Journal of Molecular Modeling最新文献

{"title":"(TD)DFT investigation of donor influence on the electronic and photovoltaic properties of D-π-A-π-A quinoxaline dyes","authors":"Malúcia M. Soeiro,&nbsp;Nathália M. P. Rosa,&nbsp;Itamar Borges Jr.","doi":"10.1007/s00894-026-06944-9","DOIUrl":"10.1007/s00894-026-06944-9","url":null,"abstract":"<div><h3>Context</h3><p>The design of efficient metal-free organic dyes is crucial for improving the performance of dye-sensitized solar cells (DSSCs). In this work, we investigated the influence of different donor groups on the electronic, photophysical, and photovoltaic properties of two D-<i>π</i>-A-<i>π</i>-A quinoxaline-based dyes, QX-DMA and QX-TPA. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations with solvation in tetrahydrofuran (THF) were employed to examine structure–property relationships. The optimized geometries exhibit high planarity along the conjugated backbone, favoring <i>π</i>-conjugation and intramolecular charge transfer. The results indicate that QX-TPA exhibits superior photovoltaic parameters, including a higher electron injection efficiency, greater regeneration driving force, and lower charge recombination, which are attributed to the extended electronic delocalization promoted by the triphenylamine (TPA) group. Electronic analysis shows that the lowest singlet excited state (<span>({S}_{1})</span>) is a bright HOMO → LUMO transition with pronounced electron–hole separation. Owing to its electron-donating group and more extended <i>π</i>-delocalization, QX-TPA displays enhanced charge-transfer character, larger reorganization energy, and a significantly longer excited-state lifetime, indicating improved charge stabilization and slower recombination rate compared with QX-DMA. These molecular properties suggest enhanced photovoltaic performance, with QX-TPA-based DSSCs achieving nearly twice the power conversion efficiency of QX-DMA devices, mainly due to a higher short-circuit current density.</p><h3>Methods</h3><p>The geometrical and electronic properties of all systems were investigated using density functional theory with the B3LYP exchange–correlation functional combined with the 6-311G(d,p) basis set. The functionals B3LYP-D3(BJ), CAM-B3LYP, <i>ω</i>B97X, and M06-2X were also tested. Time-dependent DFT calculations were performed at the same level of theory to describe the first ten singlet excited states (<span>({S}_{1} - {S}_{10})</span>). THF solvation effects were accounted for using the conductor-like polarizable continuum model (CPCM). All calculations were carried out using the ORCA 6.0 program package. Charge-transfer properties were analyzed using the TheoDORE program, whereas molecular orbital fragmentation analysis employed the Multiwfn (version 3.8) program package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06944-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148981736","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":"Structure-guided identification of histone deacetylase 11 inhibitors for targeted chemotherapy through long-timescale molecular dynamics simulation","authors":"Koustav Maiti,&nbsp;Deotima Chakraborty,&nbsp;Chandra Sekar Ponnusamy,&nbsp;Heshine Gnanasekar,&nbsp;Nevedha Ravindran,&nbsp;Bhavani Sridharan,&nbsp;Mahesh Velusamy","doi":"10.1007/s00894-026-06893-3","DOIUrl":"10.1007/s00894-026-06893-3","url":null,"abstract":"<div><h3>Context</h3><p>Histone deacetylase 11 (HDAC11), the sole member of class IV histone deacetylases, is an emerging epigenetic target in cancer therapy. In this study, an integrated computational approach involving ADMET screening, molecular docking, and molecular dynamics simulations was employed to identify potential HDAC11 inhibitors from 35 known HDAC inhibitors. Based on combined docking and pharmacokinetic analyses, five compounds were shortlisted for detailed evaluation. Mocetinostat exhibited the highest binding affinity toward HDAC11 (−8.70 kcal/mol) with acceptable pharmacokinetic properties (LogP: 2.25; TPSA: 99.11 Ų), while Belinostat showed the safest toxicity profile (LD50: 6000 mg/kg; Class 6). Resminostat also demonstrated favorable drug-likeness with moderate toxicity (LD50: 957 mg/kg; Class 4). Comparative MD analyses over 500 ns revealed high structural stability for the Nanatinostat-HDAC11 and Resminostat-HDAC11 complexes by lower RMSD, reduced residue fluctuations, and more stable hydrogen bond interactions. These findings highlight promising HDAC11 inhibitors for further experimental validation in anticancer drug development.