Journal of Molecular Modeling最新文献

{"title":"Coarse-grained force field parameters for natural product-based small molecules: from structural mapping to pharmaceutical applications.","authors":"Yumei Yan, Xiaowen Wu, Minfang Feng, Xingxing Dai, Bingxuan Li, Xinhui Peng, Guoqing Li, Yueyang Xie, Zhixun Li, Rui Li, Xinyuan Shi","doi":"10.1007/s00894-026-06983-2","DOIUrl":"https://doi.org/10.1007/s00894-026-06983-2","url":null,"abstract":"<p><strong>Context: </strong>Natural product-derived bioactive small molecules represent a major source of lead compounds for drug discovery and pharmaceutical innovation. The performance of drug delivery systems is fundamentally governed by intermolecular noncovalent interactions, yet their multiscale characterization remains computationally challenging. All-atom molecular dynamics (AA-MD) simulations provide atomic-level mechanistic resolution but are limited by their high computational cost, whereas coarse-grained molecular dynamics (CG-MD) simulations offer improved computational efficiency but lack standardized and transferable parameters for structurally diverse natural product-derived small molecules. In this study, we developed a Martini 3-based CG modeling framework for natural product-derived small molecules. Coarse-grained mapping rules were established for four representative scaffolds, including phenylpropanoids, quinones, flavonoids, and terpenoids, and a CG force-field parameter set was developed for 24 representative bioactive natural products. The models and parameters were systematically validated using two complementary criteria based on structural descriptors and energetic metrics. The resulting CG models were further applied to investigate β-cyclodextrin inclusion mechanisms and predict transdermal penetration enhancement effects, which successfully reproduced the experimentally observed macroscopic trends. These results demonstrate the reliability, transferability, and practical utility of the developed parameter set. Overall, this work established a standardized CG simulation strategy for natural product-derived small molecules and provided efficient computational guidance for the rational design and optimization of drug delivery systems for natural product-derived drugs.</p><p><strong>Methods: </strong>All-atom simulations were performed using the GROMOS 54a7 force field. Coarse-grained models were subsequently constructed based on the Martini 3.0 force field framework, and bonded parameters were obtained through iterative optimization using the Swarm-CG software. Structural rationality was validated by comparing the radius of gyration (Rg), solvent-accessible surface area (SASA), and distributions of bond lengths, bond angles, and dihedral angles between CG and AA models. Thermodynamic properties were validated by calculating the solvation free energy (ΔGₛₒₗ) using the free energy perturbation method. Finally, drug delivery system models were established to explore β-cyclodextrin inclusion mechanisms and predict the penetration-enhancing effects of transdermal penetration enhancers, thereby evaluating the applicability of the developed models. The reliability of the constructed systems, workflow, and model parameters was assessed by comparing the simulated encapsulation and penetration-enhancement efficiencies with the corresponding experimental values.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149222985","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":"A first-principles study of the adsorption behavior of chloride and sulfate ions on the surface of calcite in carbonated cement-based materials","authors":"Junting Dong,&nbsp;Liang Peng,&nbsp;Hao Zhu,&nbsp;Ming Lin,&nbsp;Jingshang Lin","doi":"10.1007/s00894-026-06995-y","DOIUrl":"10.1007/s00894-026-06995-y","url":null,"abstract":"<div><h3>Background</h3><p>Carbonation converts calcium-bearing hydration products in cementitious materials into calcium carbonate phases, with calcite being the most stable product. However, the role of calcite in regulating chloride- and sulfate-bearing species at carbonated cement–water interfaces remains unclear.</p><h3>Methods</h3><p>First-principles calculations were performed to investigate the adsorption of NaCl, CaCl₂, Na₂SO₄, and CaSO₄ on the calcite surface in an aqueous environment. Optimized structures, adsorption energies, interatomic distances, and projected densities of states were analyzed.