Journal of Molecular Modeling最新文献

{"title":"Revisiting chemical kinetics for H + CH4 → H2 + CH3 using variational transition state theory: comparison with global dynamics calculations","authors":"Edson F. V. de Carvalho,&nbsp;Marcelo A. P. Pontes,&nbsp;Luiz F. A. Ferrão,&nbsp;Francisco B. C. Machado,&nbsp;Orlando Roberto-Neto","doi":"10.1007/s00894-026-06930-1","DOIUrl":"10.1007/s00894-026-06930-1","url":null,"abstract":"<div><h3>Context</h3><p>For both the forward and reverse reaction, there are no accurate rate constants at the VTST/MT level using potential energy surfaces built with the density functional theory (DFT) approach. Calculations of rate constants in function of temperature are carried out for the elementary reaction H + CH₄ → H₂ + CH₃ using variational transition state theory with multidimensional tunneling corrections (VTST/MT) with density functional theory (DFT) and are compared with previous global dynamics calculations reported in the literature. Calculations show that the dual-level method based on an M06-2X PES is capable of providing an accurate framework to compute thermal rate constants in comparison with global dynamics methods.</p><h3>Methods</h3><p>The CCSD(T) method with the aug-cc-pVnZ (<i>n</i> = 3–5) basis set is employed to characterize the stationary states for the forward and reverse reactions and the M06-2X and ωB97X-D DFTs are used to generate potential energy surfaces (PESs) in the VTST/MT calculations. At the CVT/μOMT level and using the M06-2X PES, the rate constants at 300 and 600 K are 2.54 × 10⁻¹⁹ and 2.92 × 10⁻¹⁵ cm³ molecule⁻¹ s⁻¹, which are in excellent agreement with the multi-configurational time-dependent Hartree (MCTDH) calculations (1.9 × 10⁻¹⁹ and 2.9 × 10⁻¹⁵ cm³ molecule⁻¹ s⁻¹). For the reverse H₂ + CH₃ reaction, CVT/μOMT shows good agreement with results using CCSD(T) and analytical PESs. The kinetic isotope effect (KIE) (k^CH4+H/k^CH4+D) at 500, 600, and 700 K are 0.65, 0.71, and 0.77 in good agreement with experimental data, respectively equal to 0.8 ± 0.2, 0.9 ± 0.2, and 1.0 ± 0.2.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06930-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148918004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transition-metal functionalization of carbon nanotubes enables dual-mode transport and rapid aqueous release of 2-mercaptopyridine: A first-principles study","authors":"Bahjat S. Hameed,&nbsp;Faeq A. AL-Temimei,&nbsp;Zainab S. Hussain","doi":"10.1007/s00894-026-06937-8","DOIUrl":"10.1007/s00894-026-06937-8","url":null,"abstract":"<div><h3>Context</h3><p>Targeted delivery of the chemotherapeutic 2-mercaptopyridine (2-MP) requires robust carriers to mitigate rapid systemic degradation. Because pristine carbon nanotubes (CNTs) exhibit weak drug retention, this study investigates transition-metal-doped (Co, Sc, Ru, V) CNTs as dual-action nanocarriers and electrochemical sensors. While pristine CNTs display weak physisorption with adsorption energy <span>({E}_{ads}= -36.52)</span> kcal/mol, transition-metal doping induces robust coordinate covalent chemisorption. Ru-doped CNTs exhibit optimal thermodynamic stability with <span>({E}_{ads}= 43.56)</span> kcal/mol and extended gas-phase drug retention with recovery time <span>(tau =828)</span> s, preventing premature payload leakage. Conversely, in competitive aqueous media, these functionalized carriers facilitate rapid, diffusion-controlled release. Furthermore, 2-MP encapsulation triggers a highly sensitive 34.32% modulation in the HOMO–LUMO energy gap of Co-CNTs in water. These findings establish metal-functionalized CNTs as stable, responsive platforms for targeted 2-MP delivery and real-time electrochemical tracking.</p><h3>Methods</h3><p>Computational investigations were performed using Gaussian 09. Geometry optimizations, vibrational frequency analyses, and single-point energy calculations were executed via density functional theory (DFT) utilizing the M06-2X hybrid meta-GGA functional to account for non-covalent dispersion interactions. A mixed basis set approach was applied with 6-311G(d,p) for non-metal atoms and the LanL2DZ effective core potential for transition metals. Aqueous physiological environments were simulated using the polarizable continuum model (PCM). The physical nature of host–guest interactions was characterized through advanced topological population analyses, specifically utilizing the quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDG), and electron localization function (ELF) embedded in Multiwfn 3.8.