Pub Date : 2025-11-27DOI: 10.1016/j.jmgm.2025.109234
Qinghua Yang , Maodong Guo , Xiao Zhu
Ursolic acid (UA) exhibits anti-inflammatory and anti-tumor properties. Developing a nanodrug delivery system for UA can improve its bioavailability. Transition metal sulfides, owing to their distinctive physicochemical characteristics, have emerged as the predominant two-dimensional nanostructures utilized in the advancement of nanodrug delivery systems in recent years. This study employs first-principles calculations to assess the viability of monolayer PtS2 as a carrier for UA. The results indicate that monolayer PtS2 exhibits structural stability as a UA carrier, with an adsorption energy of −3.84 eV. Mulliken charge analysis reveals that UA donates 0.34 |e| to PtS2. Additionally, the application of strain induces a redshift in the optical absorption peak of monolayer PtS2, thereby enhancing its optical absorption capabilities. Furthermore, monolayer PtS2 displays favorable temperature-controlled release properties when utilized as a delivery vehicle for Ursolic acid. These results offer theoretical insights that could inform the development of innovative drug carriers and significantly contribute to the treatment of inflammatory bowel disease.
{"title":"Theoretical calculations of monolayer PtS2 as a drug delivery carrier for ursolic acid","authors":"Qinghua Yang , Maodong Guo , Xiao Zhu","doi":"10.1016/j.jmgm.2025.109234","DOIUrl":"10.1016/j.jmgm.2025.109234","url":null,"abstract":"<div><div>Ursolic acid (UA) exhibits anti-inflammatory and anti-tumor properties. Developing a nanodrug delivery system for UA can improve its bioavailability. Transition metal sulfides, owing to their distinctive physicochemical characteristics, have emerged as the predominant two-dimensional nanostructures utilized in the advancement of nanodrug delivery systems in recent years. This study employs first-principles calculations to assess the viability of monolayer PtS<sub>2</sub> as a carrier for UA. The results indicate that monolayer PtS<sub>2</sub> exhibits structural stability as a UA carrier, with an adsorption energy of −3.84 eV. Mulliken charge analysis reveals that UA donates 0.34 |e| to PtS<sub>2</sub>. Additionally, the application of strain induces a redshift in the optical absorption peak of monolayer PtS<sub>2</sub>, thereby enhancing its optical absorption capabilities. Furthermore, monolayer PtS<sub>2</sub> displays favorable temperature-controlled release properties when utilized as a delivery vehicle for Ursolic acid. These results offer theoretical insights that could inform the development of innovative drug carriers and significantly contribute to the treatment of inflammatory bowel disease.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109234"},"PeriodicalIF":3.0,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145617525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-25DOI: 10.1016/j.jmgm.2025.109233
Sattar Arshadi , Mina Salary , Omid Marvi
This study employs density functional theory (DFT) with Grimme's D3-BJ dispersion correction to investigate the adsorption of six hazardous industrial gases (HIGas) including cyanogen chloride (CNCl), formaldehyde (CH2O), cyanogen (C2N2), hydrogen cyanide (HCN), dichloroacetylene (C2Cl2), and phosgene (COCl2) on a magnesium-porphyrin nanoring sensor (NR4P4Mg4). The interactions are characterized as physical and reversible, with BSSE corrected adsorption energies ranging from −1.90 to −18.36 kcal/mol. Gas adsorption induces a significant band gap increase of approximately 122 %, substantially reducing electrical conductivity, while maintaining adsorption distances of 2.16–3.09 Å consistent with physisorption. The calculated recovery times spanning picoseconds to microseconds indicate rapid adsorption-desorption cycles. Electronic structure analysis through Natural Bond Orbital (NBO) and Frontier Molecular Orbital (FMO) calculations reveals consistent electron transfer from gas molecule HOMOs to the nanoring's LUMO. The presence of four distinct adsorption sites enables saturation-free detection of HIGas, with demonstrated resilience against atmospheric interference from nitrogen and humidity.
{"title":"First-principles design of a Mg-porphyrin nanoring sensor via dipole moment and dispersion energy engineering for high-sensitivity detection of hazardous industrial gases","authors":"Sattar Arshadi , Mina Salary , Omid Marvi","doi":"10.1016/j.jmgm.2025.109233","DOIUrl":"10.1016/j.jmgm.2025.109233","url":null,"abstract":"<div><div>This study employs density functional theory (DFT) with Grimme's D3-BJ dispersion correction to investigate the adsorption of six hazardous industrial gases (HI<sub>Gas</sub>) including cyanogen chloride (CNCl), formaldehyde (CH<sub>2</sub>O), cyanogen (C<sub>2</sub>N<sub>2</sub>), hydrogen cyanide (HCN), dichloroacetylene (C<sub>2</sub>Cl<sub>2</sub>), and phosgene (COCl<sub>2</sub>) on a magnesium-porphyrin nanoring sensor (NR<sub>4</sub>P<sub>4</sub>Mg<sub>4</sub>). The interactions are characterized as physical and reversible, with BSSE corrected adsorption energies ranging from −1.90 to −18.36 kcal/mol. Gas adsorption induces a significant band gap increase of approximately 122 %, substantially reducing electrical conductivity, while maintaining adsorption distances of 2.16–3.09 Å consistent with physisorption. The calculated recovery times spanning picoseconds to microseconds indicate rapid adsorption-desorption cycles. Electronic structure analysis through Natural Bond Orbital (NBO) and Frontier Molecular Orbital (FMO) calculations reveals consistent electron transfer from gas molecule HOMOs to the nanoring's LUMO. The presence of four distinct adsorption sites enables saturation-free detection of HI<sub>Gas</sub>, with demonstrated resilience against atmospheric interference from nitrogen and humidity.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109233"},"PeriodicalIF":3.0,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145610622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-25DOI: 10.1016/j.jmgm.2025.109232
Vahid Afsharnia, Ali Mohammad Yadollahi
This study investigates the effects of edge hydrogenation and length changes on the electronic and magnetic properties of armchair PSI (Ψ)-graphene nanoribbons (AΨGNRBs) and zigzag PSI (Ψ)- graphene nanoribbons (ZΨGNRBs) with changing the length and a repetition number from 1 to 10. Density Functional Theory (DFT) and Generalized Gradient Approximation (GGA-1/2) were used for this purpose. The Perdew-Burke-Ernzerhof (PBE) method was used to calculate the exchange-correlation energy. Results demonstrated that hydrogenation of AΨGNRBs causes a band gap of about 0.73 eV with slight changes due to the varied length of the nanoribbon (NRB), but with a constant value of 0.7366 in repetitions from 4 to 10. They are utilized in the fields of optoelectronics, photonics, LEDs, lasers, sensors, and photonic devices. This NRB is a non-magnetic N-type semiconductor. It is used in transistors, and quantum devices that require precise electronic (rather than spintronic) control. However, ZΨGNRBs with changing the length and a repetition number from 1 to 10 are non-magnetic conductors, and edge hydrogenation does not cause a band gap. These nanostructures are compatible with conventional electronic (non-spintronic) devices. The formation energy of hydrogen-passivated AΨGNRBs and ZΨGNRBs is lower than that of the non-passivated counterparts, indicating greater stability of the passivated NRBs. Moreover, the formation energy of AΨGNRBs from 1 to 10 repetitions is lower than that of ZΨGNRBs. This significant reduction in the formation energy indicates greater stability and a more optimal structure of AΨGNRBs compared to ZΨGNRBs. This issue is of critical importance in the design of nanomaterials.
{"title":"Comparison of electronic and magnetic properties of armchair and zigzag Ψ-graphene nanoribbons","authors":"Vahid Afsharnia, Ali Mohammad Yadollahi","doi":"10.1016/j.jmgm.2025.109232","DOIUrl":"10.1016/j.jmgm.2025.109232","url":null,"abstract":"<div><div>This study investigates the effects of edge hydrogenation and length changes on the electronic and magnetic properties of armchair PSI (Ψ)-graphene nanoribbons (AΨGNRBs) and zigzag PSI (Ψ)- graphene nanoribbons (ZΨGNRBs) with changing the length and a repetition number from 1 to 10. Density Functional Theory (DFT) and Generalized Gradient Approximation (GGA-1/2) were used for this purpose. The Perdew-Burke-Ernzerhof (PBE) method was used to calculate the exchange-correlation energy. Results demonstrated that hydrogenation of AΨGNRBs causes a band gap of about 0.73 eV with slight changes due to the varied length of the nanoribbon (NRB), but with a constant value of 0.7366 in repetitions from 4 to 10. They are utilized in the fields of optoelectronics, photonics, LEDs, lasers, sensors, and photonic devices. This NRB is a non-magnetic N-type semiconductor. It is used in transistors, and quantum devices that require precise electronic (rather than spintronic) control. However, ZΨGNRBs with changing the length and a repetition number from 1 to 10 are non-magnetic conductors, and edge hydrogenation does not cause a band gap. These nanostructures are compatible with conventional electronic (non-spintronic) devices. The formation energy of hydrogen-passivated AΨGNRBs and ZΨGNRBs is lower than that of the non-passivated counterparts, indicating greater stability of the passivated NRBs. Moreover, the formation energy of AΨGNRBs from 1 to 10 repetitions is lower than that of ZΨGNRBs. This significant reduction in the formation energy indicates greater stability and a more optimal structure of AΨGNRBs compared to ZΨGNRBs. This issue is of critical importance in the design of nanomaterials.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"143 ","pages":"Article 109232"},"PeriodicalIF":3.0,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145610621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-21DOI: 10.1016/j.jmgm.2025.109230
Yi-Zhe Wang , Tzu-En Lin , Yu-Shan Tsai , Hsuan-Hsuan Lo , Chia-Ning Yang
Ketosteroid isomerase (KSI), a highly conserved enzyme in the β-ketoacyl metabolic pathway, exhibits temperature-dependent functional adaptations across species. In this study, we investigated the temperature sensitivity of mesophilic KSI from Pseudomonas putida using molecular dynamics simulations. Since KSI functions as a dimer, we simulated both monomeric and dimeric forms at its optimal catalytic temperature (303 K) and at an elevated, non-optimal temperature (338 K) to evaluate how temperature and dimerization affect activation. We focused on the dynamics of three catalytically important residues—Y16, D40, and D103—where Y16 is located on the mobile α1-helix not involved in the dimer interface, D40 lies at the edge of the dimer interface, and D103 resides at the center of the core β-sheet structure that remains static in both monomeric and dimeric states. In the monomeric form at 303 K, the Y16–D40, Y16–D103, and D40–D103 pairs exhibit broader and longer separation distances than the optimal range for catalysis. Dimerization stabilizes D40, resulting in a narrower D40–D103 separation that falls within the catalytically competent range. The relatively unchanged mobility of Y16 upon dimerization suggests that Y16 undergoes an induced-fit adjustment upon substrate binding. At 338 K, although dimerization partially corrects the D40–D103 geometry, the increased conformational flexibility of Y16 indicates a reduced likelihood of achieving the substrate-induced active-site reorganization. Together, our results demonstrate that dimerization is essential for achieving the geometric organization required for catalytic activity and that elevated temperature disrupts this coordination, rendering KSI inactive.
{"title":"Molecular dynamics insights into dimerization-dependent catalysis and thermal adaptation of mesophilic ketosteroid isomerase from Pseudomonas putida","authors":"Yi-Zhe Wang , Tzu-En Lin , Yu-Shan Tsai , Hsuan-Hsuan Lo , Chia-Ning Yang","doi":"10.1016/j.jmgm.2025.109230","DOIUrl":"10.1016/j.jmgm.2025.109230","url":null,"abstract":"<div><div>Ketosteroid isomerase (KSI), a highly conserved enzyme in the β-ketoacyl metabolic pathway, exhibits temperature-dependent functional adaptations across species. In this study, we investigated the temperature sensitivity of mesophilic KSI from <em>Pseudomonas putida</em> using molecular dynamics simulations. Since KSI functions as a dimer, we simulated both monomeric and dimeric forms at its optimal catalytic temperature (303 K) and at an elevated, non-optimal temperature (338 K) to evaluate how temperature and dimerization affect activation. We focused on the dynamics of three catalytically important residues—Y16, D40, and D103—where Y16 is located on the mobile α1-helix not involved in the dimer interface, D40 lies at the edge of the dimer interface, and D103 resides at the center of the core β-sheet structure that remains static in both monomeric and dimeric states. In the monomeric form at 303 K, the Y16–D40, Y16–D103, and D40–D103 pairs exhibit broader and longer separation distances than the optimal range for catalysis. Dimerization stabilizes D40, resulting in a narrower D40–D103 separation that falls within the catalytically competent range. The relatively unchanged mobility of Y16 upon dimerization suggests that Y16 undergoes an induced-fit adjustment upon substrate binding. At 338 K, although dimerization partially corrects the D40–D103 geometry, the increased conformational flexibility of Y16 indicates a reduced likelihood of achieving the substrate-induced active-site reorganization. Together, our results demonstrate that dimerization is essential for achieving the geometric organization required for catalytic activity and that elevated temperature disrupts this coordination, rendering KSI inactive.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109230"},"PeriodicalIF":3.0,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145604569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-19DOI: 10.1016/j.jmgm.2025.109228
Sotirios Touliopoulos, Nicholas M. Glykos
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures is a measure of the overall proximity between the proteins’ atoms and it can vary notably among different structures. However, even single domain proteins do not exhibit uniform packing throughout their structure. Protein cores in the interior tend to be more tightly packed compared to the protein surface and the presence of cavities and voids can disrupt that internal tight packing too.
Many different methods have been used to measure the quality of packing in proteins, identify factors that influence it, and their possible implications. In this work, we examine atomic density distributions derived from 21,255 non-redundant protein structures and show that statistically significant differences between those distributions are present. The biomolecular assembly unit was chosen as a representative for these structures. Addition of hydrogen atoms and solvation was also performed to emulate a faithful representation of the structures in vitro.
Several protein structures deviate significantly and systematically from the average packing behavior. Hierarchical clustering indicated that there are groups of structures with similar atomic density distributions. Search for common features and patterns in these clusters showed that some of them include proteins with characteristic structures such as coiled-coils and cytochromes. Certain classification families such as hydrolases and transferases have also a preference to appear more frequently in dense and loosely-packed clusters respectively.
Regarding factors influencing packing, our results support knowledge that larger structures have a smaller range in their density values, but tend to be more loosely packed, compared to smaller proteins. We also used indicators, like crystallographic water molecules abundance and B-factors as estimates of the stability of the structures to reveal its relationship with packing.
{"title":"Atomic density distributions in proteins: structural and functional implications","authors":"Sotirios Touliopoulos, Nicholas M. Glykos","doi":"10.1016/j.jmgm.2025.109228","DOIUrl":"10.1016/j.jmgm.2025.109228","url":null,"abstract":"<div><div>Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures is a measure of the overall proximity between the proteins’ atoms and it can vary notably among different structures. However, even single domain proteins do not exhibit uniform packing throughout their structure. Protein cores in the interior tend to be more tightly packed compared to the protein surface and the presence of cavities and voids can disrupt that internal tight packing too.</div><div>Many different methods have been used to measure the quality of packing in proteins, identify factors that influence it, and their possible implications. In this work, we examine atomic density distributions derived from 21,255 non-redundant protein structures and show that statistically significant differences between those distributions are present. The biomolecular assembly unit was chosen as a representative for these structures. Addition of hydrogen atoms and solvation was also performed to emulate a faithful representation of the structures <em>in vitro</em>.</div><div>Several protein structures deviate significantly and systematically from the average packing behavior. Hierarchical clustering indicated that there are groups of structures with similar atomic density distributions. Search for common features and patterns in these clusters showed that some of them include proteins with characteristic structures such as coiled-coils and cytochromes. Certain classification families such as hydrolases and transferases have also a preference to appear more frequently in dense and loosely-packed clusters respectively.</div><div>Regarding factors influencing packing, our results support knowledge that larger structures have a smaller range in their density values, but tend to be more loosely packed, compared to smaller proteins. We also used indicators, like crystallographic water molecules abundance and B-factors as estimates of the stability of the structures to reveal its relationship with packing.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109228"},"PeriodicalIF":3.0,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145575961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-19DOI: 10.1016/j.jmgm.2025.109229
Sabir Ali Siddique , Shanza Fatima , Muhammad Bilal Ahmed Siddique , