Pub Date : 2026-01-07DOI: 10.1007/s00894-025-06617-z
Ayoub Lahmidi, Soumia Chliyah, Sanaa Rabii, Samir Chtita, M’hammed EL Kouali, Abdelkbir Errougui
Context
Understanding the behavior of potassium carbonate (K2CO3) in water is essential for improving its performance in various chemical and industrial applications. The physicochemical properties of K2CO3 aqueous solutions determine its reactivity, stability, and efficiency in processes such as CO2 capture and alkaline electrochemistry. In this study, we combined molecular dynamics simulations and spectroscopic experiments to elucidate the microstructural, dynamic, and dielectric behaviors of the {K2CO3–H2O} system across concentrations ranging from 0.11 to 1.07 mol.kg−1 at T = 298.15 K. The analyses reveal strong ion-water correlations, coordination changes within hydration shells, and concentration-dependent variations in ionic mobility and dielectric constant. Experimental FTIR and NMR measurements validated the simulated structures and provided deeper insights into the hydration mechanisms and ion–water interactions governing the dissolution and transport properties of K2CO3 in water.
Methods
Classical molecular dynamics simulations were performed using GROMACS 2020.6 with the CHARMM36 force field for ions and the SPC/E water model. Ionic interactions were modeled through long-range Coulombic and short-range Lennard–Jones potentials. Systems spanning 0.11–1.07 mol.kg−1 were equilibrated for 100 ns in both NVT and NPT ensembles, followed by 100 ns production runs at 298 K and 1 bar using the PME algorithm for electrostatics. FTIR spectra were recorded on a Spectrum Two instrument in ATR mode over the 400–4000 cm−1 range, and 13C NMR spectra were acquired using a JEOL 500 MHz spectrometer in D2O, providing experimental validation of the simulation-derived structural insights.
{"title":"Molecular dynamics simulations and spectroscopic study of the microstructural solvation shells, transport, and dielectric properties of the {K2CO3–H2O} system at various concentrations","authors":"Ayoub Lahmidi, Soumia Chliyah, Sanaa Rabii, Samir Chtita, M’hammed EL Kouali, Abdelkbir Errougui","doi":"10.1007/s00894-025-06617-z","DOIUrl":"10.1007/s00894-025-06617-z","url":null,"abstract":"<div><h3>Context</h3><p>Understanding the behavior of potassium carbonate (K<sub>2</sub>CO<sub>3</sub>) in water is essential for improving its performance in various chemical and industrial applications. The physicochemical properties of K<sub>2</sub>CO<sub>3</sub> aqueous solutions determine its reactivity, stability, and efficiency in processes such as CO2 capture and alkaline electrochemistry. In this study, we combined molecular dynamics simulations and spectroscopic experiments to elucidate the microstructural, dynamic, and dielectric behaviors of the {K<sub>2</sub>CO<sub>3</sub>–H<sub>2</sub>O} system across concentrations ranging from 0.11 to 1.07 mol.kg<sup>−1</sup> at T = 298.15 K. The analyses reveal strong ion-water correlations, coordination changes within hydration shells, and concentration-dependent variations in ionic mobility and dielectric constant. Experimental FTIR and NMR measurements validated the simulated structures and provided deeper insights into the hydration mechanisms and ion–water interactions governing the dissolution and transport properties of K<sub>2</sub>CO<sub>3</sub> in water.</p><h3>Methods</h3><p>Classical molecular dynamics simulations were performed using GROMACS 2020.6 with the CHARMM36 force field for ions and the SPC/E water model. Ionic interactions were modeled through long-range Coulombic and short-range Lennard–Jones potentials. Systems spanning 0.11–1.07 mol.kg<sup>−1</sup> were equilibrated for 100 ns in both NVT and NPT ensembles, followed by 100 ns production runs at 298 K and 1 bar using the PME algorithm for electrostatics. FTIR spectra were recorded on a Spectrum Two instrument in ATR mode over the 400–4000 cm<sup>−1</sup> range, and <sup>13</sup>C NMR spectra were acquired using a JEOL 500 MHz spectrometer in D<sub>2</sub>O, providing experimental validation of the simulation-derived structural insights.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145904422","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}
Pub Date : 2026-01-06DOI: 10.1007/s00894-025-06592-5
Yunju Zhang, Meilian Zhao, Cen Yao, Zhiguo Wang, Yuxi Sun
Context
H-abstraction and C≡C 1,3-cycloaddition mechanisms were discovered for the O3 + CH≡CCH2OH reaction. The computations manifested that the primary reaction channel is 1,3-cycloaddition involving O3 addition to the C≡C triple bond of CH≡CCH2OH to generate primary ozonide (IM1), which dissociated to generate two different Criegee intermediates (reactions of CI1 and CI2). The subsequent CI1 and CI2 were also detailedly investigated. The rate coefficients were also investigated at 200–3000 K and 10−10–1010 atm. At normal temperature and pressure, the rate coefficient was 4.46 × 10−19 cm3 molecule−1 s−1 with an atmospheric lifetime of 25.95 days. The current computation results have significant implications in the atmospheric chemistry of ozone oxidation of unsaturated alcohols.
