Pub Date : 2025-12-22DOI: 10.1007/s00894-025-06607-1
K. Boubendira, A. Saoudi
Context
III–V semiconductors such as aluminum phosphide (AlP) and boron phosphide (BP) are promising materials for high-power and high-temperature optoelectronic applications due to their wide band gaps, excellent thermal stability, and strong covalent bonding. However, their ternary alloys, particularly Al₁₋ₓBₓP, remain scarcely investigated in terms of their structural, electronic, thermodynamic, and thermal properties. Understanding these characteristics is essential to assess the alloy’s potential for device applications and to establish reliable theoretical data for future experimental validation.
Methods
The present study employs first-principles calculations based on density functional theory (DFT) within the generalized gradient approximation (GGA–PBE) to investigate the structural, electronic, thermodynamic, and thermal properties of zinc-blende AlP, BP, and their ternary alloy Al₁₋ₓBₓP (x = 0.25, 0.50, 0.75). The equilibrium lattice parameters, band structures, density of states (DOS), formation energies, and thermodynamic parameters were systematically analyzed to evaluate alloy stability and temperature-dependent behavior.
{"title":"Structural, electronic, thermodynamic, and thermal properties of zinc-blende AlP, BP, and their Al₁₋ₓBₓP ternary alloy","authors":"K. Boubendira, A. Saoudi","doi":"10.1007/s00894-025-06607-1","DOIUrl":"10.1007/s00894-025-06607-1","url":null,"abstract":"<div><h3>Context</h3><p>III–V semiconductors such as aluminum phosphide (AlP) and boron phosphide (BP) are promising materials for high-power and high-temperature optoelectronic applications due to their wide band gaps, excellent thermal stability, and strong covalent bonding. However, their ternary alloys, particularly Al₁₋ₓBₓP, remain scarcely investigated in terms of their structural, electronic, thermodynamic, and thermal properties. Understanding these characteristics is essential to assess the alloy’s potential for device applications and to establish reliable theoretical data for future experimental validation.</p><h3>Methods</h3><p>The present study employs first-principles calculations based on density functional theory (DFT) within the generalized gradient approximation (GGA–PBE) to investigate the structural, electronic, thermodynamic, and thermal properties of zinc-blende AlP, BP, and their ternary alloy Al₁₋ₓBₓP (<i>x</i> = 0.25, 0.50, 0.75). The equilibrium lattice parameters, band structures, density of states (DOS), formation energies, and thermodynamic parameters were systematically analyzed to evaluate alloy stability and temperature-dependent behavior.</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":"145802862","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/s00894-025-06589-0
Prashant Kurkute, Sakshi Wagh, Komal Nandode, Amit Gangwal, Sumit Sonawane, Vedant Shimpi, Azim Ansari, Yogeeta O. Agrawal, Mrunali Patil, Mohd Usman MohdSiddique MS
Context
Overexpression of Epidermal Growth Factor Receptor (EGFR) is commonly found in triple negative breast cancer. This subtype does not contain the oestrogen receptors (ER), progesterone receptors (PR), and HER2 amplification. The wide scope of biological activities and varied structural classes of natural phenolic compounds paves significant opportunities for drug discovery. The modern drug discovery process combines natural phenolic compounds and computational or AI techniques to develop novel drugs. Considering this fact, EGFR inhibitors were designed based upon the multiscale computational studies of natural phenolic compounds to identify the potent anticancer molecules for triple negative breast cancer (TNBC).
Method
Preliminary screening of all natural phenolic compounds (containing 440 phenolic compounds) was done by molecular docking studies using the glide utility of Maestro tools. The top scoring molecules were further subjected to MD simulation studies by using Desmond software. The obtained trajectory files were processed through R Studio software for data analysis employing PCA analysis, cluster analysis, and DCCM calculation. Then, binding free energies of complexes were determined by MMGBSA calculation, and drug likeliness of molecules were checked by in silico ADME calculation. These obtained in silico generated data were analysed, and it was concluded that the identified molecules bearing phenolic compounds would be a promising scaffold for EGFR inhibitors and anticancer drugs for TNBC. However, experimental results are needed to prove the obtained results.
