Journal of Molecular Modeling最新文献

{"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}

{"title":"A new method to build an initial configuration for molecular modeling","authors":"Alexander V. Teplukhin","doi":"10.1007/s00894-026-06998-9","DOIUrl":"10.1007/s00894-026-06998-9","url":null,"abstract":"<div><h3>Context</h3><p>Generally, the initial structures of large simulated systems containing discoid, tree-like, fiber-like etc. molecules obtained using conventional methods have very low density. So, their compression to target values is a special stage of data preparation, performed by multi-step protocols that require a lot of calendar and computer time. A new method for generating initial configurations of large-scale molecular models is presented, using the concept of “parallel 4D universes” to densely pack components into the basic cell of the simulated system. Examples of constructing simulated systems containing millions of atoms are given.</p><h3>Methods</h3><p>Monte Carlo simulations were performed using Metropolis sampling procedure for NVT ensemble. A software package was developed by author implementing a domain decomposition strategy to speed up the calculations. Short-range atom–atom potential functions were used to model van der Waals and electrostatic interactions as well as quadratic potential to incorporate the covalent bonds/angles deformation energy and the penalty functions to separate overlapping molecular fragments.</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":"149178605","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":"Force transfer in the glycosylated human CLEC-2–podoplanin PLAG interface","authors":"Yao Zhang,&nbsp;Han Ni Soe,&nbsp;Zhipeng Xu","doi":"10.1007/s00894-026-07010-0","DOIUrl":"10.1007/s00894-026-07010-0","url":null,"abstract":"<div><h3>Context</h3><p>Platelet C-type lectin-like receptor 2 (CLEC-2) binds an O-glycosylated podoplanin PLAG-region peptide through a side-face interface. The crystal structure defines the local glycan and peptide interactions, while their respective contributions to interfacial stability and mechanical load transmission require further mechanistic resolution. Here, atomistic simulations of the experimentally resolved CLEC-2–podoplanin glycopeptide complex were used to examine how these two ligand components contribute to interfacial mechanics. The sialylated Thr52 glycan formed a persistent recognition anchor, whereas the podoplanin Glu47/Asp48 segment together with the CLEC-2 Arg107/Arg152/Arg157 region constituted the principal load-transfer pathway during normal pulling. Consistently, deglycosylation produced smaller changes in equilibrium contacts and constant-force survival lower bounds than mutations of the acidic peptide residues or receptor arginines. These results indicate a functional separation within the interface, in which the Thr52 glycan primarily stabilizes local recognition, while interactions between the acidic peptide residues and CLEC-2 arginines dominate mechanical load transmission.</p><h3>Methods</h3><p>The 3WSR CLEC-2–podoplanin glycopeptide complex was simulated in GROMACS using CHARMM36m protein and CHARMM carbohydrate parameters. Independent equilibrium replicas were used to assess complex stability, periodic-image separation, and peptide and glycan contact occupancies. Constant-velocity SMD was retained as a relative forced separation comparison, while constant-force SMD was used as a lower-bound survival comparison under normal load. The analysis includes WT, deglycosylated, podoplanin E47A/D48A, CLEC-2 R152A/R157A, and single CLEC-2 R107A, R152A, and R157A systems.</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":"149178684","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":"Integrating quantum chemical descriptors and Monte Carlo simulations for analytical quality assurance of antineoplastic agents under gamma sterilization","authors":"Abdelmoneim Saleh,&nbsp;Nayim Sepay,&nbsp;Zehra Üstün,&nbsp;Ümit Kara","doi":"10.1007/s00894-026-07013-x","DOIUrl":"10.1007/s00894-026-07013-x","url":null,"abstract":"<div><h3>Context</h3><p>The sterilization of antineoplastic agents remains a critical challenge due to the high sensitivity of active pharmaceutical ingredients (APIs) to ionizing radiation. This study proposes a virtual validation protocol (VVP)—introduced here as a conceptual, computational screening framework rather than a regulatory recognized validation procedure—intended to support analytical quality assurance by prioritizing and guiding experimental stability testing rather than replacing it, thereby reducing the reliance on