</p><h3>Methods</h3><p>The HDAC11 protein structure was prepared and optimized along with ligand structures prior to docking. Pharmacokinetic properties and drug-likeness of all 35 selected HDAC inhibitors were predicted using the SwissADME web server, and toxicity profiles were assessed using the Protox-II server. Molecular docking was performed using PyRx with the AutoDock Vina scoring function. Protein-ligand interactions were analyzed using PyMOL and Discovery Studio visualizers. Molecular dynamics simulations were conducted using GROMACS with the CHARMM27 force field and TIP3P water model. A total of 3.5 µs of molecular dynamics simulations were performed, including a 500 ns production run and triplicate 100 ns validation runs for each complex. MD trajectory analyses, including RMSD, RMSF, radius of gyration, solvent-accessible surface area, hydrogen bond analysis, and kernel density estimation, were used to evaluate structural stability and interaction dynamics.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148981785","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":"Probing the interactions between cations and borazine analogue complexes","authors":"Guixiu Wang,&nbsp;Rongxiu Zhu,&nbsp;Jing Jia","doi":"10.1007/s00894-026-06956-5","DOIUrl":"10.1007/s00894-026-06956-5","url":null,"abstract":"<div><h3>Context</h3><p>The bond nature of X⁺  − E₁₃ upon X⁺  − E₁₃ = NL₂ (X = H, Li, Na, K, Al, Cu, Ag, E₁₃ = B, Al, Ga, In, and L = H, F, OH, CH₃, SiH₃) complexation was investigated theoretically. The well characterized covalency order of these cations H⁺  &gt; Cu⁺  &gt; Ag⁺  &gt; Al⁺  &gt; Li⁺  &gt; Na⁺  &gt; K⁺ was used as a criterion to estimate the characteristics of X⁺ − E₁₃ binding. The topological analysis is valid for all the X⁺ − E₁₃ = NL₂, except X⁺ − Al = NL₂. localized orbital locator study reveals that this is due to the non-uniform distribution of electron density and longer distance between X⁺ − Al. Orbital components of these complexes were quantified. The associated charge transfer and NOCV orbital energies reveal bonding strength follows as H⁺  &gt; Ag⁺  &gt; Cu⁺ &gt; Al⁺  &gt; Li⁺  &gt; Na⁺  &gt; K⁺. Two more bonding orbitals between Cu⁺ and E₁₃ = NL₂ share interaction energies, as well as charge transfer, leaving the major pairwise orbital bonding energies and charge transfer lesser than those of Ag⁺. CDA analysis demonstrates no orbital bonding between X⁺ and E₁₃ = NL₂ (X = Li, Na, K), weak orbital bonding for the interactions in the other compunds, especially strong orbital bonding between  H⁺  and E₁₃ = NL₂. All the result demonstrated that E₁₃ = NL₂ series act as qualified Lewis bases upon X⁺ − E₁₃ = NL₂ complexation, and the covalency of X⁺ − E₁₃ follows the traditional criterion.</p><h3>Methods</h3><p>The structural optimizations of cation/molecule interactions of X⁺ − E₁₃ = NL₂ were optimized at the level of M062X/def2tzvp using Gaussian 09 program. The nature of X⁺ − E₁₃ was investigated by Quantum Theory of Atoms in Molecules (QTAIM). Specifically, the signs of Laplacian density (<span>({nabla }^{2}rho)</span>) and energy density <i>H</i>(r) were used to discriminate covalency from non-covalency; the electron density <i>ρ</i>(<i>r</i>) was used to detect the bonding strength. Localized orbital locator (LOL) was used to show the color-filled maps of the electron densities of some species of interest. Charge decomposition analysis (CDA) and natural orbital o for chemical valence (NOCV) calculations were also performed. AIM, MESP, the plotting of the color-filled maps of LOL, CDA, and NOCV calculations were performed with the Multiwfn software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148981804","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":"Tool wear mechanism in diamond tools of single-crystal silicon machining: a molecular dynamics study","authors":"Nafiseh Mahdiyar,&nbsp;Seyed Vahid Hosseini,&nbsp;Mehdi Heidari","doi":"10.1007/s00894-026-06936-9","DOIUrl":"10.1007/s00894-026-06936-9","url":null,"abstract":"<div><h3>Context</h3><p>Single-crystal silicon is a critical material in optical and semiconductor manufacturing; however, its inherent brittleness poses persistent challenges in ultra-precision machining. This study employs classical molecular dynamics (MD) simulations to investigate the atomic-scale wear mechanisms of diamond tools during the nanomachining of single-crystal silicon. The investigation focuses on high-pressure phase transformation (HPPT) of silicon, interfacial chemical interactions consistent with SiC-like local bonding at the tool–workpiece interface, progressive sp³-to-sp²-like structural transitions and amorphization in the diamond tool, and the tribological consequences of rake-face defects—specifically voids and protrusions—on friction, temperature, material removal rate (MRR), machined surface quality, and tool structural integrity.