{"title":"Computational screening of natural phenolic compounds as potential EGFR inhibitors against triple negative breast cancer","authors":"Prashant Kurkute, Sakshi Wagh, Komal Nandode, Amit Gangwal, Sumit Sonawane, Vedant Shimpi, Azim Ansari, Yogeeta O. Agrawal, Mrunali Patil, Mohd Usman MohdSiddique MS","doi":"10.1007/s00894-025-06589-0","DOIUrl":"10.1007/s00894-025-06589-0","url":null,"abstract":"<div><h3>Context</h3><p>Overexpression of Epidermal Growth Factor Receptor (EGFR) is commonly found in triple negative breast cancer. This subtype does not contain the oestrogen receptors (ER), progesterone receptors (PR), and HER2 amplification. The wide scope of biological activities and varied structural classes of natural phenolic compounds paves significant opportunities for drug discovery. The modern drug discovery process combines natural phenolic compounds and computational or AI techniques to develop novel drugs. Considering this fact, EGFR inhibitors were designed based upon the multiscale computational studies of natural phenolic compounds to identify the potent anticancer molecules for triple negative breast cancer (TNBC).</p><h3>Method</h3><p>Preliminary screening of all natural phenolic compounds (containing 440 phenolic compounds) was done by molecular docking studies using the glide utility of Maestro tools. The top scoring molecules were further subjected to MD simulation studies by using Desmond software. The obtained trajectory files were processed through R Studio software for data analysis employing PCA analysis, cluster analysis, and DCCM calculation. Then, binding free energies of complexes were determined by MMGBSA calculation, and drug likeliness of molecules were checked by <i>in silico</i> ADME calculation. These obtained <i>in silico</i> generated data were analysed, and it was concluded that the identified molecules bearing phenolic compounds would be a promising scaffold for EGFR inhibitors and anticancer drugs for TNBC. However, experimental results are needed to prove the obtained results.</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":"145802877","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 : 2025-12-17DOI: 10.1007/s00894-025-06610-6
Habtamu F. Etefa, Francis B. Dejene
Context
The structural and electronic modifications induced by tin (Sn) doping in cubic nickel oxide (NiO) were investigated through a combined computational and experimental approach. Sn incorporation into the NiO lattice is of significant interest for tailoring its optoelectronic properties toward enhanced energy conversion and photocatalytic applications. Experimentally synthesized NiO nanoparticles confirmed the theoretical predictions, showing that increasing Sn concentration (0–12.5%) leads to lattice distortion and bandgap narrowing. The observed bandgap reduction, from 2.89 eV (pure NiO) to 2.56 eV (12.5% Sn-NiO), was attributed to a Fermi level shift and the introduction of defect states, demonstrating that Sn doping effectively tunes the electronic structure of NiO.
Methods
Theoretical investigations were conducted using spin-polarized density functional theory with Hubbard correction (DFT + U) within the Quantum ESPRESSO (v7.2) framework to elucidate the electronic properties. The cubic NiO (a = 4.22 Å) was modeled with a 2 × 2 × 2 supercell using the Perdew–Burke–Ernzerhof (PBE) functional under generalized gradient approximation (GGA) and ultrasoft pseudopotentials from PSLibrary 1.0.0. Convergence tests yielded cutoffs of 50 Ry (wavefunction) and 400 Ry (charge density) with a 7 × 7 × 7 Monkhorst–Pack grid. A Hubbard U of 6.0 eV was applied to Ni 3d orbitals to correct correlation effects. Sn doping (3.125–12.5%) was introduced by substituting Ni atoms, and all structures were optimized using the Broyden–Fletcher–Goldfarb–Shanno (BFGS) algorithm. Electronic band structures and density of states (DOS) were calculated along high-symmetry paths to analyze the doping-induced modifications in NiO’s electronic properties.
{"title":"Tuning the band gap and optical characteristics of NiO nanoparticles via tin (Sn) doping: a combined experimental and DFT investigation","authors":"Habtamu F. Etefa, Francis B. Dejene","doi":"10.1007/s00894-025-06610-6","DOIUrl":"10.1007/s00894-025-06610-6","url":null,"abstract":"<div><h3>Context</h3><p>The structural and electronic modifications induced by tin (Sn) doping in cubic nickel oxide (NiO) were investigated through a combined computational and experimental approach. Sn incorporation into the NiO lattice is of significant interest for tailoring its optoelectronic properties toward enhanced energy conversion and photocatalytic applications. Experimentally synthesized NiO nanoparticles confirmed the theoretical predictions, showing that increasing Sn concentration (0–12.5%) leads to lattice distortion and bandgap narrowing. The observed bandgap reduction, from 2.89 eV (pure NiO) to 2.56 eV (12.5% Sn-NiO), was attributed to a Fermi level shift and the introduction of defect states, demonstrating that Sn doping effectively tunes the electronic structure of NiO.</p><h3>Methods</h3><p>Theoretical investigations were conducted using spin-polarized density functional theory with Hubbard correction (DFT + U) within the Quantum ESPRESSO (v7.2) framework to elucidate the electronic properties. The cubic NiO (<i>a</i> = 4.22 Å) was modeled with a 2 × 2 × 2 supercell using the Perdew–Burke–Ernzerhof (PBE) functional under generalized gradient approximation (GGA) and ultrasoft pseudopotentials from PSLibrary 1.0.0. Convergence tests yielded cutoffs of 50 Ry (wavefunction) and 400 Ry (charge density) with a 7 × 7 × 7 Monkhorst–Pack grid. A Hubbard <i>U</i> of 6.0 eV was applied to Ni 3d orbitals to correct correlation effects. Sn doping (3.125–12.5%) was introduced by substituting Ni atoms, and all structures were optimized using the Broyden–Fletcher–Goldfarb–Shanno (BFGS) algorithm. Electronic band structures and density of states (DOS) were calculated along high-symmetry paths to analyze the doping-induced modifications in NiO’s electronic properties. \u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145766737","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 : 2025-12-16DOI: 10.1007/s00894-025-06602-6
Xiao-Feng Qing, Xiao Liu, Qing Han, Jia-Jun Ma, Li-Juan Ran, Fei Zhou, Hongli Wang, Bo Dai, Ni-Na Ge
Context