extensive trial-and-error laboratory work. Obtained results identify mercaptopurine as a significant outlier due to the “trap effect” induced by its sulfur-containing structure (<i>Z</i>_eff  = 14.20 at 0.015 MeV), which causes rapid radiation reducing. In line with the ISO 11137 dose homogeneity principle (± 10% acceptance criterion), a computationally derived packaging-thickness threshold of 1.80 mm is predicted for mercaptopurine, subject to experimental confirmation. In contrast, compounds with lower effective atomic numbers, such as capecitabine, permit greater packaging flexibility, with thickness limits up to 3.80 mm. Additionally, the projected adiabatic temperature rise remains below 37 °C in all cases, well beneath the thresholds of conventional thermal sterilization, indicating that the process avoids thermal degradation and can be regarded as a “cold” process in the thermal sense. This thermal finding concerns heat-induced damage only; preservation of chemical integrity against direct radiolysis is a separate question that requires experimental confirmation. This approach provides a sustainable, cost-effective, and non-destructive roadmap for pharmaceutical quality control.</p><h3>Methods</h3><p>The protocol integrates density functional theory (DFT) and Monte Carlo (MCNPX) simulations. Molecular structures were optimized at the ωB97XD/def2TZVP level to determine spectroscopic behaviors and evaluate chemical reactivity through HOMO–LUMO energy gaps. Simultaneously, radiation interaction parameters were modeled across a 0.015–15 MeV energy range and validated against theoretical XCOM data.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178714","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":"Atomic-level engineering of multifunctional BixC16 nanocages for hydrogen storage, thermoelectric energy conversion, spintronics, and nanoelectronic applications","authors":"Belqees Hassan,&nbsp;Manahil E. E. Mofdal","doi":"10.1007/s00894-026-07012-y","DOIUrl":"10.1007/s00894-026-07012-y","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;The development of stable carbon-based nanomaterials with tunable electronic, magnetic, thermoelectric, and hydrogen storage properties is important for emerging energy conversion and nanoelectronic technologies. Here, Bi-doped C&lt;sub&gt;16&lt;/sub&gt; nanocages, Bi&lt;sub&gt;x&lt;/sub&gt;C&lt;sub&gt;16&lt;/sub&gt; (&lt;i&gt;x&lt;/i&gt; = 1–4), corresponding to Bi concentrations of 5.8, 11.1, 15.7, and 20.0 wt%, were systematically investigated. Negative formation energies, phonon spectra without imaginary modes, and 300 K ab initio molecular dynamics simulations confirm the energetic, dynamical, and thermal stability of the considered nanocages. Increasing Bi incorporation produces progressive structural expansion and bond elongation while maintaining the integrity of the C&lt;sub&gt;16&lt;/sub&gt; framework. Strong Bi-6p/C-2p hybridization modifies the electronic structure and enhances spin polarization. The magnetic anisotropy energy and Curie temperature increase with Bi concentration, reaching approximately 3.8 meV cell&lt;sup&gt;−1&lt;/sup&gt; and 920 K, respectively, for Bi&lt;sub&gt;x&lt;/sub&gt;C&lt;sub&gt;16&lt;/sub&gt;. Bi doping also enhances thermoelectric performance, with a maximum Seebeck coefficient of 340 μV K⁻&lt;sup&gt;1&lt;/sup&gt; and a peak ZT of 2.78 at 1200 K&lt;b&gt;.&lt;/b&gt; Hydrogen storage calculations yield maximum gravimetric and volumetric capacities of 6.7 wt% and 67.4 g H&lt;sub&gt;2&lt;/sub&gt; L⁻&lt;sup&gt;1&lt;/sup&gt;, respectively. Among the investigated systems, it exhibits the most favorable combination of stability, magnetic properties, thermoelectric performance, and hydrogen storage capability, highlighting its potential for multifunctional energy and nanoelectronic applications.&lt;/p&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;The structural, electronic, magnetic, thermodynamic, hydrogen storage, and thermoelectric properties of Bi-doped C&lt;sub&gt;16&lt;/sub&gt; nanocage were investigated using spin-polarized density functional theory (DFT) calculations implemented in the CASTEP package [1, 2]. The electron exchange-correlation interactions were described using the generalized gradient approximation (GGA) within the Perdew–Burke–Ernzerhof (PBE) functional. The interaction between valence electrons and ionic cores was treated using ultrasoft pseudopotential, while the electronic wave functions were expanded using a plane-wave basis set with a kinetic energy cutoff of 600 eV, which was confirmed to provide converged total energies and forces [3]. Geometry