Pub Date : 2026-01-14DOI: 10.1007/s00894-025-06627-x
Hangwei Cao, Minfu Liao, Xiongying Duan, Fei Huang, Linyuan Fan
Context
Polyimide (PI) is a key arc-resistant material, yet its molecular-level degradation under fault-arc plasma remains unclear. Here, arc-ablation experiments were combined with multi-scale simulations to elucidate its decomposition pathways. FTIR results indicate that high-energy plasma particles exceed the maximum bond dissociation energy of PI, causing highly disordered scission distinct from thermal decomposition. Bond-order and BDE analyses were used to identify vulnerable sites, followed by ReaxFF/ZBL molecular dynamics and Fukui function analysis to probe reaction pathways. The results show that C–C and N–C bonds between imide and phenyl rings, as well as aromatic ether C–O–C linkages, are the most susceptible to cleavage. Nitrogen atoms display strong nucleophilicity, inducing C–N bond rupture and ring opening; the resulting formation of additional N–H groups explains the intensified and broadened N–H bands in the FTIR spectra. In contrast, electrophilic oxygen preferentially attacks aromatic ether bonds, generating short-chain fragments that drive rapid mass loss. These consistent experimental and computational insights establish an atomic-scale path of PI degradation under arc plasma.
Methods
The modeling process was carried out using BIOVIA Materials Studio. Lmp2arc was used to convert .car files to .data files. The calculations for the polyimide bond order were performed using the DMol3 module of Materials Studio, with LDA-PWC selected for the generalization. This paper employs a hybrid ReaxFF and ZBL force field in LAMMPS to simulate ion bombardment of the PI surface (including the atoms) in an electric arc. Gaussian 16.0 was utilized to optimize the geometry at the B3LYP/6-31G(d,p) level. Fukui function calculations were performed for polyimide using Multiwfn, based on the electron wave function generated by Gaussian 16.0.
{"title":"From arc testing to theoretical insight: ReaxFF MD and DFT unravel polyimide degradation mechanisms","authors":"Hangwei Cao, Minfu Liao, Xiongying Duan, Fei Huang, Linyuan Fan","doi":"10.1007/s00894-025-06627-x","DOIUrl":"10.1007/s00894-025-06627-x","url":null,"abstract":"<div><h3>Context</h3><p>Polyimide (PI) is a key arc-resistant material, yet its molecular-level degradation under fault-arc plasma remains unclear. Here, arc-ablation experiments were combined with multi-scale simulations to elucidate its decomposition pathways. FTIR results indicate that high-energy plasma particles exceed the maximum bond dissociation energy of PI, causing highly disordered scission distinct from thermal decomposition. Bond-order and BDE analyses were used to identify vulnerable sites, followed by ReaxFF/ZBL molecular dynamics and Fukui function analysis to probe reaction pathways. The results show that C–C and N–C bonds between imide and phenyl rings, as well as aromatic ether C–O–C linkages, are the most susceptible to cleavage. Nitrogen atoms display strong nucleophilicity, inducing C–N bond rupture and ring opening; the resulting formation of additional N–H groups explains the intensified and broadened N–H bands in the FTIR spectra. In contrast, electrophilic oxygen preferentially attacks aromatic ether bonds, generating short-chain fragments that drive rapid mass loss. These consistent experimental and computational insights establish an atomic-scale path of PI degradation under arc plasma.</p><h3>Methods</h3><p>The modeling process was carried out using BIOVIA Materials Studio. Lmp2arc was used to convert .car files to .data files. The calculations for the polyimide bond order were performed using the DMol3 module of Materials Studio, with LDA-PWC selected for the generalization. This paper employs a hybrid ReaxFF and ZBL force field in LAMMPS to simulate ion bombardment of the PI surface (including the atoms) in an electric arc. Gaussian 16.0 was utilized to optimize the geometry at the B3LYP/6-31G(d,p) level. Fukui function calculations were performed for polyimide using Multiwfn, based on the electron wave function generated by Gaussian 16.0.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145964900","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 : 2026-01-14DOI: 10.1007/s00894-025-06619-x
Gonçalo V. S. M. Carrera, Carlos E. S. Bernardes, Ana V. M. Nunes, Teresa Casimiro, João Sotomayor, Ana Aguiar-Ricardo
Context
The access to the molecular assemblage on the melting transition is fundamental to phase-change material’s design, particularly when applied to renewable and intermittent energy sources, and the investigation of physical/chemical/biological processes. The development of new methods to obtain this information is, consequently, highly desired. This framework is fertile ground for the establishment of machine learning–based models with both predictive and interpretable profiles. However, such models are difficult to establish. This work describes the implementation of a Random Forest interpretable approach set on the specific tree paths followed by a given chemical system (molecule) for the relationship between its descriptors/melting point value. The descriptors involve all combinations of atom pairs of a generical molecular chemical system. The combined use of Random Forest molecule’s specific tree paths and descriptor concept enables the built model the capacity to highlight the most important combinations of pairs of atoms/interactions inherent to molecular assembly on melting stage. As proof of concept, this procedure was applied to investigate the organization of 2-(2,4-dichlorophenoxy)acetic acid (2,4-D) molecules at their melting point, with the results validated with thermo-regulated FTIR and computational chemistry approaches.