</p><h3>Results</h3><p>NaCl and CaCl₂ interact with calcite mainly through localized Ca–Cl and Ca–O contacts, with adsorption energies of−1.47 and\u0000−1.72 eV, respectively. Na₂SO₄ exhibits substantially stronger adsorption, with an adsorption energy of−6.18 eV. This interaction arises from multidentate coordination between sulfate oxygen atoms and surface calcium sites, together with sodium-mediated interfacial bridging. The characteristic distances, including Ca–O = 2.101 Å for Na₂SO₄, Ca–Cl = 2.882 Å for NaCl, and Ca–O/Ca–Cl = 2.329/2.786 Å for CaCl₂, further distinguish the adsorption modes of sulfate and chloride species. Projected density of states analysis indicates that the interfacial interactions are primarily governed by surface calcium states and oxygen-rich groups within carbonate and sulfate units.</p><h3>Conclusions</h3><p>Calcite formed during cement carbonation is unlikely to strongly immobilize chloride salts. However, it may provide active interfacial sites that promote sulfate enrichment at carbonated cement–water interfaces. </p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149190000","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 insights into the cooperative effects of rigid π-bridges and auxiliary acceptors on the photovoltaic properties of D-π-A′-π-A sensitizers","authors":"Dilihumaer Aizezi,&nbsp;Nan Yang,&nbsp;Xiatiguli Kahaer,&nbsp;Haitao Sun,&nbsp;Yu Wang,&nbsp;Jiaqi Li,&nbsp;Xiaoning Wang,&nbsp;Mei Xiang,&nbsp;Bumaliya Abulimiti","doi":"10.1007/s00894-026-07011-z","DOIUrl":"10.1007/s00894-026-07011-z","url":null,"abstract":"<div><h3>Context</h3><p>The photovoltaic performance of dye-sensitized solar cells (DSSCs) is critically governed by the energy-level alignment, excited-state charge-transfer dynamics, and dye–TiO₂ interfacial interaction of the sensitizer. In this work, nine D-π-A′-π-A organic dyes based on an aminofluorene donor, 2-(2,4-difluorophenyl)pyridine as the auxiliary acceptor (A′), and cyanoacrylic acid as the terminal acceptor, with thiophene, selenophene, or acetylene as the π-bridge, were theoretically investigated to elucidate the cooperative effects of π-bridge engineering and substituent modification on photovoltaic performance. The computed results show that the acetylene-bridged nitro-substituted dye (F-NO₂) exhibits the narrowest HOMO–LUMO gap (1.69 eV) with an absorption maximum at 597 nm, while the selenophene-bridged nitro dye (F-Se-NO₂) reaches the longest absorption wavelength (832 nm) but with a low oscillator strength (0.14) and marginal electron injection driving force (−0.03 eV). In contrast, the unsubstituted acetylene dye (F) shows the most balanced performance: highest light-harvesting efficiency (1.00), strongest injection driving force (−1.66 eV), and highest open-circuit voltage (0.95 V). Adsorption energy calculations reveal that selenophene-based dyes exhibit significantly more negative Eads values (ranging from −7.89 to −19.05 eV) compared with thiophene-based (−0.54 to −1.36 eV) and acetylene-based (−0.82 to −3.54 eV) counterparts, indicating stronger interfacial binding to the TiO₂ surface. These findings indicate that π-bridge engineering and substituent modification cooperatively regulate molecular properties, yet enhanced charge separation and spectral broadening are often accompanied by reduced injection driving force or voltage output, highlighting the need for balanced optimization. This study provides quantitative structure–property relationships for the rational design of D-π-A′-π-A sensitizers.</p><h3>Methods</h3><p>Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were performed using Gaussian 16. Ground-state geometries were optimized at the B3LYP/6-31+G(d,p) level with Grimme’s D3 dispersion correction, and excited-state properties were calculated at the CAM-B3LYP/6-31+G(d,p) level in solvent with the IEFPCM solvation model. A (TiO₂)₉ cluster was employed to model the TiO₂ surface, and dye@TiO₂ complexes were optimized at the B3LYP/def2-SVP level with D3 correction. Molecular geometries, frontier molecular orbitals, absorption spectra, light-harvesting efficiency, electron injection driving force, open-circuit voltage, and adsorption energies were systematically calculated. Molecular visualizations were generated using Multiwfn 3.8.