Methods
All calculations of electronic structure and energy in this study are implemented using Gaussian09. The geometries of all species for the O3 + CH≡CCH2OH reaction and subsequent reactions were optimized using the M06-2X method with the 6-311++G(d,p) basis set. All stationary points were determined for local minima and transition states through vibrational analysis, and connections of the transition states between designated reactants and products were proven through intrinsic reaction coordinate (IRC) computations. The energies for the potential energy surfaces (PES) were refined through the single-point computations using the CCSD(T)/cc-pVTZ level of theory. The rate constants for the title reaction and subsequent reactions had been computed with RRKM theory.
{"title":"Theoretical study on the formation of Criegee intermediates from ozonolysis of CH≡CCH2OH","authors":"Yunju Zhang, Meilian Zhao, Cen Yao, Zhiguo Wang, Yuxi Sun","doi":"10.1007/s00894-025-06592-5","DOIUrl":"10.1007/s00894-025-06592-5","url":null,"abstract":"<div><h3>Context</h3><p>H-abstraction and C≡C 1,3-cycloaddition mechanisms were discovered for the O<sub>3</sub> + CH≡CCH<sub>2</sub>OH reaction. The computations manifested that the primary reaction channel is 1,3-cycloaddition involving O<sub>3</sub> addition to the C≡C triple bond of CH≡CCH<sub>2</sub>OH to generate primary ozonide (IM1), which dissociated to generate two different Criegee intermediates (reactions of CI1 and CI2). The subsequent CI1 and CI2 were also detailedly investigated. The rate coefficients were also investigated at 200–3000 K and 10<sup>−10</sup>–10<sup>10</sup> atm. At normal temperature and pressure, the rate coefficient was 4.46 × 10<sup>−19</sup> cm<sup>3</sup> molecule<sup>−1</sup> s<sup>−1</sup> with an atmospheric lifetime of 25.95 days. The current computation results have significant implications in the atmospheric chemistry of ozone oxidation of unsaturated alcohols. </p><h3>Methods</h3><p>All calculations of electronic structure and energy in this study are implemented using Gaussian09. The geometries of all species for the O<sub>3</sub> + CH≡CCH<sub>2</sub>OH reaction and subsequent reactions were optimized using the M06-2X method with the 6-311++G(d,p) basis set. All stationary points were determined for local minima and transition states through vibrational analysis, and connections of the transition states between designated reactants and products were proven through intrinsic reaction coordinate (IRC) computations. The energies for the potential energy surfaces (PES) were refined through the single-point computations using the CCSD(T)/cc-pVTZ level of theory. The rate constants for the title reaction and subsequent reactions had been computed with RRKM theory.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145905285","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}
Pub Date : 2026-01-06DOI: 10.1007/s00894-025-06586-3
Saisha Islam, Liana R. Cutter, Mary A. Biggs, Sophia A. Frantzeskos, Ipsita A. Banerjee
<div><h3>Context</h3><p>Vascular endothelial growth factor receptor-2 (VEGFR-2) and interleukin 13 receptor subunit-2 (IL13Rα2) are major drug targets due to their overexpression in several cancers that lead to tumor cell proliferation, metastasis, and poor prognosis. In this work, we have designed novel peptides that have the potential for dual targeting of both VEGFR-2 and IL13Rα2. Using the tumor homing peptide ACGEMGWVRCGGGS (pep1IL) as a starting point, we designed seven new peptides through single point variations within the sequences. The binding affinities and stabilities of the peptides were evaluated through molecular docking and molecular dynamics (MD) simulations. Our results indicated that among the peptide variants, ACGHMGWVRCGGGS and ACGEMGWVRCGGGT formed the most stable complexes with VEGFR-2 and IL13Rα2 respectively, while ACGEMGWVSCGGGS displayed strong binding with both receptors. In general, binding occurred with residues encompassing the D2 and D3 domains of VEGFR-2 and D1, D2, and D3 domains of IL13Rα2. Of particular note is the importance of MET143 and THR229 residues of IL13Rα2 that were critical in binding of most of the peptides. For VEGFR-2, several of the designed peptides formed hydrogen bonds with residues including TYR 165, SER 193, TYR 194, and ASN253 which have been implicated in mediating binding with VEGF-A/C/D. Thus, some of the peptides may act as competitive inhibitors, that may potentially play a role in impeding angiogenic signaling. We also designed the corresponding disulfide-bridged peptides that were docked with both receptors. MD simulations were run for two of the most optimal of those peptides and the disulfide-bridged serine variant sequence showed stable binding with both receptors. MM-GBSA results demonstrated that Van der Waals and electrostatic interactions played a key role in binding. Additionally, ACGEMGWVRCGGGT showed specificity, toward IL13Rα2 receptor and stronger binding than the original tumor homing peptide. Likewise, ACGDMGWVRCGGGS and ACGHMGWVRCGGGS showed significantly stronger binding with VEGFR-2 compared to IL13Rα2. Thus, this study shows the potential of our approach to design selective peptide variants that can be utilized for tumor targeting. Moreover, the designed peptides may be further explored in conjugation with anti-cancer drugs for future synthesis and therapeutic applications.</p><h3>Methods</h3><p>To determine the complete 3D structure of the extracellular domains of VEGFR-2 and IL13RA2, the AlphaFold 3 web server was used. Unbound (apo) receptor simulations were run using DESMOND to ensure the stability of the receptors. AntiCP web server was used to predict the anticancer potential of the peptides, while ADMETlab3.0 web server was used to determine the drug likeliness of the peptides. PEP-FOLD3 and MolProbity web servers were utilized to determine structural information about the peptides. Monte Carlo simulations were done using the MCPep server to predict membrane
