Journal of Molecular Modeling最新文献

{"title":"Construction and validation of pharmacophore model of calcitonin gene-related peptide receptor antagonists using ligand- and structure-based approaches","authors":"Thangaraj Devadoss, Shvetank Bhatt, Punniyakoti Veeraveedu Thanikachalam, Pawan Gupta","doi":"10.1007/s00894-026-06975-2","DOIUrl":"10.1007/s00894-026-06975-2","url":null,"abstract":"<div><h3>Context</h3><p>Calcitonin gene-related peptide (CGRP) is a valid target for migraine disorder. Antagonizing the CGRP receptor elicits beneficial effects in migraine, although several CGRP receptor antagonists are currently available in clinical practice, a well-defined pharmacophore model has not yet been proposed. Particularly appropriate distances between the pharmacophoric elements are not reported. Therefore, a three-point pharmacophore model was constructed based on the common structural features present in the clinically available CGRP receptor antagonists. To evaluate the proposed pharmacophore elements and model, their presence is mapped onto the reported molecules, and the distances between the elements are measured. A total of 27 molecules is shortlisted based on CGRP receptor antagonistic potency. Among them, 21 molecules possessed the proposed pharmacophore elements, and in the remaining 6 molecules, only one pharmacophore element was not matched with the proposed model. The distances between the pharmacophore elements were measured; among the 21 molecules, only five molecules (<b>3, HTL0022562, BMS-694153, 19, and BMS-846372</b>) possessed slight to moderate deviations. Based on the proposed pharmacophore model, new molecules (<b>T1-T5</b>) were designed as CGRP receptor antagonists. To validate the proposed model, the clinically existing and designed molecules were docked into the active site of the CGRP receptor. In the designed molecules, <b>T3</b> (-10.3 kcal/mol) followed by <b>T5</b> (-9.8 kcal/mol) exhibited binding affinity. Though the docking score of these novel molecules is less as compared to standard molecules: 6ZHO-lig (-13.6 kcal/mol) and as Zavegepant (-11.3 kcal/mol). These molecules exhibit the common interactions (H-bonding with Thr2122 and pi-pi with Trp2121) as standard molecules. During MDS studies till 500 ns, standard molecules: 6ZHO-lig and Zavegepant followed the docking results of higher binding affinity as compared to novel designed molecules <b>T3</b> and <b>T5</b>. However, different MDS parameters exhibited satisfactory stability of these molecules into the active site of CGRP. The <b>T3</b> and <b>T5</b> molecules displayed satisfactory pharmacokinetic properties in the SwissADME prediction tool. Further, optimization of these early-stage hits is required to improve the binding affinity and ADME profile. The ligand- and structure-based approaches support the reliability of the proposed pharmacophore model. In conclusion, the constructed pharmacophore model will serve as a template for the design of new molecules as CGRP receptor antagonists.</p><h3>Methods</h3><p>The most common structural features of clinically available CGRP receptor antagonists were considered as pharmacophoric elements of CGRP receptor antagonists. Using ACDLABS-2021 2.1/3D Viewer (CHARMM parameterization) software, the distances between pharmacophore elements were measured. The designed molecules were tested for binding m","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":"149178535","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 Insights of Refrigerants (R-32, R-125, R-134a) In Amino acid based Ionic Liquids","authors":"Brundha Devi A,&nbsp;Sweta Jha,&nbsp;Praveenkumar Sappidi","doi":"10.1007/s00894-026-06999-8","DOIUrl":"10.1007/s00894-026-06999-8","url":null,"abstract":"<div><h3>Context</h3><p>The separation of refrigerant mixtures is an important challenge in the development of sustainable cooling technologies, and ionic liquids (ILs) have emerged as promising alternative absorbents because of their tunable physicochemical properties. In this work, molecular-level interactions between three hydrofluorocarbon refrigerants (R-32, R-125, and R-134a) and amino acid (AA)–based ILs were investigated to understand their separation behavior. The ILs consisted of tetrabutylphosphonium ([TBP]) as the common cation paired with leucine ([LEU]) and isoleucine ([ILE]) anions. Structural, dynamic, and thermodynamic analyses revealed distinct differences in the behavior of the refrigerants within the IL environment. Among the three refrigerants, R-32 exhibited self-diffusivity approximately one order of magnitude higher than that of R-125 and R-134a in both ILs, indicating greater molecular mobility. RDF and interaction analyses showed that the [TBP] cation forms stronger intermolecular interactions with the refrigerants than the amino acid anions. Free-energy calculations further demonstrated that R-134a exhibits approximately 75% more favorable (i.e., more negative) solvation free energy than R-32 in [TBP][ILE], suggesting a stronger affinity for this IL. These findings provide molecular-level insights into refrigerant-IL interactions and support the rational selection of amino acid–based ILs for efficient refrigerant separation.</p><h3>Methods</h3><p>MD simulations were performed to investigate the structural organization, diffusion behavior, and thermodynamic properties of refrigerants in amino acid–based ILs. Systems containing R-32, R-125, and R-134a dissolved in [TBP][LEU] and [TBP][ILE] were simulated under equilibrium conditions. Structural properties were characterized using RDF and coordination analyses, while molecular mobility was evaluated using MSD and self-diffusion coefficient calculations. Thermodynamic behavior was examined by calculating the solvation free energy of the refrigerants in each IL. All MD simulations and trajectory analyses were carried out using the force field and simulation software described in the manuscript.</p><h3>Graphical abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></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":"149178704","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":"Sequential oxidative transformation of the chalcopyrite (001)-S surface by H(_{2})O and O(_{2}): electronic structure insights from DFT calculations","authors":"Guilherme Randow Nascimento,&nbsp;Selma Fabiana Bazan,&nbsp;Heitor Avelino de Abreu,&nbsp;Guilherme Ferreira de Lima","doi":"10.1007/s00894-026-06972-5","DOIUrl":"10.1007/s00894-026-06972-5","url":null,"abstract":"<div><h3>Context</h3><p>Chalcopyrite (CuFeS<span>(_{2})</span>) is the primary copper mineral worldwide, yet its hydrometallurgical extraction remains severely hindered by slow leaching kinetics, commonly attributed to surface passivation. Understanding the atomistic events governing the early stages of chalcopyrite surface oxidation is essential for developing more efficient and sustainable copper extraction technologies. In this work, a four-step oxidative mechanism on the CuFeS<span>(_{2})</span> <span>({textbf {(001)}})</span>-S surface was investigated and characterized electronically. O<span>(_{2})</span> co-adsorption with H<span>(_{2})</span>O on Fe sites triggers charge transfer into antibonding <span>(varvec{uppi }^{varvec{*}})</span> orbitals, activating O<span>(_{2})</span> into a superoxide-like intermediate. Subsequent proton transfer yields Fe-OOH and Fe-OH species, followed by the dissociative adsorption of a second H<span>(_{2})</span>O molecule onto the S-S dimer, forming S<span>(_{2})</span>OH intermediates accompanied by S-Cu bond elongation from <span>({textbf {2.35}})</span> to <span>({textbf {3.62}})</span> Å. In the final step, H<span>(_{2})</span>O adsorption on copper drives significant interfacial charge redistribution, with electronic states near the Fermi level progressively localized on oxygenated intermediates. Overall, iron, copper, and sulfur play distinct but electronically coupled roles in the progressive oxidative transformation of the chalcopyrite surface, providing atomistic insight into the early stages of passivation under hydrometallurgical conditions.