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149189977","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":"Phytochemical modulation of DNMT1-mediated DNA methylation: computational insights into breast cancer","authors":"Tripti Gangwar,&nbsp;Abhimanyu Kumar Jha","doi":"10.1007/s00894-026-06979-y","DOIUrl":"10.1007/s00894-026-06979-y","url":null,"abstract":"<div><h3>Context</h3><p>Aberrant DNA methylation, particularly DNMT1-mediated hypermethylation of tumor suppressor and DNA repair genes, contributes to breast cancer progression. The limitations associated with existing DNMT inhibitors highlight the need for alternative and potentially safer epigenetic modulators. Here, we developed a computational workflow to identify phytochemicals targeting the catalytic methyltransferase domain of DNMT1. Screening of the SelleckChem phytochemical library identified Echinacoside (-9.56 kcal/mol), 1,2,3,4,6-O-Pentagalloylglucose (-9.49 kcal/mol), and Complanatoside A (-9.24 kcal/mol) as promising candidates based on favourable docking and interaction profiles. Among them, 1,2,3,4,6-O-Pentagalloylglucose exhibited most favorable predicted binding free energy (− 105.31 ± 5.51 kcal/mol) and maintained stable interactions throughout 500 ns molecular dynamics simulation. DFT, PCA, FEL, and QM/MM analyses further supported its favorable electronic characteristics and conformational stability within the DNMT1 catalytic pocket.</p><h3>Methods</h3><p>Structure-based virtual screening, molecular docking, DFT, 500 ns molecular dynamics simulations, MM/GBSA, PCA, FEL, and QM/MM analyses were integrated to characterize ligand binding, stability, and electronic interactions. These findings represent purely in silico predictions and require experimental validation to establish the DNMT1 inhibitory potential of the identified compounds and their therapeutic relevance.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149189997","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":"Adsorption mechanism of neutral and protonated HQAP on Fe(110): a DFT, Monte Carlo and molecular dynamics study","authors":"Brahim Amjoud,&nbsp;Soufiane Zerraf,&nbsp;Amrane Younesse,&nbsp;Younes Abboud","doi":"10.1007/s00894-026-07008-8","DOIUrl":"10.1007/s00894-026-07008-8","url":null,"abstract":"<div><h3>Context</h3><p>The adsorption of 8-quinolinol-5-azoantipyrine (HQAP) on Fe(110) was investigated to clarify the interfacial behavior of representative neutral and carbonyl-protonated models. Although pKa-based speciation indicated that multiply protonated species dominate under strongly acidic conditions, neutral HQAP-AE and monoprotonated HQAP-OcarbonylH+ were retained for a restricted molecular comparison. Monte Carlo searches identified low-energy starting configurations, and molecular dynamics and radial distribution function analyses showed persistent Fe–N/O proximity over 2000 ps. The nearest-Fe contact of the azo nitrogen on the antipyrine side was shorter in the protonated model over both analysis windows. Other differences depended on the site and time window. The results support persistent multipoint interfacial contacts without demonstrating covalent bonding, chemisorption or a general ranking of adsorption strength.</p><h3>Methods</h3><p>Density functional theory (DFT) calculations were performed using the DMol³ module in Materials Studio 2023 with the GGA-PBE functional and DNP basis set; aqueous calculations used COSMO. Monte Carlo (MC) searches using Adsorption Locator supplied the initial adsorbed configurations for molecular dynamics (MD) using Forcite and COMPASS III. The molecular charge of HQAP-OcarbonylH+ was retained and balanced by an additional chloride counterion. Production comprised two consecutive 1000 ps NVT segments at 303 K using the Andersen thermostat and a 0.25 fs time step. Radial distribution functions (RDFs) and nearest-Fe distances were compared over 1000–2000 ps and the common final 1500–2000 ps window.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149189963","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":"Interaction mechanisms of MXene with bacterial division proteins: towards efficient antibacterial materials","authors":"Tahereh Ghaed-Sharaf,&nbsp;Akbar Omidvar","doi":"10.1007/s00894-026-07015-9","DOIUrl":"10.1007/s00894-026-07015-9","url":null,"abstract":"<div><h3>Context</h3><p>The rising threat of bacterial infections, coupled with the rise of antibiotic-resistant strains, has driven the search for alternative antibacterial strategies that do not rely on traditional chemical agents. Among these, antibacterial materials, particularly those based on two-dimensional nanomaterials, have emerged as promising platforms for preventing bacterial adhesion and proliferation. In this context, MXenes, a class of transition metal carbides and nitrides, have recently gained attention for their potent antibacterial properties. However, the molecular-level mechanisms by which MXenes interact with key bacterial components remain poorly understood. This study employs classical molecular dynamics (MD) simulations to investigate the interactions of Ti₃C₂O₂ MXene with bacterial membrane proteins such as FtsP and EnvC, which are involved in bacterial cell division. Results indicate that both examined proteins adsorb onto the MXene surface. Specific amino acids close to the Ti₃C₂O₂ MXene surface are identified as the main interaction sites that are the driving force for the adsorption of the proteins. Our findings demonstrate that Ti₃C₂O₂ MXene effectively interacts with bacterial membrane proteins, with FtsP exhibiting stronger adsorption than EnvC. These protein–surface interactions could be relevant to the antibacterial activity of Ti₃C₂O₂ MXene and may contribute to its potential effects on bacterial cell division.