Method
This approach combines the Random Forest algorithm and atom-pair-based descriptor’s pattern, set for a generical molecule, in order to find a straightforward structure–property relationship. The unique tree paths followed by a given molecule highlight new specific measures addressing a causality relationship involving its descriptors and the melting point profile. This machine learning approach was validated with thermo-regulated FTIR, interaction energies, and molecular dynamics techniques.
{"title":"The use of an interpretable machine-learning approach to disclose the molecular assemblage on melting transition","authors":"Gonçalo V. S. M. Carrera, Carlos E. S. Bernardes, Ana V. M. Nunes, Teresa Casimiro, João Sotomayor, Ana Aguiar-Ricardo","doi":"10.1007/s00894-025-06619-x","DOIUrl":"10.1007/s00894-025-06619-x","url":null,"abstract":"<div><h3>Context</h3><p>The access to the molecular assemblage on the melting transition is fundamental to phase-change material’s design, particularly when applied to renewable and intermittent energy sources, and the investigation of physical/chemical/biological processes. The development of new methods to obtain this information is, consequently, highly desired. This framework is fertile ground for the establishment of machine learning–based models with both predictive and interpretable profiles. However, such models are difficult to establish. This work describes the implementation of a Random Forest interpretable approach set on the specific tree paths followed by a given chemical system (molecule) for the relationship between its descriptors/melting point value. The descriptors involve all combinations of atom pairs of a generical molecular chemical system. The combined use of Random Forest molecule’s specific tree paths and descriptor concept enables the built model the capacity to highlight the most important combinations of pairs of atoms/interactions inherent to molecular assembly on melting stage. As proof of concept, this procedure was applied to investigate the organization of 2-(2,4-dichlorophenoxy)acetic acid (2,4-D) molecules at their melting point, with the results validated with thermo-regulated FTIR and computational chemistry approaches.</p><h3>Method</h3><p>This approach combines the Random Forest algorithm and atom-pair-based descriptor’s pattern, set for a generical molecule, in order to find a straightforward structure–property relationship. The unique tree paths followed by a given molecule highlight new specific measures addressing a causality relationship involving its descriptors and the melting point profile. This machine learning approach was validated with thermo-regulated FTIR, interaction energies, and molecular dynamics techniques.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145964861","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 : 2026-01-13DOI: 10.1007/s00894-025-06624-0
Abdelmounaim Laassouli, Mohamed Karouchi, Abdelkebir Ejjabli, Hamza Errahoui, Aymane El Haji, Youssef Lachtioui, Omar Bajjou
Context
Perovskite hydrides are promising candidates for optoelectronic and hydrogen-related technologies, where B-site substitution offers an effective route to tune functional properties. We investigate BaNaH3X (X = Ni, Pd, Pt) to clarify how moving down Group 10 modifies structure–property relationships relevant to light harvesting and charge transport. All three compounds are predicted to be stable in the hexagonal P6₃/mmc phase with systematic lattice expansion from Ni to Pt. Hybrid-functional (HSE06) calculations show an indirect band gap of 1.43 eV for BaNaH3Ni and wider gaps of 2.51 eV and 2.43 eV for BaNaH3Pd and BaNaH3Pt, respectively, accompanied by broader band dispersion, lower carrier effective masses, and higher estimated mobilities. The calculated optical response reveals strong visible–UV absorption, large refractive indices, energy-loss peaks near 11–12 eV, and low reflectivity over the solar-relevant range, identifying BaNaH3Ni as a high-index hydride and BaNaH3Pd/Pt as attractive candidates for UV/visible optoelectronic applications.