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148910434","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":"Atomistic insight into dislocation behaviors in ultra-lightweight Mg-Li-Al alloys","authors":"Yi Yao,&nbsp;Guoqiang Liu,&nbsp;Yangzhou Ma,&nbsp;Guangsheng Song","doi":"10.1007/s00894-026-06943-w","DOIUrl":"10.1007/s00894-026-06943-w","url":null,"abstract":"<div><h3>Context</h3><p>Mg-Li alloys are among the lightest structural materials and exhibit excellent ductility, but their relatively low strength limits broader applications. Alloying, such as with Al, is an effective approach for strengthening Mg-Li alloys. However, the dislocation behavior in BCC Mg-Li alloys remains poorly understood. In this study, we first developed a highly accurate machine-learning potential (MLP) for Mg-Li-Al alloys. The developed MLP was subsequently applied to investigate the dislocation behavior of three representative alloys, Mg-38Li, Mg-38Li-2Al, and Mg-38Li-4Al (a.t.%). The results show that both alloys exhibit split screw dislocation core structures. Al addition is associated with more tortuous, intermittent edge dislocation motion and lower edge dislocation mobility. It also reduces screw dislocation velocity, although the reduction is smaller than that for edge dislocations. Screw dislocations are substantially less mobile than edge dislocations over the investigated stress range. The simulations further indicate that kink-pair activity on multiple planes and the resulting cross-kink configurations may contribute to the low screw dislocation mobility. These findings provide atomistic evidence for how minor Al additions modify dislocation motion in the modeled BCC Mg-Li alloys.</p><h3>Methods</h3><p>DFT calculations were performed using the VASP package to generate the training dataset for MLP development. The exchange–correlation interactions were described using the PBE form of the GGA. The MLP was developed and trained using the GRACE framework. All molecular dynamics simulations were subsequently carried out in LAMMPS employing the trained MLP. Atomistic models for the dislocation dynamics simulations were generated using Atomsk, while dislocation structures and their evolution were characterized using the dislocation extraction algorithm (DXA) implemented in OVITO.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148910407","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":"Comparative molecular dynamics of two cyclic peptide inhibitors bound to the Zika virus NS2B/NS3 protease","authors":"Camilla Vitoria Silva Marinho,&nbsp;Maycon Vinicius Damasceno de Oliveira,&nbsp;Anderson H. Lima","doi":"10.1007/s00894-026-06945-8","DOIUrl":"10.1007/s00894-026-06945-8","url":null,"abstract":"<div><h3>Context</h3><p>The Zika virus NS2B/NS3 protease is an important antiviral target, and macrocyclic peptide inhibitors represent promising scaffolds because they combine multibasic recognition motifs with conformational restriction. Here, we investigated two structurally related cyclic peptide inhibitors, referred to as CP1 and CP2, which share a conserved macrocyclic framework but differ in the chemical nature of their linker substituents. Molecular dynamics simulations showed that both peptides display broad intramolecular distance distributions in aqueous solution, indicating that key crystallographic contacts are not intrinsically maintained in the unbound state. Upon binding to the protease, CP2 adopted a more defined conformational ensemble and preserved a short intramolecular contact compatible with its crystallographic arrangement, whereas CP1 lost its crystallographic d2 contact and sampled a broader bound-state distribution. CP2 also showed a more focused interaction network involving residues from the catalytic and substrate-recognition regions and more favorable binding free-energy estimates.</p><h3>Methods</h3><p>Molecular dynamics simulations were performed for each cyclic peptide in aqueous solution and bound to the Zika virus NS2B/NS3 protease using Amber 20. The protein was described with the ff14SB force field, the cyclic peptides with GAFF2, and the systems were solvated with the TIP3P water model. Three independent 500 ns simulations were performed for each system. Trajectories were analyzed using structural clustering, intramolecular distance distributions, residue-level interaction analysis, and MM/PBSA and MM/GBSA binding free-energy calculations.