{"title":"An in silico approach to peptide-based dual-receptor targeting for IL13RA2 and VEGFR-2 extracellular domain","authors":"Saisha Islam, Liana R. Cutter, Mary A. Biggs, Sophia A. Frantzeskos, Ipsita A. Banerjee","doi":"10.1007/s00894-025-06586-3","DOIUrl":"10.1007/s00894-025-06586-3","url":null,"abstract":"<div><h3>Context</h3><p>Vascular endothelial growth factor receptor-2 (VEGFR-2) and interleukin 13 receptor subunit-2 (IL13Rα2) are major drug targets due to their overexpression in several cancers that lead to tumor cell proliferation, metastasis, and poor prognosis. In this work, we have designed novel peptides that have the potential for dual targeting of both VEGFR-2 and IL13Rα2. Using the tumor homing peptide ACGEMGWVRCGGGS (pep1IL) as a starting point, we designed seven new peptides through single point variations within the sequences. The binding affinities and stabilities of the peptides were evaluated through molecular docking and molecular dynamics (MD) simulations. Our results indicated that among the peptide variants, ACGHMGWVRCGGGS and ACGEMGWVRCGGGT formed the most stable complexes with VEGFR-2 and IL13Rα2 respectively, while ACGEMGWVSCGGGS displayed strong binding with both receptors. In general, binding occurred with residues encompassing the D2 and D3 domains of VEGFR-2 and D1, D2, and D3 domains of IL13Rα2. Of particular note is the importance of MET143 and THR229 residues of IL13Rα2 that were critical in binding of most of the peptides. For VEGFR-2, several of the designed peptides formed hydrogen bonds with residues including TYR 165, SER 193, TYR 194, and ASN253 which have been implicated in mediating binding with VEGF-A/C/D. Thus, some of the peptides may act as competitive inhibitors, that may potentially play a role in impeding angiogenic signaling. We also designed the corresponding disulfide-bridged peptides that were docked with both receptors. MD simulations were run for two of the most optimal of those peptides and the disulfide-bridged serine variant sequence showed stable binding with both receptors. MM-GBSA results demonstrated that Van der Waals and electrostatic interactions played a key role in binding. Additionally, ACGEMGWVRCGGGT showed specificity, toward IL13Rα2 receptor and stronger binding than the original tumor homing peptide. Likewise, ACGDMGWVRCGGGS and ACGHMGWVRCGGGS showed significantly stronger binding with VEGFR-2 compared to IL13Rα2. Thus, this study shows the potential of our approach to design selective peptide variants that can be utilized for tumor targeting. Moreover, the designed peptides may be further explored in conjugation with anti-cancer drugs for future synthesis and therapeutic applications.</p><h3>Methods</h3><p>To determine the complete 3D structure of the extracellular domains of VEGFR-2 and IL13RA2, the AlphaFold 3 web server was used. Unbound (apo) receptor simulations were run using DESMOND to ensure the stability of the receptors. AntiCP web server was used to predict the anticancer potential of the peptides, while ADMETlab3.0 web server was used to determine the drug likeliness of the peptides. PEP-FOLD3 and MolProbity web servers were utilized to determine structural information about the peptides. Monte Carlo simulations were done using the MCPep server to predict membrane ","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145909685","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}
Pub Date : 2026-01-06DOI: 10.1007/s00894-025-06621-3
Febdian Rusydi, Etika Dessi Susanti, Ira Puspitasari, Rizka Nur Fadilla, Roichatul Madinah, Wun F. Mark-Lee
Context
The extensive conformational space of flexible molecules poses a significant challenge for predicting chemical reactivity through quantum chemical methods. For curcumin, whose keto–enol tautomerization is crucial to its biological activity and associated with its therapeutic potential in conditions such as Alzheimer’s disease, selecting meaningful conformers is particularly challenging. Traditional strategies for conformer selection that rely on variations in torsion angles may result in an excessive number of conformers. Our previously developed fragmentation-based strategy addresses this issue but may overlook critical conformers in highly flexible molecules. In this study, we developed an integrated workflow and yielded a diverse yet manageable set of conformers, enabling a refined energy profile of curcumin tautomerization with reduced activation energy, thereby aligning the results more closely with the experimental values than our previous estimates. Beyond curcumin, our findings demonstrate that the integration of machine-learning-assisted clustering with electronic structure calculations provides an efficient and transferable strategy for capturing conformational diversity in flexible molecular systems.