</p><h3>Methods</h3><p>Classical MD simulations were performed using LAMMPS software, employing the Tersoff potential for Si–Si and C–C interactions and the Morse potential for Si–C interactions. Three tool conditions were systematically compared: a defect-free (ideal) tool, a void-containing tool, and a protrusion-bearing tool. Key simulation parameters included a cutting speed of 80 m/s, uncut chip thickness of 10 Å, tool edge radius of 20 Å, and rake angle of − 25°. Analyses encompassed stress tensor evaluation, silicon coordination number tracking, radial distribution function (RDF) analysis, temperature evolution, friction force statistics, MRR, atomic surface roughness (R_a), and two-scale fractal dimension characterization of surface defects.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148981782","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 docking and molecular dynamics investigation of novels thiazolopyrimidines binding to canonical and alternative allosteric sites of kinesin Eg5","authors":"Vinícius S. Cunha,&nbsp;Arlan S. Gonçalves,&nbsp;Reginaldo B. dos Santos,&nbsp;Ricardo M. Kuster","doi":"10.1007/s00894-026-06958-3","DOIUrl":"10.1007/s00894-026-06958-3","url":null,"abstract":"<div><h3>Context</h3><p>Human kinesin Eg5 is essential for bipolar spindle assembly, and most allosteric inhibitors bind to the canonical pocket formed by the α2 helix, loop 5, and the α3 helix. Eleven thiazolo[3,2-<i>a</i>]pyrimidinethiones were evaluated as ligands for two sites in Eg5: this canonical pocket and an alternative region near loop 8. All derivatives showed favorable docking poses at both sites, with average energies of -7.95 and -7.79 kcal.mol⁻¹ for the loop 5 and loop 8 sites, respectively, whereas monastrol favored loop 5 by 1.6 kcal.mol⁻¹. Compounds <b>1a</b> and <b>2d</b> remained associated with both sites during 500 ns simulations, with ligand root-mean-square deviations between 1.00 and 1.53 Å. MM-PBSA estimates ranged from -26.02 to -22.92 kcal.mol⁻¹, compared with -22.14 kcal.mol⁻¹ for monastrol. RMSF calculations revealed site- and ligand-dependent redistribution of mobility in loop 5, loop 8, Switch I, Switch II, the microtubule-binding site, the cover-neck bundle, and the neck linker. These results indicate that this scaffold is promising for the exploration of alternative allosteric sites in Eg5, although experimental confirmation is required.</p><h3>Method</h3><p>The Switch II segment was reconstructed with SWISS-MODEL and evaluated with PDBsum. The structures were prepared with PDB2PQR, AutoDockTools, and Open Babel. Redocking compared AutoDock Vina, QuickVina 2, and QuickVina-W, and QuickVina-W with exhaustiveness 32 was selected. Six systems were simulated for 500 ns in GROMACS using the OPLS-AA/L force field, TIP3P water, and ligand parameters obtained with ACPYPE. Visual Molecular Dynamics was used for trajectory measurements, Discovery Studio Visualizer for interaction analysis, and g_mmpbsa for binding-energy estimation and per-residue decomposition.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06958-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148975442","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":"Charge-dipole bound anion-anion complexes","authors":"Jane S. Murray,&nbsp;Timothy Clark","doi":"10.1007/s00894-026-06947-6","DOIUrl":"10.1007/s00894-026-06947-6","url":null,"abstract":"<div><h3>Background</h3><p>At short range, charge-dipole interactions, which scale with <i>R</i>^<i>−2</i>, can override the more conceptually familiar charge-charge ones, which scale with <i>R</i>^<i>−1</i>. This can lead to metastable minima for complexes between ions of like charge, but also be designed to create, as shown here, thermodynamically stable anion-anion complexes. We show that such complexes can be stable to dissociation into their component anions, and to autoionization.</p><h3>Methods</h3><p>Geometries were optimized at the MP2/aug-cc-pVTZ level, and optimized structures confirmed to be minima or transition states by calculating the normal vibrations within the harmonic approximation at this level. Energies were refined using these geometries for CCSD(T) calculations with the same basis set. MP2/aug-cc-pVTZ single points with the complexed chloride ion represented by a point charge were used to demonstrate the charge-dipole nature of the bonding interaction. All calculations used Gaussian16.