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13550072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148904950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical investigation of g-C3N6 as an anode material for sodium-ion batteries for emergency energy in subway","authors":"Ning Liu,&nbsp;Wei Gao","doi":"10.1007/s00894-026-06934-x","DOIUrl":"10.1007/s00894-026-06934-x","url":null,"abstract":"<div><h3>Context</h3><p>Sodium-ion batteries (SIBs) are rich in resources and low in cost, exhibiting great potential for emergency energy storage in high-density public facilities such as subway stations. This study, based on density functional theory (DFT), systematically explores the theoretical performance of g-C₃N₆ and its sulfur-doped derivative (S-g-C₃N₆) as anode materials for SIBs. Electronic structure analysis revealed that pristine g-C₃N₆ is a direct-bandgap semiconductor with a bandgap of 2.601 eV, whereas S doping significantly reduced the bandgap to 0.326 eV. The most stable adsorption site for Na atoms on the g-C₃N₆ surface was found to be above the C atom, with an adsorption energy of −1.732 eV. Diffusion barrier calculations revealed that the minimum migration barriers for Na ions on the g-C₃N₆ and S-g-C₃N₆ surfaces are as low as 0.072 and 0.068 eV, respectively. The corresponding theoretical specific capacities reach 1339.2 and 1164.2 mAh/g, respectively. The average OCV was approximately 0.700 V, which is favorable for achieving a high energy density. In summary, g-C₃N₆-based materials, particularly after S doping modification, combine high specific capacity, excellent conductivity, and ultrafast ion diffusion kinetics, making them highly promising anode candidates intended for emergency energy storage in subway stations.</p><h3>Methods</h3><p>Both model optimization and property calculations were performed using the CASTEP module. The exchange-correlation interactions among electrons were treated using the PBE functional under the GGA. For the analysis of band structures and projected density of states, a more accurate HSE06 hybrid functional was further employed for correction to obtain more precise bandgap values. The cutoff energy was set to 600 eV. The maximum interatomic force was set below 0.001 eV/Å, the maximum displacement below 0.001 Å, and the internal stress below 0.001 GPa.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148904986","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":"Molecular modeling and quantum chemical calculation study of derived peptides from a Bowman-Birk inhibitor in complexes with trypsin","authors":"Luiz F. M. A. Benício,&nbsp;Érica C. M. Nascimento,&nbsp;Sonia M. de Freitas,&nbsp;João B. L. Martins","doi":"10.1007/s00894-026-06931-0","DOIUrl":"10.1007/s00894-026-06931-0","url":null,"abstract":"<div><h3>Context</h3><p>Bowman-Birk inhibitors (BBIs) are cysteine-rich proteins that inhibit trypsin and chymotrypsin proteases. Derived from soybeans, these natural BBIs have been identified as potential anticarcinogenic agents. Recent studies of the black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) demonstrated that peptides derived from the BBI family may retain their structure and inhibitory activity. Therefore, this study aimed to investigate the effects of solvent on BTCI-derived peptides and their inhibitory activity against trypsin. The results show that cyclic peptides exhibit reduced conformational flexibility, enhanced reactivity (narrower HOMO–LUMO gap), and LUMO localized at the disulfide bonds, in contrast to the linear peptide Ptry6. Non-covalent interactions were evaluated using the Independent Gradient Model based on Hirshfeld partitioning (IGMH). Molecular electrostatic potential maps and the IGMH confirmed that the cyclic architecture concentrates electropositive donor regions at key residues (Thr2, Lys3, Ser4, and Ile5), whereas Ptry6 displays only weak van der Waals contacts. Docking studies against trypsin showed strong hydrogen-bond and electrostatic interactions between cyclic peptides and residues involved in the catalytic mechanism. Predicted inhibition constants obtained from docking studies closely match experimental data. These findings suggest that electronic redistribution upon solvation governs peptide–trypsin affinity, highlighting Ptry9L as the most promising BTCI-derived inhibitor for further biotechnological development.