Methods
Our workflow incorporates extended tight-binding (xTB) metadynamics for comprehensive conformer sampling, Coulomb matrix descriptors with t-SNE dimensionality reduction for structural encoding, clustering to identify representative structures, and DFT validation of ground and transition states. We used the second generation of xTB (GFN2-xTB) in the gas phase and implicit solvent with analytical linearized Poisson-Boltzmann (ALPB), which implemented in CREST. For the clustering algorithms, we utilized K-means and agglomerative clustering and monitored the Davies-Bouldin Index (DBI), Silhouette scores, and the elbow method to determine the optimal number of clusters. The exchange-correlation functional/basis set used for DFT calculations was APFD/6-311++G(d,p), which integrated into the Gaussian 16 software.
{"title":"Probing curcumin reactive conformers in keto-enol tautomerization enhanced by clustering with t-SNE","authors":"Febdian Rusydi, Etika Dessi Susanti, Ira Puspitasari, Rizka Nur Fadilla, Roichatul Madinah, Wun F. Mark-Lee","doi":"10.1007/s00894-025-06621-3","DOIUrl":"10.1007/s00894-025-06621-3","url":null,"abstract":"<div><h3>Context</h3><p>The extensive conformational space of flexible molecules poses a significant challenge for predicting chemical reactivity through quantum chemical methods. For curcumin, whose keto–enol tautomerization is crucial to its biological activity and associated with its therapeutic potential in conditions such as Alzheimer’s disease, selecting meaningful conformers is particularly challenging. Traditional strategies for conformer selection that rely on variations in torsion angles may result in an excessive number of conformers. Our previously developed fragmentation-based strategy addresses this issue but may overlook critical conformers in highly flexible molecules. In this study, we developed an integrated workflow and yielded a diverse yet manageable set of conformers, enabling a refined energy profile of curcumin tautomerization with reduced activation energy, thereby aligning the results more closely with the experimental values than our previous estimates. Beyond curcumin, our findings demonstrate that the integration of machine-learning-assisted clustering with electronic structure calculations provides an efficient and transferable strategy for capturing conformational diversity in flexible molecular systems.</p><h3>Methods</h3><p>Our workflow incorporates extended tight-binding (xTB) metadynamics for comprehensive conformer sampling, Coulomb matrix descriptors with t-SNE dimensionality reduction for structural encoding, clustering to identify representative structures, and DFT validation of ground and transition states. We used the second generation of xTB (GFN2-xTB) in the gas phase and implicit solvent with analytical linearized Poisson-Boltzmann (ALPB), which implemented in CREST. For the clustering algorithms, we utilized K-means and agglomerative clustering and monitored the Davies-Bouldin Index (DBI), Silhouette scores, and the elbow method to determine the optimal number of clusters. The exchange-correlation functional/basis set used for DFT calculations was APFD/6-311++G(d,p), which integrated into the Gaussian 16 software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145905321","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}
Pub Date : 2026-01-03DOI: 10.1007/s00894-025-06550-1
Dilan Nawzad Mamakhan, Nabil Adil Fakhre
Context
This study examines the adsorption behavior of dibenzothiophene (DBT) on nitrogen-doped titanium dioxide (N-doped TiO₂) to evaluate its potential in photocatalytic desulfurization. The work focuses on structural stability, charge transfer, electronic properties, and dynamic interactions of the hybrid system. The findings show that nitrogen doping reduces the TiO₂ band gap, enhances charge redistribution, and improves adsorption affinity. Molecular dynamics simulations confirm the strong thermal stability of the DBT/N-doped TiO₂ composite, while recovery time calculations highlight its rapid sensing and reusability. These results underscore the promise of N-doped TiO₂ as an efficient material for sulfur pollutant removal.