</p><h3>Methods</h3><p>MD simulations were performed using GROMACS 2022.2 with the CHARMM27 force field for proteins (FtsP: 2UXT, EnvC: 4BH5) and literature-derived parameters for Ti₃C₂O₂. Systems were solvated in TIP3P water, neutralized, and simulated for 200 ns at 310 K. Adsorption was analyzed through contact area and interaction energies (LJ/Coulomb), while protein stability/flexibility was assessed via RMSD, RMSF, and <i>Rg</i> using VMD and GROMACS tools.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149189819","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":"Development and application of a new structural modeling approach for FTIR analysis of gelatin via PM3 calculations","authors":"Prateek Pathak,&nbsp;Djalila Boudemagh,&nbsp;Maria Grishina","doi":"10.1007/s00894-026-07002-0","DOIUrl":"10.1007/s00894-026-07002-0","url":null,"abstract":"<div><h3>Context</h3><p>Gelatin is a widely used material; however, its precise structure has not yet been resolved by X-ray diffraction. To predict its properties, including the adsorption of phytocomponents and associated biological effects, a reliable structural model is essential. Since experimental data are limited, computational methods that account for interactions between polypeptide chains, water, and other molecules represent a viable approach. In this study, the available experimental FTIR spectrum of gelatin was used as a benchmark to validate the modeling results.</p><h3>Methods</h3><p>A new express method Infant for global minimum search applicable for large molecular systems is proposed. This approach estimates intramolecular energies using the MM3 force field and intermolecular interactions via the presented Model of Effective Radii of Atoms (MERA). The method was applied to model various structural fragments of gelatin, including hydrated and non-hydrated single-, double-, and triple-helix α-chains. The IR spectra of the obtained fragments were calculated using the semi-empirical quantum chemical method PM3. High accuracy in reproducing the experimental FTIR spectrum of gelatin was demonstrated, confirming the reliability of the proposed structural models.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149189962","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":"DFT studies on the anti-static and decomposition mechanisms of high energy materials in the charged and damp environment: a case study of RDX, HMX, TNAZ and TATB","authors":"Qiong Wu,&nbsp;Zhihao Zheng,&nbsp;Weihua Zhu","doi":"10.1007/s00894-026-07004-y","DOIUrl":"10.1007/s00894-026-07004-y","url":null,"abstract":"<div><h3>Context</h3><p>High-energy materials are susceptible to decomposition and detonation under electrostatic stimulus, leading to severe accidents. To address this safety concern, the antistatic and decomposition mechanisms of high-energy materials under charged and humid conditions were investigated theoretically, with RDX, HMX, TNAZ, and TATB as model compounds. The results demonstrate that all four compounds possess large band gaps, resulting in low electrical conductivity and, consequently, low electrostatic sensitivity. The four compounds exhibit different tolerances to positive and negative charges: TNAZ exhibits greater tolerance to negative charges than to positive charges, whereas RDX and HMX exhibit poor tolerance to both negative and positive charges. The initial decomposition pathway involves cleavage of the N-NO₂ bond for RDX, TNAZ, and HMX, which is attributed to the uneven charge distribution on the nitro groups. In contrast, TATB exhibits significantly greater charge tolerance, owing to cooperative charge delocalization across the entire molecular skeleton. The antistatic performance is generally enhanced under humid conditions, which is attributed to charge sharing with water molecules. Furthermore, both UV–Vis and IR spectra are significantly altered upon charging or humidification, providing spectroscopic fingerprints for the detection of these materials under operational conditions.