Journal of Molecular Modeling最新文献

{"title":"Study on the electronic structure and molecular response mechanism of triazole derivatives under electric field regulation.","authors":"Mengjie Bo, Zikai Gao, Zhihui Gu, Peng Ma","doi":"10.1007/s00894-025-06452-2","DOIUrl":"10.1007/s00894-025-06452-2","url":null,"abstract":"<p><strong>Context: </strong>This article selects three excellent energetic materials: [4,4'-Bi-4H-1,2,4-triazole]-3,3'-diamine (1); 5H-1,2,4-triazolo [4,3-b] [1,2,4] triazole-3,6-diamine (2); and 4,4'-(1E)-1,2-diazenediylbis [4H-1,2,4-triazol-3-amine] (3). Use density functional theory to study molecular structure, surface electrostatic potential, molecular frontier orbitals, and density of states. The X-axis EEF is enhanced by 1 and 3, but weakened by 2; the Y-axis EEF has an enhancing effect on 2, but weakens 1 and 3. Under the X/Z-axis EEF, the polar surface area expands and the Y-axis slightly decreases; 2 forms a uniform negative potential region in the first half of the Z-axis strong electric field; the polar surface area of X-axis increases, while the Y/Z-axis significantly decreases. The EEF reconstructs the HOMO/LUMO spatial distribution and reduces the energy gap, significantly enhancing reaction activity. In summary, the EEF can precisely regulate the bond stability, surface charge distribution, and electronic excitation characteristics of energetic materials through the synergistic effect of direction and intensity, providing a theoretical basis for the safe storage, transportation, and active design of energetic materials.</p><p><strong>Methods: </strong>Using density functional theory, the B3LYP/6-311 + G(d,p) method was employed for structural optimization. After optimizing convergence, ensure that there are no imaginary frequencies to obtain a stable structure. Wave function analysis was performed using Multiwfn 3.8 and VMD 1.9.3. The EEF strength ranged from 0 to 0.02 a.u., with a growth gradient of 0.005 a.u.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"229"},"PeriodicalIF":2.5,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144768252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical study of the reactivity of oligo-pyrrole derivatives linked at their ends to the Magnesol, Ferrol, and Zinkol fragments: NBO, DFT, and TD-DFT calculations.","authors":"Mohammed Zenati, Madani Hedidi, Abdelkader M Elhorri, Hicham Mahdjoub-Araibi, Assia Laib","doi":"10.1007/s00894-025-06443-3","DOIUrl":"10.1007/s00894-025-06443-3","url":null,"abstract":"<p><strong>Context: </strong>This study compares the electronic and structural properties of oligopyrroles (OPn) grafted with metal rings (Magnesol OPnMg, Ferrol OPnFe, and Zinkol OPnZn) with those of standard oligopyrroles (OPn). In the context of the polymerization of oligomers from n = 1 to n = 15, the parameters of global reactivity and excited states obey exponential equations (ƒ(x) = A + B Exp^-R(x)), allowing values to be predicted to infinity. The corresponding infinity results reveal that energy gaps (ΔE_H-L) vary between 3.14 and 5.20 eV, while chemical hardnesses (η) oscillate between 1.507 and 2.60 eV, with overall electrophilicity (ω) and nucleophilicity (Nu) of 0.74-1.40 eV and 5.47-5.53 eV, respectively. The new oligopyrrole derivatives show increases in intramolecular charge transfer (ICT) and UV-Vis absorptions in the violet (λ_max between 407 and 431 nm). NBO analysis shows a reduction in hydrogen charges in the -NH groups of oligopyrroles based on metal derivatives, enhancing their nucleophilicity. In addition, these molecules display better solubility, with favorable solvation energies (ΔG_solv) (24-35 kcal-mol^-1) compared to OPn. Finally, metal-based derivatives show stronger interactions with formaldehyde (HCHO) in aqueous media than OPn, demonstrating interaction energy differences (E_int) ranging from 0.7 to 1.40 kcal-mol^-1.</p><p><strong>Methods: </strong>All calculations were performed using the Gaussian 16 program. The selected functionals are: B3LYP, CAM-BLYP, B3LYP-D3, CAM-BLYP-D3, and TD-CAM-BLYP. The basis-sets used are: 6-31 +  + G(d,p) and LanL2DZ. Finally, the natural bond orbital (NBO) method was used in this study.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"226"},"PeriodicalIF":2.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design and performance evaluation of nitrogen-rich bis-six-membered fused ring energetic materials via density functional theory.","authors":"Qian Zhang, You-Xiang Guo, Tao Long, Lan-Ying Xu, Yan Huang","doi":"10.1007/s00894-025-06453-1","DOIUrl":"10.1007/s00894-025-06453-1","url":null,"abstract":"<p><strong>Context: </strong>Density functional theory (DFT) calculations at the M06-2X/def2-TZVP level were employed to design bis-six-membered nitrogen-rich fused ring energetic materials. Six neutral derivatives (I-2-4, I-3-4, I-3-5, II-2-4, II-3-4, and II-3-5) achieved energy densities exceeding 2.0 g/cm³, with energetic salts reaching unprecedented values up to 3.3 g/cm³. Non-covalent interaction isosurfaces quantified van der Waals forces in crystal packing, while decomposition pathway simulations for II-3-2 identified a low O-NO₂ BDE (20.24 kcal/mol) coexisting with high thermal stability ( <math><msub><mi>T</mi> <mtext>bp</mtext></msub> </math> = 765.3 °C), governed by autocatalytic kinetics ( <math><mrow><mi>Δ</mi> <mi>G</mi></mrow> </math> = 24.7 kcal/mol and <math><mrow><mi>Δ</mi> <mi>G</mi></mrow> </math> = 8.44 kcal/mol). The DFT-derived performance matrix ( <math><mi>ρ</mi></math> > 2.02 g/cm³, <math><msub><mi>T</mi> <mtext>bp</mtext></msub> </math> > 600 °C, HOFs > 3500 kJ/mol) provides a transferable protocol for balancing energy and safety in molecular modeling of advanced energetics.</p><p><strong>Method: </strong>The DFT-based geometric optimization and frequency analyses of the designed molecules were determined using M06-2x/def2-TZVP method at Gaussian 09 package suite of programs. The heats of formation (HOF) for all molecules were obtained using an atomization reaction. The kinetic energy ( <math><mrow><mi>Δ</mi> <msub><mi>E</mi> <mrow><mtext>HOMO</mtext> <mo>-</mo> <mtext>LUMO</mtext></mrow> </msub> </mrow> </math> ), electrostatic potential (ESP), and other related calculations were computed using Multiwfn_3.8_dev software. The visualization of the weak interaction between dimers was accomplished using VMD 1.9.3 program.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"225"},"PeriodicalIF":2.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanistic insights into the evolution of microscopic molecular structures of bituminous coal and lignite during carbonization: a ReaxFF molecular dynamics study.","authors":"Kejiang Li, Xiangyu He, Jianliang Zhang, Chunhe Jiang, Shan Ren, Zhen Sun, Qingsong Zou","doi":"10.1007/s00894-025-06438-0","DOIUrl":"10.1007/s00894-025-06438-0","url":null,"abstract":"<p><strong>Context: </strong>The development of the carbon network in coal during carbonization significantly affects the quality of the resulting coke. A detailed understanding of the atomic-scale mechanisms governing coal carbonization is crucial for optimizing the coking process. This research employed ReaxFF molecular dynamics simulations to examine the carbonization processes of two coal types: bituminous coal and lignite. During carbonization, large molecular clusters produced by pyrolysis undergo cross-linking through carbon-carbon bonds, forming a carbon network that expands outward. The carbonization effects of the two coal molecular models were compared, showing that the carbonization process of bituminous coal was more stable, yielding better results. Additionally, based on the observed expansion of the carbon network within coal molecules during the simulation, the growth mechanism of the carbon network was outlined. This research provides theoretical insights into the atomic-scale carbonization mechanisms of coal molecules and their application in the coking process, offering valuable references for advancing coking production technology.</p><p><strong>Methods: </strong>Molecular dynamics simulations are conducted using the LAMMPS (Large-Scale Atomic/Molecular Massively Parallel Simulator), employing a reactive force field (ReaxFF). The modeling process incorporates a cyclic annealing method for structural relaxation of the molecules. The simulation is carried out in stages, with a temperature increment of 100 K per step. OVITO post-processing software is utilized to remove gas molecules from the system. During the post-processing phase, OVITO is used to visualize and analyze the carbonization process, investigating the evolution of coal molecular products and assessing the effectiveness of the carbonization.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"227"},"PeriodicalIF":2.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Opto-electronic properties of Sn-C Co-doped β-Ga₂O₃ at different concentrations: a GGA + U study.","authors":"Lin Chen, Haixia Li, Shangju Chen","doi":"10.1007/s00894-025-06459-9","DOIUrl":"10.1007/s00894-025-06459-9","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Content: &lt;/strong&gt;This study investigates the electronic structure and optical properties of Sn-C co-doped β-Ga&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt; at different concentrations using the generalized gradient approximation (GGA + U) method within density functional theory (DFT). The results show that, compared to intrinsic β-Ga&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt;, all doped systems induce lattice distortion. Among them, the Sn-C system exhibits higher stability in both oxygen-rich and gallium-rich environments. Additionally, doping significantly reduces the band gap, with the Sn-2C doped system having the smallest band gap (0.98 eV), while both the 5 at% system and Sn-3C system display weak metallic characteristics. The static dielectric constant of the co-doped system increases with concentration, enhancing its polarization ability. The absorption spectrum shows clear redshift, with significantly improved absorption in the 150-400 nm wavelength range and a trend toward extension into the visible light region. These results suggest that Sn-C co-doping is an effective strategy for optimizing the optoelectronic properties of β-Ga&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt;, potentially enhancing its application in optoelectronic devices.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;In the first-principles calculations, density functional theory (DFT) was employed, using the Perdew-Burke-Ernzerhof (PBE) functional within the generalized gradient approximation (GGA). The calculations were performed using the Cambridge Sequential Total Energy Package (CASTEP) program, where the interaction between valence electrons and ionic cores was treated with on-the-fly generated (OTFG) ultrasoft pseudopotentials. A plane-wave basis set was constructed with a cutoff energy of 450 eV. The Brillouin zone was sampled using a 1 × 4 × 2 k-point mesh generated by the Monkhorst-Pack method, and structural optimization was carried out using the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm. During optimization, the following energy convergence criteria were set: a total energy convergence threshold of 10&lt;sup&gt;-5&lt;/sup&gt; eV/atom, a maximum internal stress of 0.05 GPa, an interatomic force less than 0.03 eV/nm, and a maximum atomic displacement limited to 10&lt;sup&gt;-3&lt;/sup&gt; Å. The valence electron configurations used in the calculations were Ga (3d&lt;sup&gt;10&lt;/sup&gt; 4s&lt;sup&gt;2&lt;/sup&gt; 4p&lt;sup&gt;1&lt;/sup&gt;), O (2s&lt;sup&gt;2&lt;/sup&gt; 2p&lt;sup&gt;4&lt;/sup&gt;), Sn (5s&lt;sup&gt;2&lt;/sup&gt; 5p&lt;sup&gt;2&lt;/sup&gt;), and C (2s&lt;sup&gt;2&lt;/sup&gt; 2p&lt;sup&gt;2&lt;/sup&gt;). It should be noted that the standard GGA method neglects the strong correlation effects of Ga 3d electrons, which leads to an underestimated band gap compared to experimental values, thereby affecting the accurate assessment of material properties. To address this issue, the GGA + U approach was adopted in this work, introducing Hubbard U corrections to more accurately describe the electronic structure of β-Ga&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt;. Specifically, a U value of 6.5 eV was applied to the O 2p electrons, and a U value of 10","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"224"},"PeriodicalIF":2.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical Study on the HCNO + C₆H₅ Reaction: Mechanism and Kinetics.","authors":"Trong Nghia Nguyen, Hue Minh Thi Nguyen","doi":"10.1007/s00894-025-06456-y","DOIUrl":"10.1007/s00894-025-06456-y","url":null,"abstract":"<p><strong>Context: </strong>The reaction between HCNO and C₆H₅ is of relevance in environments such as combustion and atmospheric chemistry, where both species are known to coexist. In this study, we report the reaction mechanism and kinetics of their gas-phase reaction. The reaction proceeds via the addition of C₆H₅ to the carbon atom of HCNO, forming a pre-reaction complex (COMP) and a low-lying transition state (T0/1) that leads to a key intermediate (IS1). IS1 decomposes into C₆H₅CH + NO (PR2), C₆H₅CNO + H (PR3), and HCN + C₆H₅O (PR4). Minor pathways include hydrogen abstraction forming C₆H₆ + CNO (PR1) and oxygen-site addition yielding IS2, which also leads to HCN + C₆H₅O (PR5). Kinetic results indicate that IS1 dominates below 1500 K at 760 Torr. At higher temperatures, PR2 (39.5-54.3%) and PR3 (6.5-35.0%) become the main channels, with a notable contribution from PR1 (6.5-19.4%) and minor yields from PR4 (< 3.0%) and PR5 (< 2.5%) over the entire temperature range at this pressure.</p><p><strong>Methods: </strong>All structures were calculated at the ROCBS-QB3, ROCCSD(T)//B3LYP, and UCCSD(T)//B3LYP levels of theory. Rate constants were evaluated using TST and RRKM/master equation methods with Eckart tunneling corrections over the 300-2500 K and 100-7600 Torr ranges.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"228"},"PeriodicalIF":2.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ultrafast terahertz-induced torque disruption of fentanyl's μ-opioid receptor binding for precision overdose reversal.","authors":"Moses G Udoisoh, Olusola Olaitan Adegoke, Amy Lebua James","doi":"10.1007/s00894-025-06447-z","DOIUrl":"10.1007/s00894-025-06447-z","url":null,"abstract":"<p><strong>Context: </strong>This study establishes a quantum-biophysical framework for non-invasive opioid overdose reversal by demonstrating ultrafast terahertz (THz) torque-mediated disruption of fentanyl-μ-opioid receptor (μOR) binding. By targeting the vibrational modes of the fentanyl-μOR complex with resonant THz pulses (1-1.5 THz, ≥ 100 kV/cm), the study examines two key binding configurations: the Asp147 salt bridge (D147) and His297 hydrogen bond (H297). The model reveals that THz-induced torque reduces the dissociation barrier by 3.2-3.8 kcal/mol through mechanical disruption of the N-H⁺···O⁻ interaction, achieving 50% unbinding within 1.2 ps at optimal frequencies. The H297 configuration dissociates 40% faster than D147, indicating a pharmacologically preferable site for intervention. A sigmoidal dose-response is observed in the 100-150 kV/cm range, enabling > 90% dissociation efficacy under non-thermal conditions. These findings offer a novel electromagnetic approach for modulating opioid pharmacodynamics and inform the development of receptor-targeted antidotes via precision bioelectromagnetic strategies. While this study demonstrates the theoretical feasibility of THz-induced dissociation, future experimental work is needed to address translational challenges such as tissue penetration and biological specificity.</p><p><strong>Methods: </strong>The study employs a quantum-classical hybrid framework combining time-dependent Schrödinger equation simulations with classical electrodynamics. Fentanyl is modeled as a confined asymmetric rotor interacting with a µOR-like potential landscape under circularly polarized THz radiation. Quantum torque is derived from angular momentum operators coupled to the electric field vector. Site-specific binding configurations (D147 and H297) are simulated with field-driven vibrational excitation and potential energy surface deformation. Dissociation dynamics and barrier modulation are quantified using Fermi's Golden Rule and time-evolved wavepacket propagation. Numerical computations were performed in Wolfram Mathematica 13.1, with molecular input parameters validated against DFT-based dipole moments, mass tensors, and force-field data extracted from experimental literature.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"221"},"PeriodicalIF":2.5,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144726382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeting SARS-CoV-2 main protease: a pharmacophore and molecular modeling approach.","authors":"Nitchakan Darai, Piyatida Pojtanadithee, Kamonpan Sanachai, Thierry Langer, Peter Wolschann, Thanyada Rungrotmongkol","doi":"10.1007/s00894-025-06441-5","DOIUrl":"10.1007/s00894-025-06441-5","url":null,"abstract":"<p><strong>Context: </strong>The COVID-19 pandemic, driven by SARS-CoV-2, has had a profound impact on global health, with severe respiratory complications being a primary concern. The main protease (Mpro) of SARS-CoV-2 plays a critical role in viral replication, making it an attractive target for therapeutic intervention. This study aimed to identify potential Mpro inhibitors using an integrated computational approach. From an initial pool of 89,200 compounds in the ChemDiv database, a systematic screening process reduced the candidates to 735 through drug-like property predictions and pharmacophore-based virtual screening. Molecular docking against four co-crystal structures of the inhibitor/Mpro complex, followed by molecular dynamics (MD) simulations and binding free energy calculations, identified E912-0363 and G740-1003 as promising candidates with binding affinities comparable to nirmatrelvir. Extended 500-ns MD simulations further established E912-0363 as a highly promising Mpro inhibitor, supporting its potential for therapeutic development as a complementary or alternative treatment to nirmatrelvir.</p><p><strong>Methods: </strong>Pharmacophore modeling and virtual screening were conducted using the ChemDiv database, reducing 89,200 compounds to 735 candidates based on drug-like property predictions. Molecular docking was performed against four SARS-CoV-2 Mpro co-crystal structures using AutoDock VinaXB and GOLD docking programs. The top five candidates (E912-0363, P635-0261, G740-1003, G069-0804, and 8602-0428) were subjected to 100-ns molecular dynamics (MD) simulations using the AMBER force field. Binding free energy calculations were performed using the MM/GBSA method. Extended 500-ns MD simulations were carried out for the most promising candidate, E912-0363, to evaluate its long-term stability and interaction with the Mpro binding site.