</p><h3>Methods</h3><p>All calculations were performed within the DFT+U framework using the PBE functional and a Hubbard correction (<span>({textbf {U = 2}})</span> eV for Fe<span>(^{3+})</span>), as implemented in <span>Quantum ESPRESSO</span> (v7.3). The CuFeS<span>(_{2})</span> (001)-S surface was modeled as a periodic slab with a <span>({textbf {15}})</span> Å vacuum layer, employing ultrasoft pseudopotentials and a plane-wave kinetic energy cutoff of <span>({textbf {60}})</span> Ry. Brillouin zone sampling used <span>({textbf {1}}varvec{times } {textbf {1}}varvec{times } {textbf {1}})</span> and <span>({textbf {4}}varvec{times } {textbf {4}}varvec{times } {textbf {1}})</span> <span>({varvec{k}})</span>-point grids for geometry optimizations and electronic property calculations, respectively. Antiferromagnetic ordering along the crystallographic <i>c</i>-axis was adopted throughout. Electronic structure characterization was performed through Bader charge analysis, projected density of states (PDOS), charge density difference maps, and integrated local density of states (ILDOS).</p><h3>Graphical abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></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":"https://link.springer.com/content/pdf/10.1007/s00894-026-06972-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178547","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":"DFT, MC, and MD investigation of H₂MoO₄ adsorption on model AISI 304 stainless steel surfaces: effects of inhibitor loading, temperature, and confined shear","authors":"Zahra Ghorbanzadeh,&nbsp;Milad Rezaei","doi":"10.1007/s00894-026-07001-1","DOIUrl":"10.1007/s00894-026-07001-1","url":null,"abstract":"<div><h3>Context</h3><p>Molybdate-based inhibitors are promising candidates for corrosion protection of stainless steels; however, the molecular mechanisms controlling their adsorption behavior under different interfacial conditions remain insufficiently understood. This study investigates the adsorption behavior of H₂MoO₄ on model surfaces relevant to AISI 304 stainless steel, focusing on the effects of inhibitor loading, temperature, and confined shear. Electronic-structure analysis revealed that oxygen-containing regions act as electron-donating sites, whereas the Mo-centered region exhibits electron-accepting characteristics. Molecular simulations showed favorable adsorption interactions on Fe(110) and a representative Cr₂O₃–Fe₂O₃–NiO passive oxide model. Increasing inhibitor loading enhanced the overall adsorption interaction, while temperature affected adsorption energetics without a monotonic trend. Under confined shear conditions, H₂MoO₄ maintained a predominantly parallel orientation relative to the surface, indicating stable adsorption behavior under the investigated conditions.</p><h3>Methods</h3><p>Density functional theory (DFT), Monte Carlo (MC), and molecular dynamics (MD) simulations were performed using Materials Studio. DFT calculations were carried out using the DMol³ module with the GGA/PBE functional and DNP basis set. HOMO, LUMO, and condensed Fukui function analyses were used to evaluate molecular reactivity. Adsorption configurations were obtained using Monte Carlo simulations with the Metropolis method and Universal force field. MD simulations were performed using the Forcite module with the Universal force field under the NVT ensemble to analyze adsorption behavior under different inhibitor loading, temperature, and confined-shear conditions.</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":"149178669","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":"Substituent-directed tuning of energetic performance and sensitivity in tetrazolo[1,2,4]triazine-based high-energy materials: a computational investigation","authors":"Arzoo Gupta,&nbsp;Renu Rani,&nbsp;Vikas D. Ghule","doi":"10.1007/s00894-026-06986-z","DOIUrl":"10.1007/s00894-026-06986-z","url":null,"abstract":"<div><h3>Context</h3><p>A nitrogen-rich fused tetrazolo[1,2,4]triazine framework was employed as a rigid and highly conjugated energetic backbone to design six energetic derivatives (A1–A6) bearing amino (–NH₂), nitramino (–NHNO₂), nitro (–NO₂), and mixed substituents. All tailored tetrazolo[1,2,4]triazine compounds exhibit high positive solid-phase heats of formation (459.19–652.40 kJ/mol), substantially exceeding those of TNT and RDX. Incorporation of oxygen-rich explosophoric groups progressively improves oxygen balance, density, and detonation performance, with compound A5 containing two –NO₂ groups exhibiting the highest detonation velocity (9.18 km/s) and detonation pressure (38.3 GPa). Bond dissociation energy, electron