Currently, boron modification represents a significant strategy for enhancing the thermal stability of phenolic resins. However, existing boron modification methods generally suffer from synthetic complexity, and the mechanism of boron’s effect on phenolic resins at the molecular level remains incompletely understood. This study investigated how 4-hydroxyphenylboronic acid pinacol ester (4-HPBAPE) doping regulates the glass transition temperature (Tg), thermal conductivity, and pyrolysis behavior of phenolic resin. Results showed that 4-HPBAPE doping increased the glass transition temperature (162 → 187 ℃), while thermal conductivity testing revealed a 10% reduction (0.2154 → 0.1920 W/(m·K)). The errors between the results obtained from MD simulation and the experimental results were all less than 10%. The char yield decreased with increasing 4-HPBAPE doping ratio. ReaxFF MD simulations demonstrated that boron modification of phenolic resins enhanced the production of light hydrocarbons (C1–C5) during pyrolysis, resulting in higher mass loss. This occurred via boron-mediated ring-opening and suppression of large aromatic cluster formation. Future efforts could focus on controlling the bonding form of boron to suppress ring-opening reactions, thereby enhancing the char yield.
Methods
The materials were characterized using Fourier transform infrared spectrometer (FTIR) and nuclear magnetic resonance spectroscopy (NMR). Thermal conductivity was measured using a DRE-2C thermal conductivity meter. Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) were performed using a synchronous thermal analyzer. Simulations were carried out with the LAMMPS and Materials Studio software package. Classical molecular dynamics (MD) simulations employed the COMPASS force field, while the reaction force field files containing C, H, O and B element were used. The post-processing of the results was implemented using OVITO and self-programmed Python scripts.
{"title":"Boron-modified phenolic resin: thermal stability and decomposition mechanisms via experiments and simulations","authors":"Xiao-Feng Qing, Xiao Liu, Qing Han, Jia-Jun Ma, Li-Juan Ran, Fei Zhou, Hongli Wang, Bo Dai, Ni-Na Ge","doi":"10.1007/s00894-025-06602-6","DOIUrl":"10.1007/s00894-025-06602-6","url":null,"abstract":"<div><h3>Context</h3><p>Currently, boron modification represents a significant strategy for enhancing the thermal stability of phenolic resins. However, existing boron modification methods generally suffer from synthetic complexity, and the mechanism of boron’s effect on phenolic resins at the molecular level remains incompletely understood. This study investigated how 4-hydroxyphenylboronic acid pinacol ester (4-HPBAPE) doping regulates the glass transition temperature (<i>T</i><sub>g</sub>), thermal conductivity, and pyrolysis behavior of phenolic resin. Results showed that 4-HPBAPE doping increased the glass transition temperature (162 → 187 ℃), while thermal conductivity testing revealed a 10% reduction (0.2154 → 0.1920 W/(m·K)). The errors between the results obtained from MD simulation and the experimental results were all less than 10%. The char yield decreased with increasing 4-HPBAPE doping ratio. ReaxFF MD simulations demonstrated that boron modification of phenolic resins enhanced the production of light hydrocarbons (C<sub>1</sub>–C<sub>5</sub>) during pyrolysis, resulting in higher mass loss. This occurred via boron-mediated ring-opening and suppression of large aromatic cluster formation. Future efforts could focus on controlling the bonding form of boron to suppress ring-opening reactions, thereby enhancing the char yield.</p><h3>Methods</h3><p>The materials were characterized using Fourier transform infrared spectrometer (FTIR) and nuclear magnetic resonance spectroscopy (NMR). Thermal conductivity was measured using a DRE-2C thermal conductivity meter. Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) were performed using a synchronous thermal analyzer. Simulations were carried out with the LAMMPS and Materials Studio software package. Classical molecular dynamics (MD) simulations employed the COMPASS force field, while the reaction force field files containing C, H, O and B element were used. The post-processing of the results was implemented using OVITO and self-programmed Python scripts.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761560","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 : 2025-12-16DOI: 10.1007/s00894-025-06600-8
Akash Moi, Md. Shahzad Khan, Anurag Srivastava, Boddepalli SanthiBhushan
Context
Ever since the experimental realization of the first free-standing layers of stanene by researchers in 2016, this potential wonder material is widely being explored for various applications. This work analyzes the implication of this novel 2D material for supercapacitor electrodes and ways to enhance its quantum capacitance and charge storage capacity via first principles simulations. The stanene nanosheet is subjected to single vacancy (SV) defect and near valence (In and Sb) doping (direct doping at the SV site, independent doping at the SV edges, and co-doping at the SV edges). The results reveal the zero band gap nature of pristine stanene similar to graphene, yet at least 7 times enhancement in quantum capacitance in comparison to pristine graphene. The incorporation of a single vacancy (SV) defect in stanene has improved its quantum capacitance and charge storage capacity by 1.54 times, at the expense of compromised thermodynamic stability. Thus, to preserve the thermodynamic stability with minimal lattice distortions and enhance the quantum capacitance as well as charge storage of SV stanene, near valence dopants are introduced at the SV site and SV edges. Our results confirm that antimony doping in stanene offers better thermodynamic stability than Indium. Moreover, the independent doping of 3 antimony atoms at SV edges offers the highest quantum capacitance of 134.21 μF/cm2 at 0.6 V, which is about 1.47 times higher than the maximum value (91 μF/cm2 for N and Ni co-doping) reported in the literature for any doping. All the SV and near valence doped stanene configurations are observed to be better suitable for the anode electrode of asymmetric supercapacitors owing to their quantum capacitance and charge storage peaks on the positive side of the electrochemical window, except for one particular configuration, i.e., the direct antimony doping at the SV site, which is better suitable for the cathode electrode of the asymmetric supercapacitor.
Methods
The DFT-based first principle simulations combined with MATLAB programming are performed to study the capacitive behavior of the electrodes. A k-point sampling of 7 × 7 × 1 is found to be sufficient for sampling the Brillouin zone in reciprocal space, and a density mesh cutoff of 80 Hartree is used to define the fineness of real space effective potential and electron density grids for solving Poisson’s equation. The Generalized Gradient Approximation (GGA) with Perdew-Burke-Ernzerhof parameterization is used as the exchange correlation functional.
{"title":"Enhanced quantum capacitance of near valence doped stanene nanosheets for asymmetric supercapacitors","authors":"Akash Moi, Md. Shahzad Khan, Anurag Srivastava, Boddepalli SanthiBhushan","doi":"10.1007/s00894-025-06600-8","DOIUrl":"10.1007/s00894-025-06600-8","url":null,"abstract":"<div><h3>Context</h3><p>Ever since the experimental realization of the first free-standing layers of stanene by researchers in 2016, this potential wonder material is widely being explored for various applications. This work analyzes the implication of this novel 2D material for supercapacitor electrodes and ways to enhance its quantum capacitance and charge storage capacity via first principles simulations. The stanene nanosheet is subjected to single vacancy (SV) defect and near valence (In and Sb) doping (direct doping at the SV site, independent doping at the SV edges, and co-doping at the SV edges). The results reveal the zero band gap nature of pristine stanene similar to graphene, yet at least 7 times enhancement in quantum capacitance in comparison to pristine graphene. The incorporation of a single vacancy (SV) defect in stanene has improved its quantum capacitance and charge storage capacity by 1.54 times, at the expense of compromised thermodynamic stability. Thus, to preserve the thermodynamic stability with minimal lattice distortions and enhance the quantum capacitance as well as charge storage of SV stanene, near valence dopants are introduced at the SV site and SV edges. Our results confirm that antimony doping in stanene offers better thermodynamic stability than Indium. Moreover, the independent doping of 3 antimony atoms at SV edges offers the highest quantum capacitance of 134.21 μF/cm<sup>2</sup> at 0.6 V, which is about 1.47 times higher than the maximum value (91 μF/cm<sup>2</sup> for N and Ni co-doping) reported in the literature for any doping. All the SV and near valence doped stanene configurations are observed to be better suitable for the anode electrode of asymmetric supercapacitors owing to their quantum capacitance and charge storage peaks on the positive side of the electrochemical window, except for one particular configuration, i.e., the direct antimony doping at the SV site, which is better suitable for the cathode electrode of the asymmetric supercapacitor.</p><h3>Methods</h3><p>The DFT-based first principle simulations combined with MATLAB programming are performed to study the capacitive behavior of the electrodes. A <i>k-point</i> sampling of 7 × 7 × 1 is found to be sufficient for sampling the Brillouin zone in reciprocal space, and a density mesh cutoff of 80 Hartree is used to define the fineness of real space effective potential and electron density grids for solving Poisson’s equation. The Generalized Gradient Approximation (GGA) with Perdew-Burke-Ernzerhof parameterization is used as the exchange correlation functional.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761783","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 : 2025-12-16DOI: 10.1007/s00894-025-06604-4
Die Gao, Qi Gao, Jianguo Zhang, Jinting Wu, Tingxing Zhao, Hongbo Li
Context
Substituents including -NH2, -NO2, -NHNO2, and -CH(NO2)2 were introduced into the N,N′-linked bis-triazole scaffold to design 72 derivatives. Density functional theory (DFT) calculations at the B3LYP/6-311+G(d, p) level were performed using the Gaussian 09 software package to evaluate critical parameters such as density, heat of formation (HOF), detonation pressure (P), detonation velocity (D), explosive energy release (Q), sensitivity, and molecular orbital energies (HOMO–LUMO) for all 72 derivatives. The results indicate that compound C3 (ρ = 1.86 g.cm−3, D = 8.77 km.s−1, P = 34.83 GPa, h50% = 39.27 cm), C12 (ρ = 1.86 g.cm−3, D = 9.11 km.s−1, P = 37.45 GPa, h50% = 29.97 cm), and D15 (ρ = 1.80 g.cm−3, D = 9.03 km.s−1, P = 36.11 GPa, h50% = 31.47 cm) exhibit potential as substitute explosive candidates for 1,3,5-trinitro-1,3,5-triazinane (RDX) (ρ = 1.80 g.cm−3, D = 8.75 km.s−1, P = 34 GPa, h50% = 26 cm).
Methods
The structural optimization, volume calculations, and electrostatic potential energy analyses were conducted using the Gaussian 09 and Multiwfn 3.8 software packages, employing the B3LYP method within density functional theory (DFT). The structures of 72 derivatives were optimized at the 6-311+G(d, p) basis set level, followed by an investigation into their detonation performance and stability characteristics.
背景：将-NH2、-NO2、-NHNO2、-CH(NO2)2等取代基引入N，N'链双三唑支架中，设计72个衍生物。使用Gaussian 09软件包进行B3LYP/6-311+G（d, p）水平的密度泛函数理论（DFT）计算，以评估所有72个衍生物的密度、形成热（HOF）、爆轰压力(p)、爆轰速度(d)、爆炸能量释放(Q)、灵敏度和分子轨道能（HOMO-LUMO）等关键参数。结果表明,复合C3(ρ= 1.86 g.cm-3, km.s-1 D = 8.77, P = 34.83的绩点,h50% = 39.27厘米),C12(ρ= 1.86 g.cm-3, km.s-1 D = 9.11, P = 37.45的绩点,h50% = 29.97厘米),和D15(ρ= 1.80 g.cm-3, km.s-1 D = 9.03, P = 36.11的绩点,h50% = 31.47厘米)表现出潜在的替代炸药候选人1,3,5-trinitro-1, 3, 5-triazinane (RDX)(ρ= 1.80 g.cm-3, km.s-1 D = 8.75, P = 34 GPa, h50% = 26厘米)。方法：采用密度泛函理论（DFT）中的B3LYP方法，利用Gaussian 09和Multiwfn 3.8软件包进行结构优化、体积计算和静电势能分析。在6-311+G（d, p）基集水平上对72种衍生物进行了结构优化，并对其爆轰性能和稳定性进行了研究。
{"title":"Investigation into the performance characteristics of N,N′-bonded bis-triazole derivatives","authors":"Die Gao, Qi Gao, Jianguo Zhang, Jinting Wu, Tingxing Zhao, Hongbo Li","doi":"10.1007/s00894-025-06604-4","DOIUrl":"10.1007/s00894-025-06604-4","url":null,"abstract":"<div><h3>Context</h3><p>Substituents including -NH<sub>2</sub>, -NO<sub>2</sub>, -NHNO<sub>2</sub>, and -CH(NO<sub>2</sub>)<sub>2</sub> were introduced into the <i>N,N</i>′-linked bis-triazole scaffold to design 72 derivatives. Density functional theory (DFT) calculations at the B3LYP/6-311+G(d, p) level were performed using the Gaussian 09 software package to evaluate critical parameters such as density, heat of formation (HOF), detonation pressure (<i>P</i>), detonation velocity (<i>D</i>), explosive energy release (<i>Q</i>), sensitivity, and molecular orbital energies (HOMO–LUMO) for all 72 derivatives. The results indicate that compound C3 (<i>ρ</i> = 1.86 g.cm<sup>−3</sup>, <i>D</i> = 8.77 km.s<sup>−1</sup>, <i>P</i> = 34.83 GPa, <i>h</i><sub>50%</sub> = 39.27 cm), C12 (<i>ρ</i> = 1.86 g.cm<sup>−3</sup>, <i>D</i> = 9.11 km.s<sup>−1</sup>, <i>P</i> = 37.45 GPa, <i>h</i><sub>50%</sub> = 29.97 cm), and D15 (<i>ρ</i> = 1.80 g.cm<sup>−3</sup>, <i>D</i> = 9.03 km.s<sup>−1</sup>, <i>P</i> = 36.11 GPa, <i>h</i><sub>50%</sub> = 31.47 cm) exhibit potential as substitute explosive candidates for 1,3,5-trinitro-1,3,5-triazinane (RDX) (<i>ρ</i> = 1.80 g.cm<sup>−3</sup>, <i>D</i> = 8.75 km.s<sup>−1</sup>, <i>P</i> = 34 GPa, <i>h</i><sub>50%</sub> = 26 cm).</p><h3>Methods</h3><p>The structural optimization, volume calculations, and electrostatic potential energy analyses were conducted using the Gaussian 09 and Multiwfn 3.8 software packages, employing the B3LYP method within density functional theory (DFT). The structures of 72 derivatives were optimized at the 6-311+G(d, p) basis set level, followed by an investigation into their detonation performance and stability characteristics.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761763","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 : 2025-12-16DOI: 10.1007/s00894-025-06608-0
Zilian Tian, Lu Yang, Jianlin He
Context
Two-dimensional transition-metal dichalcogenides such as WSe2 are promising platforms for tunable optoelectronic devices. Here, first-principles molecular modeling is used to examine how substitutional Si doping combined with shear strain tunes the electronic and optical properties of monolayer WSe2. Si dopants introduce localized states that reduce the band gap from 1.599 to 1.029 eV and enhance low-energy absorption. Shear strain applied along orthogonal in-plane directions (xy and yx) further induces direction-dependent electronic localization and band-gap renormalization, giving rise to anisotropic optical absorption. These results provide mechanistic insight and a simple strategy for tailoring the optoelectronic response of WSe2-based materials.