</p><h3>Methods</h3><p>BTCI peptides were studied using quantum-chemical calculations and molecular docking. Three peptides—a cyclic nonapeptide in both L- and D-configurations (Ptry9L, Ptry9D) and a linear hexapeptide (Ptry6)—were optimized in vacuo and in implicit aqueous solvent using density functional theory at B3LYP-D3/Def2-SVP and B3LYP-D3/6-311+G(d,p) levels with D3 dispersion correction. Frontier molecular orbital analyses (HOMO–LUMO gaps and orbital localization) and IGMH revealed that the disulfide bond stabilizes cyclic peptides.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13546364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148896260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Finite-difference analysis of excitonic spectra in monolayer transition-metal dichalcogenides/hBN heterostructures","authors":"Dalel Helel,&nbsp;Mourad Debbichi","doi":"10.1007/s00894-026-06908-z","DOIUrl":"10.1007/s00894-026-06908-z","url":null,"abstract":"<div><h3>Context</h3><p>We theoretically study the excitonic properties in semiconductor transition metal dichalcogenide monolayers (ML-TMDs)(WSe<span>(_{2})</span>, WS<span>(_{2})</span>, MoSe<span>(_{2})</span>, MoS<span>(_{2})</span>, and MoTe<span>(_{2})</span>) encapsulated in hexagonal boron nitride (hBN). Excitonic binding energies and full non-hydrogenic Rydberg series (<i>s</i>, <i>p</i>, and <i>d</i> states) are calculated. As a first validation, the binding energies of the 1<i>s</i>-5<i>s</i> states of WSe<span>(_{2})</span>/hBN are reproduced to less than 2 meV (<span>(&lt;1%)</span>) over the entire range of thicknesses <span>(N in [0,infty [)</span>, and the separation <span>(Delta _{12}= 127{.}8)</span> meV reproduces the experimental value without adjusted parameters. We further derive a generalized two-sided dielectric potential <span>(V(r, N_textrm{top}, N_textrm{bot}))</span> that captures the asymmetric encapsulation geometry, and compute the two-dimensional map <span>(E_textrm{b}(N_textrm{top},N_textrm{bot}))</span> for WSe<span>(_{2})</span>. A new analysis of Coulomb engineering shows that E<span>(_{b})</span>(1<i>s</i>) varies by up to a factor of three across experimentally accessible dielectric environments, while the ratio <span>(E_{b}(2s)/E^{b}(1s))</span> serves as a sensitive probe of the non-hydrogenic character. Moreover, Berry-curvature corrections lift the angular-momentum degeneracy of <i>p</i>-and <i>d</i>-type excitons by 2–8 meV, with M-based compounds showing larger effects. Finally, the quadratic Stark polarizability under an out-of-plane electric field is computed via exact <span>(s-p)</span> coupling, with results depending sensitively on <i>N</i> and the material parameters. These results provide a unified quantitative framework directly applicable to studies on van der Waals heterostructures.</p><h3>Methods</h3><p>The generalized Rytova-Keldysh (RK) Schrödinger equation is solved using a cell-centered finite-difference scheme on a fine real-space grid (<i>N</i> = 2000 points, <span>(xi _{max})</span> = 50), with the calculations incorporating both Coulomb engineering effects and an applied out-of-plane electric field. Topological Berry phase corrections are subsequently introduced: the differential Berry curvature between the conduction and valence bands computed within the bulk Dirac model is averaged over the exciton momentum distribution through a Bessel-Hankel transform, yielding an energy shift that scales linearly with the azimuthal quantum number <i>m</i>.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148871851","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":"Hybrid organic–inorganic CH3NH3MnS3 : a multifunctional material for energy conversion, radiation protection, and hydrogen storage","authors":"Belqees Hassan,&nbsp;Manahil. E. E. Mofdal","doi":"10.1007/s00894-026-06926-x","DOIUrl":"10.1007/s00894-026-06926-x","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;Hybrid organic–inorganic chalcogenides have emerged as promising multifunctional materials due to their structural flexibility and tunable physical properties, making them attractive candidates for energy-conversion, optoelectronic, environmental, and radiation-protection technologies. In this study, the structural, electronic, mechanical, optical, thermodynamic, radiation-shielding, and hydrogen-storage properties of