localization, interaction region indicator, and quantum theory of atoms in molecules analyses reveal that substitution of -NH₂, -NO₂, and -NHNO₂ groups strongly modulates bond strength, charge distribution, and intermolecular interactions. The fused tetrazolo[1,2,4]triazine framework retains aromaticity and π-electron delocalization despite functional group modification. Overall, the results demonstrate that mixed -NH₂ and -NHNO₂/-NO₂ substitution on tetrazolo[1,2,4]triazine backbone provides an effective strategy for tuning the energy–performance–sensitivity balance, with amino groups favoring reduced sensitivity and nitro/nitramino groups enhancing energetic performance.</p><h3>Methods</h3><p>The optimization and energy calculations of designed tetrazolo[1,2,4]triazine derivatives were performed at the B3LYP/6-311 + G(d,p) and M06-2X/def2-TZVPP levels of theory, utilizing the Gaussian 09 software package. The molecular surface properties were analyzed by employing Multiwfn software. The EXPLO5 (V7.01.01) thermochemical code was used to predict the detonation properties.</p><h3>Graphical abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149132945","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":"Machine learning prediction of thermal sensitivity for energetic materials based on multi-source feature fusion","authors":"Xuan Zhang,&nbsp;Zheng-Tang Liu,&nbsp;Qi-Jun Liu","doi":"10.1007/s00894-026-06996-x","DOIUrl":"10.1007/s00894-026-06996-x","url":null,"abstract":"<div><h3>Context</h3><p>Thermal sensitivity, typically characterized by the thermal decomposition temperature (<i>T</i>_d), is a key parameter that reflects the thermal stability and safety of energetic materials, providing essential guidance for their engineering applications, storage, and transportation. However, traditional experimental determination methods suffer from long cycles, high costs, and significant hazards, rendering them unsuitable for efficient, large‑scale material screening. To address this bottleneck, this study systematically compares the predictive capabilities of topological features, calculated features, and their multi‑source fused features for estimating <i>T</i>_d. The results demonstrate that using only topological features in a Random Forest (RF) model yields an <i>R</i>² of 0.721, and the RMSE and MAE were 39.844 °C and 29.502 °C, respectively, whereas relying solely on calculated features gives considerably lower performance (<i>R</i>² = 0.462, RMSE = 42.391 °C, MAE = 34.836 °C). The fused features significantly improves prediction accuracy, achieving a test set <i>R</i>² of 0.799 and reducing RMSE and MAE to 31.585 °C and 24.443 °C, respectively. This enhancement is consistently observed across various machine learning models, including SVR, KRR, and AdaBoost, confirming the universal complementarity between the two feature types. Among the four models, RF combined with the SPXY sample partitioning method delivers the best overall predictive performance, providing a reliable computational tool and methodological framework for rapid and accurate <i>T</i>_d prediction of energetic materials.</p><h3>Methods</h3><p>All machine learning modeling and data processing were carried out in Python. Molecular topological features were generated using RDKit 2024.9.6. The crystal structures were obtained from the Cambridge Crystallographic Data Centre (CCDC), and subsequent first‑principles calculations were performed with the Cambridge Serial Total Energy Package (CASTEP) module in Materials Studio, employing the Perdew–Burke–Ernzerhof (PBE) functional within the generalized gradient approximation (GGA) with DFT‑D dispersion correction and norm‑conserving pseudopotentials. A plane‑wave cutoff energy of 830 eV was adopted, and geometry convergence criteria were set as follows: energy change &lt; 5 × 10⁻⁶ eV/atom, maximum force &lt; 0.01 eV/Å, maximum stress &lt; 0.02 GPa, and maximum displacement &lt; 5 × 10⁻⁴ Å. Single‑molecule calculations employed DMol³ with the same PBE functional and DNP basis set, with Grimme’s D2 dispersion correction. The SCF convergence thresholds were set to 1 × 10⁻⁵ Ha for energy, 0.002 Ha/Å for force, and 0.005 Å for displacement.