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06947-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148975448","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":"Deciphering SHP-2 conformational switching via elastic network models and transfer entropy analysis","authors":"Qinchen Si,&nbsp;Zhixiang Wu","doi":"10.1007/s00894-026-06959-2","DOIUrl":"10.1007/s00894-026-06959-2","url":null,"abstract":"<div><h3>Context</h3><p>Src homology 2 domain-containing protein tyrosine phosphatase-2 (SHP-2), a non-receptor protein tyrosine phosphatase encoded by PTPN11, functions as a central regulator of the Ras-MAPK, JAK-STAT, and PI3K-AKT signaling pathways. Its gain-of-function mutations, such as E76K, drive aberrant activation in multiple cancers, making it an attractive therapeutic target. While molecular dynamics simulations have provided atomic-level insights into SHP-2 conformational dynamics, they are computationally prohibitive for systematically characterizing large-scale domain rearrangements and allosteric communication networks. Here, we employed an equal-weighted multi-parameter Gaussian network model (ewmGNM) to investigate the two lowest-frequency modes governing the functional dynamics of SHP-2 in three key systems: the wild-type closed (autoinhibited) conformation, the oncogenic E76K mutant in its open (active) conformation, and its complex with the allosteric inhibitor SHP099. By focusing on low-frequency modes, we computed residue fluctuations, dynamic cross-correlations, and transfer entropy to map directional information flow and allosteric communication landscapes. Our results demonstrate that the E76K mutation globally increases protein flexibility and disrupts inter-domain coupling, particularly at the N-SH2/PTP interface, whereas SHP099 binding largely restores the closed state dynamics but retains mutation-induced residual flexibility. Transfer entropy analysis reveals a conformation-dependent reorganization of information flow, with the open state exhibiting that the N-SH2 domain possibly acts as a new entropy source, tentatively suggesting its potential as a novel allosteric site. These findings provide a mechanistic understanding of SHP-2 conformational regulation and offer a theoretical basis for the design of allosteric inhibitors targeting this open state site.</p><h3>Methods</h3><p>Protein crystal structures were downloaded from the Protein Data Bank. The ewmGNM and the conventional GNM were implemented using custom scripts written in MATLAB R2024b. Protein dynamics data were mapped using custom Python scripts in PyMOL.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148975531","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":"First-principles study on the structure, hydrogen storage, and physical properties of perovskite hydrides X2YH6 (X = Mg, Ca, Sr, Ba) for hydrogen storage applications","authors":"Hao-Yi Xu,&nbsp;Hai-Jun Hou,&nbsp;Hong-Li Guo,&nbsp;Shun-Ru Zhang","doi":"10.1007/s00894-026-06955-6","DOIUrl":"10.1007/s00894-026-06955-6","url":null,"abstract":"<div><h3>Context</h3><p>Based on density functional theory (DFT), this study systematically investigates the structure, hydrogen storage performance, mechanical properties, and optoelectronic properties of X₂YH₆ (X = Mg, Ca, Sr, Ba) compounds. Analysis of the elastic constants indicates that the cubic yttrium-based hydride X₂YH₆ crystals possess excellent structural stability. Furthermore, analysis of the chemical bonds of the compounds reveals that all X₂YH₆ compounds are bonded via ionic bonds, with Mg₂YH₆ being a brittle material and Ca₂YH₆, Sr₂YH₆, and Ba₂YH₆ being ductile materials. Band structure analysis further demonstrates that these materials have metallic properties. Meanwhile, the hydrogen storage capacities of X₂YH₆ (X = Mg, Ca, Sr, Ba) are 4.21, 3.46, 2.24, and 1.64 wt%, respectively. Analysis of the optical properties shows that the static reflectivities of X₂YH₆ (X = Mg, Ca, Sr, Ba) are 55.7%, 39.9%, 39.4%, and 44.8%, respectively, and the maximum absorption coefficients are 2.24 × 10⁵ (25.32 eV), 3.78 × 10⁵ (26.49 eV), 2.91 × 10⁵ (26.32 eV), and 2.47 × 10⁵ (26.34 eV), respectively, indicating that the materials have good reflectivity and absorption capacity. At the limit state of zero photon energy, the static refractive indices of Mg₂YH₆, Ca₂YH₆, Sr₂YH₆, and Ba₂YH₆ are 6.80, 4.40, 4.33, and 4.99, respectively, showing favorable refractive indices, with maximum electrical conductivities of 3.72, 6.72, 4.15, and 3.42 1/fs, respectively. The good electrical conductivity and low energy loss coefficient of the materials also indicate that they can reduce the attenuation of electronic performance in applications. This study aims to provide valuable references for subsequent research on X₂YH₆ compounds.</p><h3>Methods</h3><p>Based on DFT, and the CASTEP software is used to optimize the structure of X₂YH₆ (X = Mg, Ca, Sr, Ba) compounds. The BFGS algorithm is selected for energy minimization during the calculation process. The electron exchange–correlation interaction is described by the PBE functional under the generalized gradient approximation, and the OTFG ultrasoft pseudopotential is used to handle the interaction between the ionic core and valence electrons.