CH&lt;sub&gt;3&lt;/sub&gt;NH&lt;sub&gt;3&lt;/sub&gt;MnS&lt;sub&gt;3&lt;/sub&gt; were comprehensively investigated. The optimized structure exhibits excellent stability, while mechanical analysis confirms elastic stability and anisotropic behavior. Optical calculations reveal strong absorption across the visible and ultraviolet regions, accompanied by a high dielectric response, moderate refractive index, and low reflectivity, indicating suitability for photovoltaic and photodetection applications. Dynamical and thermal stability are verified through phonon-dispersion and thermodynamic analyses. Radiation-shielding calculations demonstrate efficient attenuation of low-energy photons with small half-value and tenth-value layers. Furthermore, hydrogen-storage investigations predict favorable adsorption energetics, a gravimetric storage capacity of approximately 13.2 wt.%, and a low diffusion barrier of about 0.32 eV, facilitating rapid hydrogen transport. These findings identify CH&lt;sub&gt;3&lt;/sub&gt;NH&lt;sub&gt;3&lt;/sub&gt;MnS&lt;sub&gt;3&lt;/sub&gt; as a versatile multifunctional material with significant potential for next-generation energy, optoelectronic, hydrogen-storage, and radiation-shielding applications.&lt;/p&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;The structural, electronic, optical, elastic, thermodynamic, radiation-shielding, and hydrogen-storage properties of CH&lt;sub&gt;3&lt;/sub&gt;NH&lt;sub&gt;3&lt;/sub&gt;MnS&lt;sub&gt;3&lt;/sub&gt; were investigated using DFT calculations implemented within the Cambridge Serial Total Energy Package (CASTEP) [1]. The exchange–correlation interactions were described using the generalized gradient approximation (GGA) within the Perdew–Burke–Ernzerhof (PBE) functional [2]. Ultrasoft pseudopotential was employed to represent the interactions between valence electrons and ionic cores [3]. The initial crystal structure was fully optimized using the Broyden–Fletcher–Goldfarb–Shanno (BFGS) minimization scheme. The convergence criteria were set to ensure high computational accuracy, with total-energy convergence of 1 × 10&lt;sup&gt;–5&lt;/sup&gt; eV atom&lt;sup&gt;−1&lt;/sup&gt;, maximum force below 0.03 eV Å&lt;sup&gt;−1&lt;/sup&gt;, maximum stress less than 0.05 GPa, and atomic displacement below 1 × 10⁻3 Å. A plane-wave cutoff energy of 500 eV and an appropriately converged Monkhorst–Pack k-point mesh were used throughout the calculations [4]. Following structural optimization, the electronic properties of CH&lt;sub&gt;3&lt;/sub&gt;NH&lt;sub&gt;3&lt;/sub&gt;MnS&lt;sub&gt;3&lt;/sub&gt; were examined through calculations of the electronic band structure and density of states (DOS). The band structure was evaluated along the high-symmetry directions of the firs","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148871850","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":"MR-CISD investigation (including extensivity corrections) of Rydberg n-3 s and n-3p states of the smallest ionized HCl-water cluster","authors":"Mariana G. Bezerra,&nbsp;Elizete Ventura,&nbsp;Silmar A. do Monte","doi":"10.1007/s00894-026-06912-3","DOIUrl":"10.1007/s00894-026-06912-3","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;The [H&lt;sub&gt;3&lt;/sub&gt;O(H&lt;sub&gt;2&lt;/sub&gt;O)&lt;sub&gt;3&lt;/sub&gt;]&lt;sup&gt;+&lt;/sup&gt;Cl&lt;sup&gt;−&lt;/sup&gt; ion-pair is the smallest cluster of ionized HCl in water. It has been demonstrated experimentally that it can be formed in conditions compatible with the interstellar medium (ISM). It is also a precursor of another ion-pair, H&lt;sub&gt;3&lt;/sub&gt;O&lt;sup&gt;+&lt;/sup&gt;(MetOH)&lt;sub&gt;3&lt;/sub&gt;Cl&lt;sup&gt;−&lt;/sup&gt;, suggested as an important prebiotic species in the ISM. Aiming to help the detection of the former ion-pair several properties of its n-3 s and n-3p singlet and triplet Rydberg states have been studied through a highly correlated &lt;i&gt;ab-initio&lt;/i&gt; method. The vertical excitation energies (ΔE&lt;sub&gt;v&lt;/sub&gt;), oscillator strengths (&lt;i&gt;f&lt;/i&gt;), dipole moments (μ), diradical character, participation ratio of natural transition orbitals (PR&lt;sub&gt;NTO&lt;/sub&gt;), single-excitation character (Ω), charge-transfer numbers and the singlet–triplet gaps (ΔE&lt;sub&gt;ST&lt;/sub&gt;) have been studied at the ground state (gs) geometry. The energies of the two lowest-lying dissociation channels have also been computed. Our highest-level