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"222"},"PeriodicalIF":2.5,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144726381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein chains in tight-binding framework.","authors":"Hamze Mousavi, Ronak Emami","doi":"10.1007/s00894-025-06450-4","DOIUrl":"10.1007/s00894-025-06450-4","url":null,"abstract":"<p><strong>Context: </strong>This research assesses the band structure and density of states for three unique conformations of protein chains, examined in both finite and infinite configurations. Under a constant temperature, the band structure and density of states reveal flat energy dispersion curves and discrete energy levels for the finite protein conformations, which are ascribed to the presence of localized states within these structures. Conversely, the infinite protein chain demonstrates a continuous band structure due to its periodic nature, resulting in narrow-gap semiconducting behavior across all conformations. The influence of temperature on the energy spectra of the systems, regardless of the configuration type, leads to alterations in both the peak heights and positions for all three protein conformations.</p><p><strong>Methods: </strong>The exploration of the electronic properties of protein chains is performed using the tight-binding Hamiltonian method in conjunction with Green's function formalism. The primary emphasis is placed on protein chains consisting of thirty-six amino acids, characterized by a straightforward structural arrangement, where amino acids are interconnected through covalent bonds, while the other two conformations exhibit a more complex structural configuration, with amino acids linked by both peptide bonds and non-covalent interactions.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"223"},"PeriodicalIF":2.5,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144726380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical investigation of solvent-polarity-dependent excited-state intramolecular proton transfer behavior for incorporated bulky -CF₃ side semi-aliphatic polyimide.","authors":"Xiaoyu Zhang, Qingfang Zhang, Yujian Zhang, Qiuhe Ren, Hengyi Yuan","doi":"10.1007/s00894-025-06442-4","DOIUrl":"10.1007/s00894-025-06442-4","url":null,"abstract":"<p><strong>Context: </strong>In this work, the molecular properties of the novel semi-aliphatic polyimide derivative with incorporating bulky -CF₃ side groups (3H-6F) in gas, chloroform and acetonitrile have been studied by DFT and TDDFT methods. The optimal reaction path could be found to regulate the occurrence of excited-state intramolecular proton transfer (ESIPT) reaction. In S₁ state, the strength of O1-H2···O3 hydrogen bond increases significantly and contributes to the ESIPT reaction providing the driving force. We calculated the infrared (IR) vibrational spectrum to analyze the movement of O1-H2 bond expansion vibration and then studied the variations of hydrogen bonding strength. In addition, from the rearrangement of frontier molecular orbital (MOs), the electron density distribution should be also an extremely important positive factor in ESIPT process. According to potential energy curves (PECs), ESIPT reaction occurs after the molecule absorbs the photon to reach the first excited state, and the hydrogen atom of the O1-H2 bond combines with the adjacent O3 atom to form an isomer. After the completion of the ESIPT reaction process, the S₁ state returns to S₀ state with recovering the original structure. The barrier size and photoexcitation characteristics in different surroundings are also compared, based on which we present that the increase of solvent polarity promotes occurrence of ESIPT reaction process for 3H-6F fluorophore.</p><p><strong>Methods: </strong>All molecular structures have been optimized using DFT and TDDFT method with B3LYP/6-311 +  + G(d,p) level by Gaussian 16 software. Vertical excitation simulations were based on TDDFT method with analyzing charge redistributions. Using Multiwfn 3.8 software, the core-valence bifurcation indexes were performed. Further, potential energy surfaces have been constructed, based on which the transition state configurations were found at the same level.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"219"},"PeriodicalIF":2.5,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}