optimization was performed using the Broyden–Fletcher–Goldfarb–Shanno (BFGS) minimization algorithm until the convergence criteria of 1.0 × 10⁻&lt;sup&gt;6&lt;/sup&gt; eV atom⁻&lt;sup&gt;1&lt;/sup&gt; for total energy, 0.01 eV Å⁻&lt;sup&gt;1&lt;/sup&gt; for maximum force, 0.02 GPa for stress, and 5.0 × 10⁻&lt;sup&gt;4&lt;/sup&gt; Å for atomic displacement were simultaneously satisfied. The isolated Bi-doped C&lt;sub&gt;16&lt;/sub&gt; nanocage was modeled within a 20 × 20 × 20 Å&lt;sup&gt;3&lt;/sup&gt; cubic supercell to eliminate interactions between periodic images. Owing to the molecular nature of the nanocage, Brillouin-zone integration was performed using a &lt;i&gt;Γ&lt;/i&gt;-poi","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178545","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":"Stacking-sequence-dependent plasticity and subsurface damage evolution in nanometric cutting of hexagonal SiC","authors":"Binbin Meng","doi":"10.1007/s00894-026-07006-w","DOIUrl":"10.1007/s00894-026-07006-w","url":null,"abstract":"<div><h3>Context</h3><p>Hexagonal SiC is a widely used third-generation semiconductor material that can be classified into several polytypes (2H, 4H, 6H and 8H) based on stacking sequence. Since crystal structure directly determines machinability, understanding the influence of stacking sequence is essential for optimising ultra-precision machining. In this study, abrasive scratching simulations were performed to systematically investigate the relationships among stacking structure, machinability and micro-slip behaviour. The results reveal that hexagonal SiC exhibits distinct fine slip behaviour, pronounced stacking-structure selectivity and local disorder characteristics, clarifying the differences in machinability across various polytypes.</p><h3>Methods</h3><p>All simulations were performed using LAMMPS with the ABOP many-body potential to describe Si–C interactions. The abrasive was modelled as a deformable body with a negative rake angle of -35.5°. The SiC workpiece had an off-axis angle of 4° relative to the basal plane, with the C-plane (000–1) as the machined surface and scratching along the [01–10] direction. Simulation results were visualised and analysed using OVITO.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178644","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":"Systematic investigation of density functional theory methods for diorganotin 1,3-dithiole-2-thione-4,5-dithiolate complexes, R2Sn(dmit)","authors":"Raíssa Ribeiro Domingues Brum,&nbsp;Jonathan B. Brum,&nbsp;Glaucio Braga Ferreira","doi":"10.1007/s00894-026-06990-3","DOIUrl":"10.1007/s00894-026-06990-3","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;Organotin complexes have been extensively studied due to their versatile structural features and potential applications in catalysis, materials science, and bioinorganic chemistry. Among them, compounds containing Sn–S interactions are of particular interest, as the tin–sulfur bond strongly affects both the stability and the electronic properties of the complexes. In addition, theoretical studies on 1,3-dithiole-2-thione-4,5-dithiolate systems have attracted considerable attention because of their potential technological applications.&lt;/p&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;Density functional theory calculations were performed to evaluate the performance of different exchange–correlation functionals in describing the structural and spectroscopic properties of R&lt;sub&gt;2&lt;/sub&gt;Sn(dmit) complexes. A total of 36 levels of theory were assessed for geometry optimization by combining 12 density functionals with three basis sets (def2-SVP, def2-TZVP, and def2-QZVP). The calculated geometric parameters were compared with experimental crystallographic data using statistical metrics including mean deviation, mean absolute deviation, standard deviation, and root mean square deviation. The results show that the choice of exchange–correlation functional has a greater influence on the accuracy of the optimized geometries than the basis-set size, with PBE/def2-SVP, BP86/def2-SVP, and M06-2X/def2-TZVP providing the best overall agreement with the experimental structures. Harmonic vibrational frequencies were corrected by linear scaling and compared with the experimental infrared spectra, demonstrating that BP86 and PBE consistently produced the lowest statistical deviations, whereas increasing the basis-set size beyond the triple-ζ level provided only marginal improvements. The &lt;sup&gt;119&lt;/sup&gt;Sn NMR chemical shifts were calculated using the ZORA, DKH, and X2C