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149132942","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 investigation of fluorination sites effects on the photovoltaic performance of D-π-A donor materials","authors":"Wenying Du,&nbsp;Dongmei Wang,&nbsp;Yueling Wang,&nbsp;Jieyi Liu","doi":"10.1007/s00894-026-06927-w","DOIUrl":"10.1007/s00894-026-06927-w","url":null,"abstract":"<div><h3>Context</h3><p>Fluorination is an effective strategy for precisely regulating the energy levels, molecular conformations, and optoelectronic properties of donor materials in organic solar cells (OSCs), thereby significantly impacting charge transport, light absorption, and device efficiency. In this work, three D-π-A-type fluorinated isomers —PBT-BDT-F, PffBT-BDT, and PffBT-BDT-FT— were theoretically investigated to elucidate the effects of different fluorine substitution positions on photovoltaic performance. The results demonstrate that fluorination on the donor unit enhances molecular planarity, light absorption, and charge transport to a greater extent than substitution on the acceptor unit or π-bridge, providing valuable guidance for optimizing fluorination sites in D-π-A type donor materials.</p><h3>Methods</h3><p>Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were performed using Gaussian 09. Ground-state geometries were optimized at the B3P86/6-31G(d) level, and excited-state properties were calculated at the PBE1PBE/6-31G(d) level in CHCl₃ solvent with the CPCM solvation model. Molecular geometries, spectral properties, electrostatic potentials, exciton binding energies, reorganization energies, and charge transfer rates were systematically calculated to evaluate the photovoltaic performance of the three isomers. Molecular visualizations were generated using GaussView 6.0, VMD, and Multiwfn.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149132943","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 synergistic mechanism of coordination compensation and structural evolution in ammonium carnallite","authors":"Yushuang Du,&nbsp;Han Zhou,&nbsp;Shengting Li,&nbsp;Rongyan Wang,&nbsp;Ze Sun,&nbsp;Guimin Lu","doi":"10.1007/s00894-026-06989-w","DOIUrl":"10.1007/s00894-026-06989-w","url":null,"abstract":"<div><h3>Context</h3><p>The preparation of anhydrous magnesium chloride is severely hindered by hydrolysis during thermal dehydration, while the ammonium carnallite route is widely adopted to mitigate this issue. However, the atomistic mechanism by which NH₄Cl regulates dehydration and suppresses hydrolysis remains unclear. In this work, a unified mechanism is revealed in which Cl^⁻ ions compensate for coordination vacancies in partially dehydrated magnesium species, while the collapse of the NH₄Cl framework facilitates water migration and inhibits rehydration, thereby enhancing structural stability. Hydrogen bonding promotes the initial removal of coordinated water, whereas progressive structural collapse lowers migration barriers and facilitates water migration. Thermodynamic analysis and thermal experiments further confirm that most crystallization water is removed above 210 °C and that controlled heating below 240 °C effectively limits hydrolysis.</p><h3>Methods</h3><p>Density functional theory (DFT) calculations were performed using the PBE functional within the generalized gradient approximation and a plane-wave basis set as implemented in VASP, with the projector-augmented wave (PAW) method and DFT-D3 dispersion corrections. Transition states were identified using the climbing image nudged elastic band (CI-NEB) method. The computational results were combined with thermodynamic analysis and thermal experiments to validate the proposed mechanism and to evaluate dehydration behavior under different temperature conditions.