Methods
Density functional theory (DFT) was employed to analyze adsorption energies, band structures, charge density, and non-covalent interactions, supported by Bader charge analysis. Molecular dynamics (MD) simulations were carried out to evaluate the thermal stability and dynamic behavior of the DBT/N-doped TiO₂ system.
{"title":"Adsorption of dibenzothiophene on N-doped TiO₂ system: a DFT and molecular dynamics study","authors":"Dilan Nawzad Mamakhan, Nabil Adil Fakhre","doi":"10.1007/s00894-025-06550-1","DOIUrl":"10.1007/s00894-025-06550-1","url":null,"abstract":"<div><h3>Context</h3><p>This study examines the adsorption behavior of dibenzothiophene (DBT) on nitrogen-doped titanium dioxide (N-doped TiO₂) to evaluate its potential in photocatalytic desulfurization. The work focuses on structural stability, charge transfer, electronic properties, and dynamic interactions of the hybrid system. The findings show that nitrogen doping reduces the TiO₂ band gap, enhances charge redistribution, and improves adsorption affinity. Molecular dynamics simulations confirm the strong thermal stability of the DBT/N-doped TiO₂ composite, while recovery time calculations highlight its rapid sensing and reusability. These results underscore the promise of N-doped TiO₂ as an efficient material for sulfur pollutant removal.</p><h3>Methods</h3><p>Density functional theory (DFT) was employed to analyze adsorption energies, band structures, charge density, and non-covalent interactions, supported by Bader charge analysis. Molecular dynamics (MD) simulations were carried out to evaluate the thermal stability and dynamic behavior of the DBT/N-doped TiO₂ system.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145886790","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}
Pub Date : 2026-01-03DOI: 10.1007/s00894-025-06616-0
Francisco M. Fernández
{"title":"Comment on: Energy and momentum eigenspectrum of the Hulthèn-screened cosine Kratzer potential using proper quantization rule and SUSYQM method","authors":"Francisco M. Fernández","doi":"10.1007/s00894-025-06616-0","DOIUrl":"10.1007/s00894-025-06616-0","url":null,"abstract":"","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145886789","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}
Synthetic ester is a high-quality lubricating base oil, and its antioxidant stability and high-temperature service life are greatly affected by antioxidants. For a considerable period, a significant number of researchers have utilized a variety of conventional methodologies, including the rotating oxygen bomb test, for the selection and evaluation of antioxidants. However, there is little systematic research on the thermal stability and antioxidant performance of these antioxidants through a combination of experiments and calculations. In this study, a range of investigative approaches, including experimental, calculation, and molecular simulation methods, were employed to assess the impact of synthetic esters (PE5) with antioxidants (1010, L57, and hybrid). Compared with PE5 base oil, the thermodynamic analysis showed the value of activation energy for PE5 samples was probably PE5 + 2% L57 ≥ PE5 + 1% 1010 + 1% L57 > PE5 + 2% 1010 ≥ PE5. These results were in consistent with the acid number changes and viscosity changes for PE5 samples. The IOT results obtained from PDSC also proved the validity of this trend. Especially, PE5 containing 1% 1010 and 1% L57 showed good antioxidant properties, indicating that the hybrid antioxidants have excellent high-temperature antioxidant performance. The molecule simulation results show L57 can effectively and quickly reach the protected point without rapid volatilization and loss, thereby achieving excellent antioxidant performance. In addition, the movement rate of the hybrid antioxidant system (1wt% 1010 + 1wt% L57) can also achieve similar results compared with L57.
Methods
The thermal stability of antioxidants was investigated by TG/DTG analysis, and the corresponding decomposition kinetic parameters were evaluated by Flynn–Wall–Ozawa (FWO) and Kissinger–Akahira–Sunose (KAS) methods. The optimization of the geometry of related molecules was performed via Gaussian 16 package at B3LYP/def2-SVP level. The single point energy was then calculated at B3LYP/def2-TZVP level. The ACPEPY script was employed to obtain the GAF force field topology file of them. Molecular dynamics simulations were performed using the GROMACS software package.