Methods
Density functional theory calculations within the generalized-gradient approximation are performed using the Perdew–Burke–Ernzerhof functional and Gaussian-type basis sets as implemented in the Materials Studio package. Substitutional Si doping is modeled in a WSe2 supercell, and shear strain is introduced by distorting the in-plane lattice vectors along the xy and yx directions. For each configuration, fully relaxed geometries are used to evaluate the electronic band structures, charge redistribution, and complex dielectric function. Optical absorption spectra are obtained from the frequency-dependent dielectric tensor within the independent-particle approximation.
{"title":"Effects of Si-doped and shear strain on the optoelectronic properties of WSe2: A first principles study","authors":"Zilian Tian, Lu Yang, Jianlin He","doi":"10.1007/s00894-025-06608-0","DOIUrl":"10.1007/s00894-025-06608-0","url":null,"abstract":"<div><h3>Context</h3><p>Two-dimensional transition-metal dichalcogenides such as WSe<sub>2</sub> are promising platforms for tunable optoelectronic devices. Here, first-principles molecular modeling is used to examine how substitutional Si doping combined with shear strain tunes the electronic and optical properties of monolayer WSe<sub>2</sub>. Si dopants introduce localized states that reduce the band gap from 1.599 to 1.029 eV and enhance low-energy absorption. Shear strain applied along orthogonal in-plane directions (xy and yx) further induces direction-dependent electronic localization and band-gap renormalization, giving rise to anisotropic optical absorption. These results provide mechanistic insight and a simple strategy for tailoring the optoelectronic response of WSe<sub>2</sub>-based materials.</p><h3>Methods</h3><p>Density functional theory calculations within the generalized-gradient approximation are performed using the Perdew–Burke–Ernzerhof functional and Gaussian-type basis sets as implemented in the Materials Studio package. Substitutional Si doping is modeled in a WSe<sub>2</sub> supercell, and shear strain is introduced by distorting the in-plane lattice vectors along the xy and yx directions. For each configuration, fully relaxed geometries are used to evaluate the electronic band structures, charge redistribution, and complex dielectric function. Optical absorption spectra are obtained from the frequency-dependent dielectric tensor within the independent-particle approximation.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761553","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}
High carbon emissions have become a major problem perplexing human society, and the use of shale for CO2 storage has a broad application prospect and significance. In this paper, a SiO2- Al2O3 heterostructure model representing clay shale is established, and the adsorption mechanisms of CO2 in clay shale are studied systematically by means of grand canonical Monte Carlo (GCMC), molecular dynamics (MD) and density functional theory (DFT). The findings indicate that the system's equilibrium shifts toward adsorption as pressure increases, enhancing gas uptake. Conversely, rising temperature favors the desorption equilibrium, thereby reducing the overall adsorption capacity. Higher water content reduces CO2 adsorption capacity in hydrous SiO2-Al2O3 nanopores. For every 5 wt% increment in water content, the CO2 adsorption amount decreases by approximately 18.6%. The density profiles show that the interaction between H2O and adsorption sites on the shale surface is stronger than that of CO2. The radial distribution functions indicate the difference of CO2 distribution between SiO2 region and Al2O3 region and reveal the effect of water on Al2O3 region is greater than that of SiO2 region. This study has an in-depth exploration of the adsorption rule and migration mechanism of CO2 in clay shale, which may contribute preliminary theoretical insights for optimizing CO2 adsorption and storage.
Method
The simulation software employed in this study is Materials Studio, and the associated force field utilized is COMPASS III. The adsorption configurations are obtained from the Sorption module and molecular dynamics simulations are performed on it by using the Forcite module with the NVT ensemble. Based on the DFT, molecular optimization and performance metrics analysis are all calculated using the DMol3 module.
