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    Journal of Molecular Modeling

    Journal of Molecular Modeling

    JournalISSN 1610-2940eISSN 0948-5023中科院 化学 4区

    年发文量

    研究主题

    论文(7584)

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    1Structure and Photophysical Properties of Copper(i) Photosensitizers: a Computational Study of Substituent Effects
    Bruno Campana Severino,Vania Martins Ramos,Ana Paula de Lima Batista

    Developing efficient and sustainable photosensitizers is crucial for advancing solar energy conversion and light-driven chemical processes. Ruthenium(II) and iridium(III) complexes have traditionally dominated this field due to their favorable photophysical properties, but their high cost has prompted the search for alternatives using earth-abundant metals. Copper(I) complexes are promising because they are cost-effective, have a tunable electronic structure, and feature a d^10 configuration that avoids low-lying metal-centered excited states. However, further improvements are needed to match the performance of Ru(II) and Ir(III) complexes, with ligand engineering playing a key role. Although there has been progress, the systematic effect of R substituents on the N ^∧ NR ligand in heteroleptic Cu(N ^∧ NR)(NacNac) complexes remains underexplored. We investigated a series of Cu(I) complexes of the type Cu(N ^∧ NR) (NacNacMe), where N ^∧ N is 2,2 ' -biquinoline and NacNac is β -diketiminate, using electronic structure calculations. The N ^∧ NR ligand was systematically substituted with R groups including -NH _2 , -OH, -CH _3 , -H, -Cl, -COOCH _3 , and -CF _3 to examine how these modifications affect the structure and photophysical properties of copper(I) photosensitizers. Ground- and excited-state properties were evaluated using density functional theory (DFT) and time-dependent DFT (TD-DFT), with excited-state character quantified using the TheoDORE program. We analyzed structural parameters, frontier orbital energies, and electronic transitions to correlate substituent electronic character with photophysical behavior. Local energy decomposition (LED) analyses based on DLPNO-CCSD(T) calculations were also performed to study metal-ligand interactions. The results indicate that strong electron-withdrawing groups such as -COOCH _3 and -CF _3 reduce the HOMO–LUMO gap and cause red shifts in charge-transfer absorption. These findings establish how substituent electronics modulate the frontier-orbital energies and charge-transfer absorption of this series of heteroleptic Cu(I) complexes, providing an electronic-structure framework for tuning their optical response.

    2026
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    2Reaction Mechanisms of Propionic Acid Pyrolysis, Hydrolysis, and H2 Production During the Thermal Decomposition in Various Alcohol Environments: a ReaxFF Molecular Dynamics
    Fatih Ahmet Celik,Yu Yang,Mücahit Yılmaz,Ezman Karabulut

    In this study, ReaxFF molecular dynamics (MD) simulations were employed to investigate the pyrolysis process and thermal decomposition of propionic acid (CH3CH2COOH) in various environments such as ethanol, methanol, propanol, and water. There were two reaction pathways in propionic acid pyrolysis through CH3CH2COOH → H + CH3CH2COO and CH3CH2COOH → OH + CH3CH2CO, leading to CO2 and CO products. Furthermore, propionate radicals are generated via the reaction C3H6O2 + C3H6O2 → H2O + C3H5O2 + C3H5O, when acid-acid molecular interactions occur. The primary cross-reaction channels between propionic acid and alcohols are C3H6O2 + CH4O → CH3 + H2O + C3H5O2, C3H6O2 + C3H8O → H2O + C3H7 + C3H5O2, C2H6O + C3H6O2 → H2O + C2H5 + C3H5O2 resulting in ethyl, methyl, and propyl propionates as well as water production. During thermal decomposition of propionic acid in various alcohol environments, the productions of CO and H2 increase, while the production of CO2 decreases. Conversely, the lowest H2 production is seen in water environment. Arrhenius equation was used for calculation of activation energies (Ea) for all systems. The activation energies of propionic acid were calculated as 163(8) kJ mol−1, 165(3) kJ mol−1, 172.58(12) kJ mol−1, and 193.05(25) kJ mol−1 in ethanol, methanol, propanol, and water solutions, respectively. Molecular dynamics (MD) simulations were performed using the Amsterdam Modeling Suite (AMS) software version 2026.103. The ReaxFF all-atom force field was used, and the parameters for carbon, hydrogen, and oxygen were taken from the CHO force-field parameter set. The numerous reactive events, reaction mechanisms, intermediate species, and product distributions were extracted from the MD trajectories by using ChemTraYzer2 developed by AMS tools. The simulations were equilibrated under NVT conditions, and the activation energies of the decomposition processes were determined using the Arrhenius equation based on the simulation data, enabling a quantitative comparison of the kinetic behavior in ethanol, methanol, propanol, and water.

    2026
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    3Electronic, Optical and Thermodynamic Properties of ZnO Monolayer under Hydrostatic Pressures: a First-Principles Study
    Sravanthi Jalasutram, Ball Mukund Mani Tripathi

    First-principles density functional theory (DFT) calculations were performed to investigate the electronic, optical, and thermodynamic properties of a ZnO monolayer under hydrostatic pressures ranging from 0 to 40 GPa. The values of bond lengths, energy band gap, and dielectric constant were deduced for the first time using the theoretical plasmon calculations, show good agreement with the computed and reported values. The structural stability of the ZnO monolayer was verified using binding energy and phonon dispersion calculations under both ambient and external pressures. The computed results reveal that the band gap decreases continuously from 1.647 eV at ambient pressure to 0 eV at 40 GPa, indicating a pressure-driven semiconductor to metal transition. The mechanical stability has been verified using elastic stiffness constants and the elastic properties were derived for 2D ZnO monolayer, are in good agreement with reported works. The calculated optical properties show the absorption edge undergoes red-shifts with pressure, primarily due to band gap narrowing, while the real part and refractive index increase as a result of enhanced electronic polarizability and lattice compression. A comparative analysis with graphene further demonstrates the high temperature dependence of thermodynamic properties of ZnO. These findings provide valuable insights into the tunable electronic, optical, and thermodynamic properties of ZnO monolayers, demonstrating their potential for deep ocean and aerospace applications. The first-principles DFT calculations were performed using Cambridge Sequential Total Energy Package (CASTEP) code. These calculations were carried out within the generalized gradient approximation (GGA) parameterized by Perdew et al. scheme, along with the ultra-soft pseudo-potential reciprocal space representation. The structure was optimized using the Broyden, Fletcher, Goldfarb, and Shannon (BFGS) scheme. The integration over the Brillouin zone was performed using a plane wave basis set with a cut-off energy of 330.00 eV.

    2026
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    4DFT and Multivariate Statistical Analysis for the Rational Design of DTP-based Hole Transport Materials
    Sania Ismaeel, Sidra Manzoor,Faheem Abbas

