sensors, and memory devices. These materials exhibit reversible switching between high-spin and low-spin states in response to external stimuli such as temperature or pressure. In this study, we investigate three Fe(II) complexes [Fe(4bt)(_3)](ClO(_4))(_2), [Fe(2bt)(_3)](ClO(_4))(_2).MeOH, and[Fe(3tpH)(_3)](ClO(_4))(_2) to understand their spin-state behavior in relation to both intramolecular and intermolecular interactions. Our computational results indicate that [Fe(2bt)(_3)](ClO(_4))(_2).MeOH and [Fe(3tpH)(_3)](ClO(_4))(_2) undergo spin-crossover transitions with temperature, whereas [Fe(4bt)(_3)](ClO(_4))(_2) stabilizes in the low spin state. Intermolecular interactions such as (pi )-(pi ) stacking and O–H contacts significantly modulate the electronic structure and spin-state energetics. By comparing isolated molecular complexes with their crystalline counterparts, we highlight the critical influence of crystal packing on the SCO mechanism. These insights contribute to the rational design of Fe(II)-based materials with tunable magnetic properties.

Methods

Spin-polarized density functional theory (DFT) calculations were carried out using the Vienna Ab initio Simulation Package (VASP). The Perdew–Burke–Ernzerhof (PBE) functional within the generalized gradient approximation (GGA) was employed, along with Grimme’s D2 dispersion correction to account for van der Waals interactions. The projector augmented wave (PAW) method was used to describe core–valence interactions. Strong correlation effects in Fe 3d orbitals were treated using the PBE+U method.