{"title":"Exploration on thermal behavior of synthetic ester with antioxidant based on thermodynamic analysis and molecular simulations","authors":"Mengke Zhang, Qin Zhao, Junming Liu, Bingbing Lai, Gaiqing Zhao, Xiaobo Wang","doi":"10.1007/s00894-025-06601-7","DOIUrl":"10.1007/s00894-025-06601-7","url":null,"abstract":"<div><h3>Context</h3><p>Synthetic ester is a high-quality lubricating base oil, and its antioxidant stability and high-temperature service life are greatly affected by antioxidants. For a considerable period, a significant number of researchers have utilized a variety of conventional methodologies, including the rotating oxygen bomb test, for the selection and evaluation of antioxidants. However, there is little systematic research on the thermal stability and antioxidant performance of these antioxidants through a combination of experiments and calculations. In this study, a range of investigative approaches, including experimental, calculation, and molecular simulation methods, were employed to assess the impact of synthetic esters (PE5) with antioxidants (1010, L57, and hybrid). Compared with PE5 base oil, the thermodynamic analysis showed the value of activation energy for PE5 samples was probably PE5 + 2% L57 ≥ PE5 + 1% 1010 + 1% L57 > PE5 + 2% 1010 ≥ PE5. These results were in consistent with the acid number changes and viscosity changes for PE5 samples. The IOT results obtained from PDSC also proved the validity of this trend. Especially, PE5 containing 1% 1010 and 1% L57 showed good antioxidant properties, indicating that the hybrid antioxidants have excellent high-temperature antioxidant performance. The molecule simulation results show L57 can effectively and quickly reach the protected point without rapid volatilization and loss, thereby achieving excellent antioxidant performance. In addition, the movement rate of the hybrid antioxidant system (1wt% 1010 + 1wt% L57) can also achieve similar results compared with L57.</p><h3>Methods</h3><p>The thermal stability of antioxidants was investigated by TG/DTG analysis, and the corresponding decomposition kinetic parameters were evaluated by Flynn–Wall–Ozawa (FWO) and Kissinger–Akahira–Sunose (KAS) methods. The optimization of the geometry of related molecules was performed via Gaussian 16 package at B3LYP/def2-SVP level. The single point energy was then calculated at B3LYP/def2-TZVP level. The ACPEPY script was employed to obtain the GAF force field topology file of them. Molecular dynamics simulations were performed using the GROMACS software package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145848638","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}
Pub Date : 2025-12-27DOI: 10.1007/s00894-025-06594-3
Tengfei Nian, Haowen Sun, Wei Li, Piyi Li
Context
Waste plastics have a significant impact on natural resources and the environment. The focus is on the interfacial adhesion behavior of three types of waste plastics—polyethylene (PE), polypropylene (PP), and Poly acrylic (PA)—with neutral silica (SiO2) aggregates, as well as the influence of graphene oxide (GO) on the asphalt-water-aggregate interface performance. The validity of the molecular dynamics simulations was assessed based on fundamental thermodynamic properties of asphalt, including density, glass transition temperature, cohesive energy density, and solubility parameters. The diffusion patterns of the four asphalt components on the SiO2 aggregate surface were analyzed using the mean square displacement (MSD), diffusion coefficient, and relative concentration distribution. The bonding strength between various waste plastics and the asphalt-aggregate interface was quantified by calculating the adhesion work. The results indicate that van der Waals forces and electrostatic forces play a crucial role in the adhesion between asphalt and minerals. The adhesion work between aged asphalt and aggregates is highest when PE plastic is added, lowest when PP plastic is added, and intermediate when PA plastic added. Upon introducing water molecules at the asphalt-aggregate interface, the interfacial adhesion work decreased significantly, indicating that water molecules exert a substantial negative impact on interfacial adhesion performance. However, after coating the aggregate surface with graphene oxide, the adhesion work at the asphalt-water-aggregate interface increased significantly, suggesting that graphene oxide enhances water damage resistance by improving interfacial polarity. This study provides molecular-level theoretical support for the recycling of waste plastics in asphalt-based materials and for the optimization of interfaces.
Methods
Molecular dynamics simulations were performed using Materials Studio software with the COMPASS II force field. The Nose thermostat and Berendsen isobaric thermostat were used to control temperature and pressure, respectively, to maintain constant temperature and pressure conditions throughout the simulation. In non-bonded interaction calculations, electrostatic forces were calculated using the Ewald method, and van der Waals forces were calculated using the Atom Based method, with a cutoff radius of 15.5 Å. The simulations were conducted using NVT and NPT ensembles, with all simulations set to fine computational precision. The constructed model was first subjected to geometric optimization (100,000 iterations), followed by annealing treatment (10 cycles with a temperature change gradient of 100 K), and then the ideal molecular structure of the model was obtained through NPT ensemble simulations.
{"title":"Regulatory mechanism of interface adhesion and moisture damage in aged SBS-modified asphalt–aggregate systems modified with waste plastic and oxidized graphene","authors":"Tengfei Nian, Haowen Sun, Wei Li, Piyi Li","doi":"10.1007/s00894-025-06594-3","DOIUrl":"10.1007/s00894-025-06594-3","url":null,"abstract":"<div><h3>Context</h3><p>Waste plastics have a significant impact on natural resources and the environment. The focus is on the interfacial adhesion behavior of three types of waste plastics—polyethylene (PE), polypropylene (PP), and Poly acrylic (PA)—with neutral silica (SiO<sub>2</sub>) aggregates, as well as the influence of graphene oxide (GO) on the asphalt-water-aggregate interface performance. The validity of the molecular dynamics simulations was assessed based on fundamental thermodynamic properties of asphalt, including density, glass transition temperature, cohesive energy density, and solubility parameters. The diffusion patterns of the four asphalt components on the SiO<sub>2</sub> aggregate surface were analyzed using the mean square displacement (MSD), diffusion coefficient, and relative concentration distribution. The bonding strength between various waste plastics and the asphalt-aggregate interface was quantified by calculating the adhesion work. The results indicate that van der Waals forces and electrostatic forces play a crucial role in the adhesion between asphalt and minerals. The adhesion work between aged asphalt and aggregates is highest when PE plastic is added, lowest when PP plastic is added, and intermediate when PA plastic added. Upon introducing water molecules at the asphalt-aggregate interface, the interfacial adhesion work decreased significantly, indicating that water molecules exert a substantial negative impact on interfacial adhesion performance. However, after coating the aggregate surface with graphene oxide, the adhesion work at the asphalt-water-aggregate interface increased significantly, suggesting that graphene oxide enhances water damage resistance by improving interfacial polarity. This study provides molecular-level theoretical support for the recycling of waste plastics in asphalt-based materials and for the optimization of interfaces.</p><h3>Methods</h3><p>Molecular dynamics simulations were performed using Materials Studio software with the COMPASS II force field. The Nose thermostat and Berendsen isobaric thermostat were used to control temperature and pressure, respectively, to maintain constant temperature and pressure conditions throughout the simulation. In non-bonded interaction calculations, electrostatic forces were calculated using the Ewald method, and van der Waals forces were calculated using the Atom Based method, with a cutoff radius of 15.5 Å. The simulations were conducted using NVT and NPT ensembles, with all simulations set to fine computational precision. The constructed model was first subjected to geometric optimization (100,000 iterations), followed by annealing treatment (10 cycles with a temperature change gradient of 100 K), and then the ideal molecular structure of the model was obtained through NPT ensemble simulations.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145831379","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}
Pub Date : 2025-12-22DOI: 10.1007/s00894-025-06611-5
Wen-Bin Wu, Qian Hu, Hua-Kang Zhou, Kai Chen
Context
The biomimetic domino cycloaddition between acylphloroglucinol and 2-hydroxyethyl-cyclohexenone has been previously established as an efficient strategy for constructing tricyclic ketal scaffolds and synthesizing the bioactive natural products, Myrtucommulone J and Myrtucommuacetalone. In this study, density functional theory (DFT) calculations were performed to elucidate the plausible reaction mechanism. The transformation proceeds via a tandem sequence involving hemiacetalization, dehydration, electrophilic attack, re-aromatization, protonation of the C = C bond, and annulation. The rate-determining step was identified as the electrophilic attack of an allylic cation on the aromatic ring of acylphloroglucinol, with an overall free energy barrier of approximately 23.5 kcal/mol. These mechanistic insights not only advance our understanding of this biomimetic cascade but also provide a foundation for the rational design of novel synthetic methodologies.
Methods
In this work, density functional theory (DFT) calculations were carried out using the Gaussian 16 software package. Geometry optimizations and vibrational frequency analyses for all stationary points were performed at the M06-2X/def2-SVP level of theory. The intrinsic reaction coordinate (IRC) calculations were employed to verify the connectivity between each transition state and its corresponding minima. Single-point energy calculations were subsequently conducted using the M06-2X functional in conjunction with the def2-TZVP basis set for all atoms. Solvent effects of toluene were incorporated through Truhlar’s SMD continuum solvation model. All optimized structures and transition states were visualized with CYLview.
{"title":"Mechanistic studies on a biomimetic cycloaddition between phloroglucinol and 2-hydroxyethyl-α,β-unsaturated ketone","authors":"Wen-Bin Wu, Qian Hu, Hua-Kang Zhou, Kai Chen","doi":"10.1007/s00894-025-06611-5","DOIUrl":"10.1007/s00894-025-06611-5","url":null,"abstract":"<div><h3>Context</h3><p>The biomimetic domino cycloaddition between acylphloroglucinol and 2-hydroxyethyl-cyclohexenone has been previously established as an efficient strategy for constructing tricyclic ketal scaffolds and synthesizing the bioactive natural products, Myrtucommulone J and Myrtucommuacetalone. In this study, density functional theory (DFT) calculations were performed to elucidate the plausible reaction mechanism. The transformation proceeds via a tandem sequence involving hemiacetalization, dehydration, electrophilic attack, re-aromatization, protonation of the C = C bond, and annulation. The rate-determining step was identified as the electrophilic attack of an allylic cation on the aromatic ring of acylphloroglucinol, with an overall free energy barrier of approximately 23.5 kcal/mol. These mechanistic insights not only advance our understanding of this biomimetic cascade but also provide a foundation for the rational design of novel synthetic methodologies.</p><h3>Methods</h3><p>In this work, density functional theory (DFT) calculations were carried out using the Gaussian 16 software package. Geometry optimizations and vibrational frequency analyses for all stationary points were performed at the M06-2X/def2-SVP level of theory. The intrinsic reaction coordinate (IRC) calculations were employed to verify the connectivity between each transition state and its corresponding minima. Single-point energy calculations were subsequently conducted using the M06-2X functional in conjunction with the def2-TZVP basis set for all atoms. Solvent effects of toluene were incorporated through Truhlar’s SMD continuum solvation model. All optimized structures and transition states were visualized with CYLview.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145802912","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}
Pub Date : 2025-12-22DOI: 10.1007/s00894-025-06613-3
Huy Duy Nguyen, Phong Hai Nguyen, Giang Huong Bach, Oanh Kim Thi Nguyen
Context
Trivalent C(_{22}) cages are explored with the recent generation of Gaussian approximation potential (GAP-20) and density functional theory (DFT) calculations. Using the GAP-20 to approximate the energy landscape significantly reduces the search time and provides superior starting structures for DFT optimization. The GAP-20, however, fails to capture the Jahn-Teller distortion. The relative GAP-20 energies are overestimated, and the vibrational modes/frequencies are poorly characterized.
Methods
Via the CALYPSO package, particle swarm optimization is employed to explore the configuration space. Energies/forces are calculated via the QUIP/LAMMPS module, employing the GAP-20. Structural relaxation follows the conjugate gradient method to a force precision of (10^{-7} text { eV}/)Å. Cage isomers are further optimized by DFT, utilizing BFGS optimization scheme, until forces are below 0.05 eV/Å. The (text {B3LYP/6-31+G}*) level of theory is applied, as implemented in the NWChem software. Vibrational analysis is performed to study the stability/infrared spectra.
背景：用最近一代的高斯近似势（GAP-20）和密度泛函理论（DFT）计算探索了三价c22笼。使用GAP-20近似能量格局显著减少了搜索时间，并为DFT优化提供了优越的起始结构。然而，GAP-20未能捕捉到扬-泰勒扭曲。相对GAP-20能量被高估，振动模式/频率特征不佳。方法：利用CALYPSO软件包，采用粒子群算法对构型空间进行寻优。能量/力通过QUIP/LAMMPS模块计算，采用GAP-20。结构松弛遵循共轭梯度法，力精度为10 - 7 eV / Å。利用BFGS优化方案对笼形异构体进行进一步的DFT优化，直至作用力小于0.05 eV/Å。在NWChem软件中，应用了B3LYP/6-31+G *水平的理论。通过振动分析研究其稳定性和红外光谱。
{"title":"Accelerating the search for carbon cluster isomers via machine learning potential","authors":"Huy Duy Nguyen, Phong Hai Nguyen, Giang Huong Bach, Oanh Kim Thi Nguyen","doi":"10.1007/s00894-025-06613-3","DOIUrl":"10.1007/s00894-025-06613-3","url":null,"abstract":"<div><h3>Context</h3><p>Trivalent C<span>(_{22})</span> cages are explored with the recent generation of Gaussian approximation potential (GAP-20) and density functional theory (DFT) calculations. Using the GAP-20 to approximate the energy landscape significantly reduces the search time and provides superior starting structures for DFT optimization. The GAP-20, however, fails to capture the Jahn-Teller distortion. The relative GAP-20 energies are overestimated, and the vibrational modes/frequencies are poorly characterized.</p><h3>Methods</h3><p>Via the CALYPSO package, particle swarm optimization is employed to explore the configuration space. Energies/forces are calculated via the QUIP/LAMMPS module, employing the GAP-20. Structural relaxation follows the conjugate gradient method to a force precision of <span>(10^{-7} text { eV}/)</span>Å. Cage isomers are further optimized by DFT, utilizing BFGS optimization scheme, until forces are below 0.05 eV/Å. The <span>(text {B3LYP/6-31+G}*)</span> level of theory is applied, as implemented in the NWChem software. Vibrational analysis is performed to study the stability/infrared spectra.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145802780","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}
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