</p><h3>Methods</h3><p>All of the calculations on the structures were carried out using the Gaussian 09 software at the M06-2X/6-311 + G(d,p) level. In addition, further calculations on the Fukui function were performed using the DMOL³ package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149189432","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":"Ab initio simulation of the absorption spectrum of Ruby and the role of vibronic coupling","authors":"Leon D. Starke,&nbsp;Amanda D. Torres,&nbsp;Alexandre B. Rocha","doi":"10.1007/s00894-026-06985-0","DOIUrl":"10.1007/s00894-026-06985-0","url":null,"abstract":"<div><h3>Context</h3><p>Ruby is a material commonly found in Nature. Its red color is due to chromium impurity in the lattice of <span>(alpha )</span>-alumina. It has several technological applications, such as lasers, thermometers, and radiation dosimeters. The study of its absorption spectrum is relevant in this context. On the other hand, vibronic coupling in solids is an important phenomenon since it can change the features of the absorption spectrum, especially when involving transition metal <i>d-d</i> electronic transitions in a quasi-octahedral environment, as in the case considered here. This work provides insight into the role of the vibronic coupling mechanism in the profile of the absorption spectrum of Ruby in the visible region.</p><h3>Methods</h3><p>The spectrum of Ruby, i.e., <span>(alpha )</span>-alumina doped with chromium, is calculated within the linear response regime applied to a PBE DFT initial calculation. Intensities are taken as the imaginary part of the frequency-dependent dielectric function, obtained by the Green-Kubo formula. The model is composed of an <span>(alpha )</span>-alumina supercell in which an aluminum atom is replaced by a chromium atom. Periodic boundary conditions were applied throughout. The vertical spectrum at the equilibrium geometry was first reported. Then, vibronic coupling effects were evaluated by carrying out distortions of the geometry along the normal modes related to the motions of chromium and its first neighbors. In addition, the effect of distortions involving combined modes was also assessed. In the last case, the modes are combined in pairs, generating hundreds of possibilities, all of which were carefully calculated. Modes (pure and combined) that change the absorption profile are clearly identified, and it is shown that they were able to change both position and intensity of the absorption peak in the visible region.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06985-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178565","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":"Hydrogen storage in alkali-decorated N-doped biphenylene: a DFT study","authors":"Shoeib Babaee Touski,&nbsp;Alireza Kokabi,&nbsp;Manouchehr Hosseini","doi":"10.1007/s00894-026-06973-4","DOIUrl":"10.1007/s00894-026-06973-4","url":null,"abstract":"<div><h3>Context</h3><p>The hydrogen storage performance of alkali-decorated nitrogen-doped biphenylene monolayers was investigated using density functional theory calculations. Two possible nitrogen substitution configurations were examined, and the 2-N structure was identified as the energetically preferred configuration. Among the investigated adsorption sites, the octagonal ring provides the most stable anchoring for Li, Na, and K atoms. The hydrogen storage properties were evaluated in terms of adsorption energy and gravimetric density. By adopting 0.2 eV per H<span>(_2)</span> as the lower limit for practical reversible adsorption, the maximum hydrogen storage capacities were determined to be 9, 12, and 11 H<span>(_2)</span> molecules for Li-, Na-, and K-decorated structures, corresponding to gravimetric densities of 5.72, 7.12, and 6.27 wt%, respectively. Furthermore, double-sided hydrogen adsorption on the Na-decorated monolayer increases the gravimetric density to 12.50 wt%. These results suggest that Na-decorated nitrogen-doped biphenylene is a promising candidate for reversible hydrogen storage applications.</p><h3>Methods</h3><p>Density functional theory calculations were performed using the SIESTA package. Exchange-correlation effects were described within the generalized gradient approximation using the Perdew–Burke–Ernzerhof functional together with Grimme’s dispersion correction. A Monkhorst–Pack <span>(21times 21times 1)</span> <i>k</i>-point mesh, a double-<span>(zeta )</span> plus polarization basis set, and an energy cutoff of 200 Ry were employed. Geometry optimizations were carried out until the total energy converged to better than <span>(10^{-5})</span> eV and the residual force on each atom was below 0.01 eV/Å.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178646","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}