Methods
First-principles density-functional theory (DFT) calculations were carried out using CASTEP. Structural optimization and ground-state properties employed GGA-PBE with OTFG norm-conserving pseudopotentials, a 500 eV plane-wave cutoff, and a Monkhorst–Pack 6 × 6 × 6 k-point mesh. Band gaps were refined using the HSE06 hybrid functional. Carrier effective masses were extracted from the converged band structures, and frequency-dependent dielectric functions and derived optical quantities were computed within the independent-particle approximation for the optimized geometries.
{"title":"Tuning optoelectronic properties in BaNaH3X (X = Ni, Pd, Pt) perovskite hydrides: a DFT-based analysis","authors":"Abdelmounaim Laassouli, Mohamed Karouchi, Abdelkebir Ejjabli, Hamza Errahoui, Aymane El Haji, Youssef Lachtioui, Omar Bajjou","doi":"10.1007/s00894-025-06624-0","DOIUrl":"10.1007/s00894-025-06624-0","url":null,"abstract":"<div><h3>Context</h3><p>Perovskite hydrides are promising candidates for optoelectronic and hydrogen-related technologies, where B-site substitution offers an effective route to tune functional properties. We investigate BaNaH<sub>3</sub>X (X = Ni, Pd, Pt) to clarify how moving down Group 10 modifies structure–property relationships relevant to light harvesting and charge transport. All three compounds are predicted to be stable in the hexagonal P6₃/mmc phase with systematic lattice expansion from Ni to Pt. Hybrid-functional (HSE06) calculations show an indirect band gap of 1.43 eV for BaNaH<sub>3</sub>Ni and wider gaps of 2.51 eV and 2.43 eV for BaNaH<sub>3</sub>Pd and BaNaH<sub>3</sub>Pt, respectively, accompanied by broader band dispersion, lower carrier effective masses, and higher estimated mobilities. The calculated optical response reveals strong visible–UV absorption, large refractive indices, energy-loss peaks near 11–12 eV, and low reflectivity over the solar-relevant range, identifying BaNaH<sub>3</sub>Ni as a high-index hydride and BaNaH<sub>3</sub>Pd/Pt as attractive candidates for UV/visible optoelectronic applications.</p><h3>Methods</h3><p>First-principles density-functional theory (DFT) calculations were carried out using CASTEP. Structural optimization and ground-state properties employed GGA-PBE with OTFG norm-conserving pseudopotentials, a 500 eV plane-wave cutoff, and a Monkhorst–Pack 6 × 6 × 6 k-point mesh. Band gaps were refined using the HSE06 hybrid functional. Carrier effective masses were extracted from the converged band structures, and frequency-dependent dielectric functions and derived optical quantities were computed within the independent-particle approximation for the optimized geometries.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145958391","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}
Coumarin derivatives (CoDe) exhibit significant biological activities, and the positions of different substituents as well as the introduction of methyl groups may influence their biological activity and efficacy. By investigating the relationship between substituent positions, methylation, and hydrogen bond properties, the specific mechanisms and rules governing hydrogen bonds in intermolecular interactions can be further elucidated. This provides a theoretical basis for the synthesis of novel coumarin derivatives with tailored hydrogen bond characteristics and biological activities, as well as a research foundation for the development of new drug molecules. Therefore, the hydrogen bonding interactions between 3-hydroxycoumarin (3-HyCo), 4-hydroxycoumarin (4-HyCo), 7-hydroxycoumarin (7-HyCo), and 7-hydroxy-4-methylcoumarin (4-Me-7-HyCo) with ethanol and water were studied using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). Firstly, the molecular structure of the coumarin (Co) monomer and the charge properties and molecular electrostatic potential extreme value of its four derivatives were analyzed. The stable complex structures of the four derivatives with ethanol and water were obtained through optimization, and the presence of hydrogen bonds in these complexes was confirmed. Secondly, the hydrogen bond lengths, frontier molecular orbitals (FMOs), interaction energies, atoms in molecules (AIM) topological parameters, and hydrogen bond vibration spectra in both the ground and excited states were examined. It was found that among the derivatives with different hydroxyl positions, the hydrogen bond structure of the 4-hydroxycoumarin complex was the most stable, and the introduction of a methyl group further enhanced the stability of the hydrogen bond structure. Finally, the hydrogen bond vibration spectra were found to undergo a red shift in the excited state, rendering the hydrogen bond structure more stable than that in the ground state.