    Conventional hole-transport materials (HTMs) in perovskite solar cells (PSCs) often suffer from limited charge transport, suboptimal energy alignment, and recombination losses. This paper presents a computational molecular-design and screening approach for DTP-based HTMs using density functional theory (DFT) and multivariate descriptor analysis. Five new derivatives of DTP (DH1–DH5) were designed through targeted control of terminal triphenylamine (TPA) units to rationally tune charge-transfer behavior, electronic structure, and interfacial properties. Among all candidates, DH1 shows favorable calculated charge-transport characteristics within the studied series, exhibiting a distinct combination of low hole reorganization energy (λh = 0.0115 eV), the highest hole-hopping rate (2.13 × 1015 s−1), enabling good charge transport. DH1 also exhibits a stabilized LUMO energy (− 3.04 eV) and a smaller band gap (1.66 eV), facilitating effective intramolecular charge transfer (ICT) and enhanced optical absorption at 599 nm. It also exhibits the highest calculated dipole moment (21.68 D), indicating pronounced molecular polarity and electronic asymmetry; however, the implications of this polarity for solid-state interfaces and film formation require further investigation. Notably, structure–property relationships within the molecular series were revealed using data-driven methods, including principal component analysis, correlation mapping, and clustering. The analysis identifies LUMO energy, dipole moment, and band gap as useful descriptors of charge-transfer efficiency and optoelectronic performance and places DH1 in a distinct region of the calculated descriptor space within this studied series. This multivariate analysis provides a descriptive view of the relationships among the calculated molecular descriptors. Combining quantum-chemical calculations with multivariate statistical analysis can provide complementary molecular-level insights for the screening and design of HTMs. The results provide molecular-level insights into DH1–DH5 and offer a useful approach for guiding the future design and investigation of HTMs for PSC applications. Density functional theory (DFT) calculations were used to investigate the structural, electronic, optical, charge-transfer, and interfacial properties of the designed DTP derivatives (DH1–DH5). Data-assisted descriptor analysis was subsequently performed using multivariate statistical techniques, including principal component analysis, correlation mapping, and clustering, to identify structure–property relationships and the descriptors most strongly associated with charge-transfer efficiency and optoelectronic performance. Machine learning-assisted donor engineering reveals significant enhancement in the optoelectronic properties of DTP-based HTMs. The optimized systems exhibit reduced band gaps, red-shifted absorption, and ultralow reorganization energies, enabling fast charge transport. Descriptor analysis identifies LUMO stabilization and dipole moment as key factors governing performance, establishing a data-driven pathway for designing efficient hole-transport materials for perovskite solar cells.

    2026
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    5Atomistic Investigation of Fatigue Behavior in Single-Crystal and Polycrystalline Aluminum Via Molecular Dynamics
    Xingsheng Peng,Shanming Fan,Mingjun Peng, Jun Li, Huarong Qi, Jianjun Yao

    This study investigates the temperature-dependent fatigue behavior of single-crystal and polycrystalline aluminum, which is important for understanding microstructural stability and damage evolution under cyclic loading. Molecular dynamics simulations were performed to examine the microstructural evolution and fatigue behavior of both materials under identical strain amplitudes at different temperatures. The results indicate that in single-crystal Al, localized irreversible cyclic plastic deformation progressively accumulates at regions where slip planes intersect, potentially serving as a precursor to fatigue damage, whereas in polycrystalline Al, plastic deformation is accompanied by grain boundary rearrangement and local structural reorganization, with localized irreversible plastic deformation primarily accumulating near grain boundaries. Elevated temperature increases the atomic kinetic energy, accelerates the rearrangement and equilibration of dislocation structures, and promotes faster attainment of a dynamic balance between hardening and softening mechanisms. By analyzing local defect characteristics, dislocation density, and grain size, this study establishes a correlation between fatigue response and underlying microscopic mechanisms and provides insights into the evolution of localized irreversible cyclic plastic deformation in both single-crystal and polycrystalline aluminum. Classical molecular dynamics simulations were performed using LAMMPS to investigate the microstructural evolution and fatigue mechanical behavior of single-crystal and polycrystalline aluminum under identical strain amplitudes across varying temperatures. The interatomic interactions of aluminum were described by an embedded-atom method (EAM) potential. The open-source visualization tool OVITO was employed to render the evolution of the corresponding microstructures and to analyze the associated mechanical responses. Furthermore, equivalent stress and strain were calculated based on the von Mises yield criterion to characterize the deformation mechanisms throughout the loading process.

    2026
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    高被引作者

    作者引用发文
    Jane S. Murray1481450
    Peter Politzer1471342
    Tim Clark865657
    David Van Der Spoel86313
    Berk Hess86081
    Erik Lindahl86081
    James J. P. Stewart81639
    Matthias Hennemann496612
    Pat Lane478310
    Monica Concha399613

    高产作者

    作者引用发文
    Tim Clark865657
    Jane S. Murray1481450
    Fu-De Ren55445
    Qijun Liu11943
    Peter Politzer1471342
    Peng ma15537
    Jerzy Leszczynski35434
    Zhengtang Liu9834
    Weihua Zhu57331
    Ricardo Gargano52330

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