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06955-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148965963","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":"Membrane interactions and pore stability of aurein 1.2 and LLAA in single- and multi-peptide systems revealed by coarse-grained molecular dynamics simulations","authors":"Roshanak Ansarihaghi","doi":"10.1007/s00894-026-06903-4","DOIUrl":"10.1007/s00894-026-06903-4","url":null,"abstract":"<div><h3>Context</h3><p>Aurein 1.2 is a short cationic antimicrobial peptide secreted by the Australian tree frog <i>Litoria aurea</i>. In this study, we investigated the membrane interactions of aurein 1.2 and its analog LLAA in single- and multi-peptide systems using model bacterial-like and eukaryotic-like lipid bilayers. LLAA exhibited stronger membrane interactions and deeper insertion than aurein, particularly in the bacterial-like membrane models. The simulations further indicated that peptide dissociation from aggregates was generally associated with increased membrane insertion. In pre-formed pore simulations, LLAA pore assemblies rapidly disassembled, whereas aurein pore assemblies remained stable for longer periods, particularly in the bacterial-like membrane models. These findings suggest that differences in peptide sequence and charge distribution are associated with distinct membrane insertion behavior, peptide organization, and the stability of pre-formed pore assemblies in the membrane models investigated.</p><h3>Methods</h3><p>Coarse-grained molecular dynamics simulations were performed using the MARTINI force field with the polarizable water model. Simulations were carried out with GROMACS for systems containing single peptides, five-peptide membrane insertion systems, and pre-formed pore assemblies in POPC, DPPC, and POPE/POPG bilayers. Peptide insertion, orientation, electrostatic interactions, clustering, pre-formed pore stability, and water occupancy were analyzed using GROMACS analysis tools together with custom VMD Tcl, Python, and C++ scripts.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148965966","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":"Rational design of ruthenium-based organic sensitizers for high-performance dye-sensitized solar cells: a comprehensive DFT and TD-DFT investigation","authors":"Faeq A. AL-Temimei","doi":"10.1007/s00894-026-06950-x","DOIUrl":"10.1007/s00894-026-06950-x","url":null,"abstract":"<div><h3>Context</h3><p>In this work, we report a detailed computational evaluation of eight organic ruthenium-based sensitizers (Dye1–Dye8) for their possible use in Dye-Sensitized Solar Cells (DSSCs). The calculated electronic and photovoltaic parameters showed a good energetic alignment for electron injections and dye regeneration, with HOMO energies from −5.483 to −4.994 eV, LUMO energies from −3.271 to −2.933 eV and open-circuit voltage values from 0.694 to 1.183 eV. The quantum chemical descriptors showed excellent electronic reactivity with global hardness values from 1.002 to 1.239 eV and softness values between 0.403 and 0.499 eV-1, indicating a high charge transfer ability and electronic flexibility. Charge distribution analyses such as MEP and ELF showed strong donor–acceptor behavior and effective electron delocalization along the molecular framework. Structural investigations by RDG, NCI, and Hirshfeld surfaces revealed that hydrogen bonding and weak intermolecular contacts considerably increase molecular stiffness, crystal packing, and intermolecular electrical communication, with H···H interactions contributing 77–80% in Dye1, Dye2, and Dye7. Further DOS/PDOS research demonstrated a substantial orbital hybridization between Ru d-orbitals and ligand orbitals, confirming effective photoinduced excitation pathways. The optical characteristics exhibited extensive absorption in the visible and near-infrared areas with λ_max values in the range of 436.891–788.532 nm, excitation energies from 1.573 to 1.721 eV, and oscillator strengths from 0.684 to 2.038, showing good light-harvesting performance. The obtained results highlight the extraordinary stability of structure, excellent electrical characteristics, and outstanding photovoltaic potential of the studied sensitizers for the development of future high-efficient DSSC devices.</p><h3>Methods</h3><p>All calculations were done with DFT and TD-DFT in Gaussian and molecular visualization in GaussView. ωB97X-D functional with LanL2DZ basis set for Ru and Ti atoms and 6-31G(d,p) for the non-metal atoms were used for geometry optimizations. Frequency calculations verified genuine minima with no imaginary frequencies. The excited-state and optical properties were calculated at the CAM-B3LYP level of theory using TD-DFT for the first 30 singlet–singlet transitions. Other analyses are MEP, ELF, RDG, NCI, Hirshfeld surface, and DOS/PDOS calculations.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148965957","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}