{"title":"Competitive adsorption mechanisms of CO2 in hydrous silica-alumina clay shale nanopores: a comprehensive exploration","authors":"Zhichao Zhang, Liehui Zhang, Yulong Zhao, Peiming Bian, Xin Chen","doi":"10.1007/s00894-025-06597-0","DOIUrl":"10.1007/s00894-025-06597-0","url":null,"abstract":"<div><h3>Context</h3><p>High carbon emissions have become a major problem perplexing human society, and the use of shale for CO<sub>2</sub> storage has a broad application prospect and significance. In this paper, a SiO<sub>2</sub>- Al<sub>2</sub>O<sub>3</sub> heterostructure model representing clay shale is established, and the adsorption mechanisms of CO<sub>2</sub> in clay shale are studied systematically by means of grand canonical Monte Carlo (GCMC), molecular dynamics (MD) and density functional theory (DFT). The findings indicate that the system's equilibrium shifts toward adsorption as pressure increases, enhancing gas uptake. Conversely, rising temperature favors the desorption equilibrium, thereby reducing the overall adsorption capacity. Higher water content reduces CO<sub>2</sub> adsorption capacity in hydrous SiO<sub>2</sub>-Al<sub>2</sub>O<sub>3</sub> nanopores. For every 5 wt% increment in water content, the CO<sub>2</sub> adsorption amount decreases by approximately 18.6%. The density profiles show that the interaction between H<sub>2</sub>O and adsorption sites on the shale surface is stronger than that of CO<sub>2</sub>. The radial distribution functions indicate the difference of CO<sub>2</sub> distribution between SiO<sub>2</sub> region and Al<sub>2</sub>O<sub>3</sub> region and reveal the effect of water on Al<sub>2</sub>O<sub>3</sub> region is greater than that of SiO<sub>2</sub> region. This study has an in-depth exploration of the adsorption rule and migration mechanism of CO<sub>2</sub> in clay shale, which may contribute preliminary theoretical insights for optimizing CO<sub>2</sub> adsorption and storage.</p><h3>Method</h3><p>The simulation software employed in this study is Materials Studio, and the associated force field utilized is COMPASS III. The adsorption configurations are obtained from the Sorption module and molecular dynamics simulations are performed on it by using the Forcite module with the NVT ensemble. Based on the DFT, molecular optimization and performance metrics analysis are all calculated using the DMol<sup>3</sup> module.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761569","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 : 2025-12-16DOI: 10.1007/s00894-025-06591-6
Mauricio Barrera, Irma Crivelli
Context
In order to increase the efficiency of dye-sensitized solar cells (DSSC), we propose to study the influence of maximizing the push–pull effect by quantifying the donor force (Ds) and the acceptor capacity (Ap) calculated as functions of the Electrophilicity, Orbital Hardness, and Polarizability. The sum of the donor force and the acceptor capacity is the inductive force, which allows the push–pull effect to be maximized. With this approach, we applied the Barrera-Crivelli-Loeb (BCL) model to a series of eleven Zinc Porphyrins to correlate the Global Efficiency Index (GEI) with the experimental measurement of Photo Conversion Efficiency (PCE). The use of this strategy together with the use of siloles and siloxanes allows the design of two new dyes, BCL 516 and BCL 520, with theoretically calculated efficiencies of 10.64% and 10.61%.
Methods
In this work, all calculations were performed with the Amsterdam Density Functional 2023 package. For geometry optimization (ground state and first singlet), the optimized Perdew-Becke-Ernzerhof exchange correlation functional was employed with a DZP basis set for H, C, N, O, S, and a Zeroth Order Regular Approximation (ZORA) – TZP basis set for Ti and Zn. Time-Dependent Density Functional Theory (TDDFT) calculations were achieved with the Statistical Average Orbital model exchange correlation potential (SAOP), including solvent effects with the Conductor-like Screening Model (COSMO). Calculations of molecular properties like electrophilicity, orbital hardness, and polarizability were carried out in the gas phase with the SAOP potential model after optimization of the target molecule with the OPBE exchange correlation functional. To determine the orbital hardness of the HOMO and LUMO, the occupation number of the frontier orbital was modified by 0.3 units.
{"title":"`Theoretical study of the enhancement of the photoconversion eficiency on zinc porphyrin dyes by combining electron donor–acceptor theory with the Barrera-Crivelli-Loeb (BCL) model","authors":"Mauricio Barrera, Irma Crivelli","doi":"10.1007/s00894-025-06591-6","DOIUrl":"10.1007/s00894-025-06591-6","url":null,"abstract":"<div><h3>Context</h3><p>In order to increase the efficiency of dye-sensitized solar cells (DSSC), we propose to study the influence of maximizing the push–pull effect by quantifying the donor force (Ds) and the acceptor capacity (Ap) calculated as functions of the Electrophilicity, Orbital Hardness, and Polarizability. The sum of the donor force and the acceptor capacity is the inductive force, which allows the push–pull effect to be maximized. With this approach, we applied the Barrera-Crivelli-Loeb (BCL) model to a series of eleven Zinc Porphyrins to correlate the Global Efficiency Index (GEI) with the experimental measurement of Photo Conversion Efficiency (PCE). The use of this strategy together with the use of siloles and siloxanes allows the design of two new dyes, BCL 516 and BCL 520, with theoretically calculated efficiencies of 10.64% and 10.61%.</p><h3>Methods</h3><p>In this work, all calculations were performed with the Amsterdam Density Functional 2023 package. For geometry optimization (ground state and first singlet), the optimized Perdew-Becke-Ernzerhof exchange correlation functional was employed with a DZP basis set for H, C, N, O, S, and a Zeroth Order Regular Approximation (ZORA) – TZP basis set for Ti and Zn. Time-Dependent Density Functional Theory (TDDFT) calculations were achieved with the Statistical Average Orbital model exchange correlation potential (SAOP), including solvent effects with the Conductor-like Screening Model (COSMO). Calculations of molecular properties like electrophilicity, orbital hardness, and polarizability were carried out in the gas phase with the SAOP potential model after optimization of the target molecule with the OPBE exchange correlation functional. To determine the orbital hardness of the HOMO and LUMO, the occupation number of the frontier orbital was modified by 0.3 units.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761562","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 : 2025-12-16DOI: 10.1007/s00894-025-06609-z
Chaofu Wu
Context
Due to the versatile properties, the hydrocarbon ladder polymers developed recently represent a class of promising materials for membrane separations of industrially relevant gas mixtures. The excellent thermomechanical properties and ultrahigh permselectivity are generally attributed to the chain rigidity of the three-dimensional (3D) ladder structures, which are not readily accessible via experiments. Therefore, this work takes advantage of molecular simulations to quantify the chain rigidity of such polymers, which exhibit quite different behaviors from the conventional polymers. It is first identified that the characteristic segments and repeating units behave like bows that are easy to press but difficult to pull. Furthermore, it is demonstrated that the subtle influences of side groups and temperature on the end-to-end distance (Re) can be well captured by these all-atomistic (AA) simulations. As suggested by the fluctuation in Re, the configuration provides an effective way to tune overall chain morphology and thus its rigidity, resulting from both the rigidity and shape of characteristic segments. These results highlight the unique rigidity of such polymers, which should inspire further development of new robust polymer membranes of gas separations.
Methods
The software named Materials Studio 4.0 was employed to construct the all-atomistic structures of model systems and to perform all the energy minimizations and molecular dynamics simulations with the Deriding force field and QEq charges, and to analyze the structural and energetic properties.
背景：由于其多用途的特性，最近开发的碳氢阶梯聚合物代表了一类有前途的材料，用于工业相关气体混合物的膜分离。优异的热机械性能和超高的过电选择性通常归因于三维（3D）阶梯结构的链刚性，这是不易通过实验获得的。因此，这项工作利用分子模拟来量化这种聚合物的链刚性，它表现出与传统聚合物完全不同的行为。首先确定了特征段和重复单元的行为像弓，容易按，但很难拉。此外，这些全原子（AA）模拟可以很好地捕捉到侧基和温度对端到端距离（Re）的微妙影响。正如Re的波动所表明的那样，该构型提供了一种有效的方法来调整整体链的形态，从而调整其刚度，这是由特征段的刚度和形状产生的。这些结果突出了这种聚合物的独特刚性，这应该激发进一步开发新的坚固的气体分离聚合物膜。方法：采用Materials Studio 4.0软件构建模型体系的全原子结构，并利用Deriding力场和QEq电荷进行全能量最小化和分子动力学模拟，分析其结构和能量性质。
{"title":"Chain rigidity of 3D-ladder polymers quantified by molecular simulations","authors":"Chaofu Wu","doi":"10.1007/s00894-025-06609-z","DOIUrl":"10.1007/s00894-025-06609-z","url":null,"abstract":"<div><h3>Context</h3><p>Due to the versatile properties, the hydrocarbon ladder polymers developed recently represent a class of promising materials for membrane separations of industrially relevant gas mixtures. The excellent thermomechanical properties and ultrahigh permselectivity are generally attributed to the chain rigidity of the three-dimensional (3D) ladder structures, which are not readily accessible via experiments. Therefore, this work takes advantage of molecular simulations to quantify the chain rigidity of such polymers, which exhibit quite different behaviors from the conventional polymers. It is first identified that the characteristic segments and repeating units behave like bows that are easy to press but difficult to pull. Furthermore, it is demonstrated that the subtle influences of side groups and temperature on the end-to-end distance (Re) can be well captured by these all-atomistic (AA) simulations. As suggested by the fluctuation in Re, the configuration provides an effective way to tune overall chain morphology and thus its rigidity, resulting from both the rigidity and shape of characteristic segments. These results highlight the unique rigidity of such polymers, which should inspire further development of new robust polymer membranes of gas separations.</p><h3> Methods</h3><p>The software named Materials Studio 4.0 was employed to construct the all-atomistic structures of model systems and to perform all the energy minimizations and molecular dynamics simulations with the Deriding force field and QEq charges, and to analyze the structural and energetic properties.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761563","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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