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149132786","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":"Valence and core ionization energies of atoms and small molecules using variational Monte Carlo with explicit correlation and Slater-type basis sets","authors":"Josué de Jesus Oliveira Araújo,&nbsp;Pedro Oliveira Mariz de Carvalho,&nbsp;Rogério Custodio","doi":"10.1007/s00894-026-06987-y","DOIUrl":"10.1007/s00894-026-06987-y","url":null,"abstract":"<div><h3>Context</h3><p>Reliable prediction of both valence and core ionization energies remains challenging because these processes involve different balances of electron correlation, orbital relaxation, and basis-set flexibility. In this work, we assess whether variational Monte Carlo (VMC) with explicit correlation and compact Slater-type basis sets can provide accurate ionization energies without fitting to experimental data. As expected from their greater flexibility, double-zeta (DZ) and Hartree–Fock limit (HFL) Slater-type basis sets provide better agreement with experiment than single-zeta (SZ), particularly for atomic ionizations and some molecular cases. For H₂O, VMC/HFL achieves a mean absolute error (MAE) of 0.42 eV, comparable to 0.39 eV from CCSD-GF/TZ2P; for CO, VMC/HFL gives an MAE of 0.67 eV. Removing the polarization functions has little effect on the core ionization energies. The calculations without polarization functions yield overall mean absolute errors of 0.65 eV for H_₂O and 0.67 eV for CO. The accuracy arises from variational optimization of the explicit-correlation parameters without fitting to experimental ionization energies, supporting VMC as a practical approach for ionization-energy estimates and for extension to larger systems.</p><h3>Methods</h3><p>Hartree–Fock wave functions with Slater-type basis sets were used as trial wave functions. For atoms, the SZ, DZ, and HFL orbital expansions were taken from the literature. For neutral molecules, Hartree–Fock calculations were performed with Gaussian 09 using Slater-type basis sets from the literature to generate the corresponding LCAO coefficients. Single valence and core ionization energies were computed with the VMC method using a nine-parameter Boys–Handy explicit correlation factor and Slater-type basis sets, with and without polarization functions. The VMC calculations and parameter optimizations were performed with computer programs developed by the authors’ research group.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06987-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149132790","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":"ReaxFF molecular dynamics study on the decomposition mechanism of AlH3 in NO2 gaseous environment","authors":"Jun Jiang,&nbsp;Shui-Ping Zhou,&nbsp;Xiang Hu,&nbsp;Nian Yang,&nbsp;Sen Xu,&nbsp;Xue-Hai Ju","doi":"10.1007/s00894-026-06988-x","DOIUrl":"10.1007/s00894-026-06988-x","url":null,"abstract":"<div><h3>Context</h3><p>As an intermediate product of propellant decomposition, NO₂ can react with AlH₃ nanoparticles (AHNPs) and significantly influence the overall combustion characteristics; however, the underlying decomposition mechanism remains unclear. In this study, ReaxFF molecular dynamics (RMD) simulations were performed to investigate the decomposition and ignition processes of AHNPs in NO₂ gaseous environment. The reaction mechanism of NO₂ decomposition to N₂ is revealed at the atomic level, and the promotional role of H, Al, and O species spilling over from AHNPs in facilitating NO₂ decomposition is clarified. Furthermore, the coupled combustion behavior of dual AHNPs is analyzed. The melting of the two AHNPs delays nanoparticle cracking, particularly at low temperatures. The apparent activation energies for NO₂ decomposition are 26.2 kJ/mol in S₁, 18.8 kJ/mol in S₂ and 23.6 kJ/mol in S₃, respectively, indicating the promoting effect of the dual AHNPs in S₂. Collectively, these microscopic insights clarify the gas-phase NO₂ and AHNPs reaction mechanism and the influence of particle number, providing a mechanistic basis for understanding the initial decomposition behavior of composite propellants.</p><h3>Methods</h3><p>The generalized gradient approximation with GGA-PBE method was used to optimize NO₂ molecular geometry using Dmol3 package. The models containing AHNPs and NO₂ are built by PACKMOL software. ReaxFF molecular dynamics simulations were used to study the decomposition of AHNPs in NO₂ atmosphere. The ReaxFF parameters are from Mei which are used to describe AlH₃. The bond order truncation cutoff is set as 0.3 to facilitate the determination of chemical bonds and products. All simulations were performed using LAMMPS software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149132717","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}