results for ΔE&lt;sub&gt;v&lt;/sub&gt; of the n-3 s singlet states are between 6.63 and 6.65 eV, while for n-3p one has 7.40 to 7.74 eV. Previous TD-DFT results are ~ 0.84 to 0.95 eV lower, but our results nicely agree with available CASPT2 results for the n-3 s states. The brighter state is the 2nd n-3 s state, with &lt;i&gt;f&lt;/i&gt; = 0.172 at the highest-level. While the gs is essentially a closed-shell state, consistent with the [H&lt;sub&gt;3&lt;/sub&gt;O(H&lt;sub&gt;2&lt;/sub&gt;O)&lt;sub&gt;3&lt;/sub&gt;]&lt;sup&gt;+&lt;/sup&gt;Cl&lt;sup&gt;−&lt;/sup&gt; ion pair, all n-3 s and n-3p singlet states have high diradical characters, consistent with their small ΔE&lt;sub&gt;ST&lt;/sub&gt; values and with their nature as charge-recombination (CR) states. For most of the cases the CR characters are consistent with a decrease of μ. A possible deactivation pathway for the n-3 s states, involving their optimized geometries and a four-states conical intersection, is discussed. Our highest-level results yield the ionic channel 0.46 eV lower than the neutral channel. Ω indicates dominant single-excitation character for all Rydberg states, while PR&lt;sub&gt;NTO&lt;/sub&gt; indicates multi-configurational character only for few n-3p states.&lt;/p&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;The multi-reference configuration interaction with singles and doubles (MR–CISD) calculations (including size-extensivity corrections) have been employed. Size-extensivity corrections have only been applied for ΔE&lt;sub&gt;v&lt;/sub&gt; and for the energies of the dissociation channels. &lt;i&gt;f&lt;/i&gt;, μ and ΔE&lt;sub&gt;ST&lt;/sub&gt; have been computed from the MR-CISD wavefunctions. PR&lt;sub&gt;NTO&lt;/sub&gt;, Ω and the charge-transfer numbers (from which the nature of the excited states in terms of local, charge-transfer or CR states are obtained) have been computed from the one-electron transition density matrix. Three basis sets have been employed. The smallest one is the Pople’s 6–31+ +G**, while the second one is a mixed basis set based on the aug-cc-pVDZ","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 9","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13538156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148878957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microscopic investigation of the optoelectronic and electronic structure characteristics of OLED derivatives with CH/N substitutions on pyridyl and phenoxide rings","authors":"Huai-Wen Tsai","doi":"10.1007/s00894-026-06778-5","DOIUrl":"10.1007/s00894-026-06778-5","url":null,"abstract":"<div><h3>Context</h3><p>Organic light-emitting materials based on tris(8-hydroxyquinoline) aluminum (Alq₃) and gallium (Gaq₃) remain benchmark emitters in OLED research due to stable emission behaviors. The present work is concerned with the molecular and optical characteristics of these compounds by introducing CH/N substitutions at different positions. A series of derivatives was constructed to evaluate the impact of structural modifications on absorption, emission, and Stokes shift. The results reveal that substitution position apparently affects electronic transitions and spectral behavior. Modifications on the pyridyl side tend to induce red shifts, whereas those on the phenoxide side result in blue shifts. Molecular orbital analyses further indicate that parent complexes exhibit multi-orbital excitations, whereas the 5n₂p derivatives show localized HOMO to LUMO + 1 transitions, leading to higher excitation energies and narrower Stokes shifts.</p><h3>Methods</h3><p>Molecular structures were constructed using GaussView and subsequently optimized by density functional theory (DFT) with the B3LYP functional and the 6-31G(d) basis set. The first singlet excited-state (S₁) geometries were optimized using the CIS method with the 3-21G* basis set. Then, based on the optimized ground- and excited-state structures, the absorption and emission spectra were obtained at the B3LYP/3-21G* level from time-dependent DFT (TD-DFT). All calculations were carried out using the Gaussian software package. The computed results have a good agreement with the experimental UV–vis and photoluminescence trends, providing confidence in the modeling approach.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 7","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148872555","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}