relativistic Hamiltonians. The double-hybrid B2PLYP-D3 functional yielded the lowest absolute errors overall within the investigated dataset. For most global and range-separated hybrid functionals (e.g., CAM-B3LYP, M06-2X, and ωB97X-D3), as well as the GGA functional BP86, the X2C Hamiltonian provided satisfactory agreement with the experimental data within the investigated dataset, yielding &lt;i&gt;R&lt;/i&gt;&lt;sup&gt;2&lt;/sup&gt; values of 0.984-0.986, regression slopes moderately close to unity, and low mean absolute deviations. The chemical-shift range covered by the investigated systems represents only a subset of the full &lt;sup&gt;119&lt;/sup&gt;Sn chemical-shift range, reflecting the specific chemical space considered in this study. Overall, the results demonstrate that computationally efficient GGA functionals provide a favorable balance between accuracy and computational cost for geometry optimization and vibrational frequencies, whereas the prediction of &lt;sup&gt;119&lt;/sup&gt;Sn NMR chemical shifts is strongly influenced by the choice of relativistic treatment, B2PLYP-D3/ZORA being the top-performing individual protocol and X2C provi","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06990-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178685","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":"GMUPC: a new package for global-minimum search of large uranyl peroxide clusters with machine learning potentials and DFT calculations","authors":"Yu Cheng,&nbsp;Xin-Yu Dai,&nbsp;Shu-Wen Zhang,&nbsp;Yang-Yang Zhang","doi":"10.1007/s00894-026-07000-2","DOIUrl":"10.1007/s00894-026-07000-2","url":null,"abstract":"<div><h3>Context</h3><p>This study presents the development of the GMUPC package, which integrates machine learning potentials (MLPs) to efficiently and accurately identify the possible structures of fullerene-like uranyl peroxide U_<i>n</i> clusters spanning a broad size range from U₂₀ to U₁₀₂₆₀. The computational workflow incorporates symmetric structure generation from Wyckoff positions, isomer perturbation, duplicate structure removal, and four distinct global optimization algorithms, including the particle swarm optimization (PSO), genetic algorithm (GA), standard basin-hopping (BH), and improved basin-hopping (IBH), to systematically explore the potential energy surfaces of large uranyl peroxide systems. We note that the symmetry-seeded structural generation within GMUPC prioritizes high-symmetry cage topologies for computational efficiency; highly distorted, low-symmetry metastable isomers with significant steric strain are less frequently sampled compared to carbon fullerene search algorithms, representing a defined limitation of the present computational framework. Structural explorations uncover non-classical fullerene-like U₂₂ clusters with unique topological structure and a series of giant icosahedral fullerene-like U_60<i>n</i>² (<i>n</i> = 1~12) clusters adhering to the isolated pentagon rule (IPR), with consistent retention of 12 pentagonal faces across all cluster sizes. Geometry analyses establish scalable evolutionary trends in cluster radius, surface area, and volume as functions of uranium atomic count, while energy analyses reveal a monotonic decrease in total energy per uranium atom with increasing cluster size. The GMUPC package enables unprecedented exploration of uranyl peroxide cluster chemistry across size scales previously inaccessible via conventional computational methods, providing atomic-level insights into structure-energy relationships and possible self-assembly principles that bridge fundamental cluster science and nuclear materials chemistry.</p><h3>Methods</h3><p>In the present study, the geometrical structures of fullerene-like uranyl peroxide U_<i>n</i> (<i>n</i> = 20~10,260) clusters were systematically explored to identify their possible thermodynamically stable geometries. Global-minimum structural searches of U_<i>n</i> (<i>n</i> = 20~60) clusters with even number of uranium atoms were independently performed using two advanced computational approaches: the recently developed GMUPC code interfaced with the multi-atomic cluster expansion (MACE) machine learning potential. For high-accuracy structural refinement, all low-energy isomers derived from preliminary searches were further re-optimized using density functional theory (DFT). The searched low-lying isomers of U₂₂ clusters were re-optimized at the DFT Perdew-Burke-Ernzerhof (PBE) functional by using the CP2K (v2024.3) package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178693","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}