Methods
All computational studies in this paper were performed using the Gaussian 16 software package (Revision B.01), while GaussView 6.0.16 was employed for the analysis and visualization of compounds. The DFT method was adopted to optimize all compounds, utilizing the B3LYP functional combined with the 6-311++G(d,p) basis set. Multiwfn 3.8 (dev) and VMD 1.9.3 software were used to analyze and create the molecular electrostatic potential extreme value diagrams and frontier molecular orbital (FMO) images. Basis set superposition error (BSSE) correction was introduced during the calculation of interaction energies. Topological analysis was conducted using Multiwfn 3.8 (dev) software, and the excited-state vibration spectra were obtained based on the TD-DFT method.
{"title":"The effects of substituent position and methylation on the hydrogen bond properties of coumarin derivatives with ethanol and water","authors":"Jiaqi Li, Zhongxin Zhang, Haitao Sun, Yu Wang, Xiatiguli Kahaer, Dilihumaer Aizezi, Mei Xiang, Bumaliya Abulimiti","doi":"10.1007/s00894-025-06615-1","DOIUrl":"10.1007/s00894-025-06615-1","url":null,"abstract":"<div><h3>Context</h3><p>Coumarin derivatives (CoDe) exhibit significant biological activities, and the positions of different substituents as well as the introduction of methyl groups may influence their biological activity and efficacy. By investigating the relationship between substituent positions, methylation, and hydrogen bond properties, the specific mechanisms and rules governing hydrogen bonds in intermolecular interactions can be further elucidated. This provides a theoretical basis for the synthesis of novel coumarin derivatives with tailored hydrogen bond characteristics and biological activities, as well as a research foundation for the development of new drug molecules. Therefore, the hydrogen bonding interactions between 3-hydroxycoumarin (3-HyCo), 4-hydroxycoumarin (4-HyCo), 7-hydroxycoumarin (7-HyCo), and 7-hydroxy-4-methylcoumarin (4-Me-7-HyCo) with ethanol and water were studied using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). Firstly, the molecular structure of the coumarin (Co) monomer and the charge properties and molecular electrostatic potential extreme value of its four derivatives were analyzed. The stable complex structures of the four derivatives with ethanol and water were obtained through optimization, and the presence of hydrogen bonds in these complexes was confirmed. Secondly, the hydrogen bond lengths, frontier molecular orbitals (FMOs), interaction energies, atoms in molecules (AIM) topological parameters, and hydrogen bond vibration spectra in both the ground and excited states were examined. It was found that among the derivatives with different hydroxyl positions, the hydrogen bond structure of the 4-hydroxycoumarin complex was the most stable, and the introduction of a methyl group further enhanced the stability of the hydrogen bond structure. Finally, the hydrogen bond vibration spectra were found to undergo a red shift in the excited state, rendering the hydrogen bond structure more stable than that in the ground state.</p><h3>Methods</h3><p>All computational studies in this paper were performed using the Gaussian 16 software package (Revision B.01), while GaussView 6.0.16 was employed for the analysis and visualization of compounds. The DFT method was adopted to optimize all compounds, utilizing the B3LYP functional combined with the 6-311++G(d,p) basis set. Multiwfn 3.8 (dev) and VMD 1.9.3 software were used to analyze and create the molecular electrostatic potential extreme value diagrams and frontier molecular orbital (FMO) images. Basis set superposition error (BSSE) correction was introduced during the calculation of interaction energies. Topological analysis was conducted using Multiwfn 3.8 (dev) software, and the excited-state vibration spectra were obtained based on the TD-DFT method.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 2","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145930745","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 : 2026-01-07DOI: 10.1007/s00894-025-06612-4
Anju, L. K. Saini, Mukesh Pandey
Context
The study of molecular stability, electronic properties, and molecular interactions, including topological analysis of 5,10,15,20-tetrakis-(4-carboxyphenyl)porphyrin (TCPP) and its derivatives, holds considerable applications and implications in material science (including sensing applications), human health, and environmental protection. Our work investigates the unique features of metallic TCPP to drive advancements in these related fields. The increase in adsorption energy and decrease in intermolecular distance confirms the efficiency of the protonation and metalation configurations in gas interaction properties and makes them potential for atmospheric monitoring applications. Additionally, we conducted an analysis of non-covalent interactions (NCI), which reveals that the Van-der-Waals (dominating) and steric type interaction occurring between studied molecules. Moreover, by examining the density of states, GCRD properties, and Koopman’s theorem; physisorption behaviour of examined materials with the gases are confirmed. The significant sensing capabilities of ZnTCPP towards C2N2 gas confirms the cyanogen recognition, offering a next generation porphyrin-inspired system for environmental surveillance and toxic pollutant remediation.
Methods
In this study, we performed DFT calculations using B3LYP hybrid functional by implementing ORCA software package. The optimization calculations of TCPP and its derivatives are performed with def2-TZVP triple-zeta basis set. For data analysis and visualization of stability, electronic and interaction properties of optimized configurations, this study employs diverse computational tools. Notably, visualization software Avogadro, molecular interaction analysis software Multiwfn are employed. By utilizing these comprehensive tools, we obtained valuable insights into GCRD properties, electronic and molecular interaction through topological analysis, including QTAIM and RDG-NCI methods.
{"title":"Quantum chemical calculation of cyanogen gas sensitivity: Unveiling the high-sensitivity ZnTCPP–C2N2 interaction","authors":"Anju, L. K. Saini, Mukesh Pandey","doi":"10.1007/s00894-025-06612-4","DOIUrl":"10.1007/s00894-025-06612-4","url":null,"abstract":"<div><h3>Context</h3><p>The study of molecular stability, electronic properties, and molecular interactions, including topological analysis of 5,10,15,20-tetrakis-(4-carboxyphenyl)porphyrin (TCPP) and its derivatives, holds considerable applications and implications in material science (including sensing applications), human health, and environmental protection. Our work investigates the unique features of metallic TCPP to drive advancements in these related fields. The increase in adsorption energy and decrease in intermolecular distance confirms the efficiency of the protonation and metalation configurations in gas interaction properties and makes them potential for atmospheric monitoring applications. Additionally, we conducted an analysis of non-covalent interactions (NCI), which reveals that the Van-der-Waals (dominating) and steric type interaction occurring between studied molecules. Moreover, by examining the density of states, GCRD properties, and Koopman’s theorem; physisorption behaviour of examined materials with the gases are confirmed. The significant sensing capabilities of ZnTCPP towards C<sub>2</sub>N<sub>2</sub> gas confirms the cyanogen recognition, offering a next generation porphyrin-inspired system for environmental surveillance and toxic pollutant remediation.</p><h3>Methods</h3><p>In this study, we performed DFT calculations using B3LYP hybrid functional by implementing ORCA software package. The optimization calculations of TCPP and its derivatives are performed with def2-TZVP triple-zeta basis set. For data analysis and visualization of stability, electronic and interaction properties of optimized configurations, this study employs diverse computational tools. Notably, visualization software Avogadro, molecular interaction analysis software Multiwfn are employed. By utilizing these comprehensive tools, we obtained valuable insights into GCRD properties, electronic and molecular interaction through topological analysis, including QTAIM and RDG-NCI methods.</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":"145904417","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 : 2026-01-07DOI: 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}
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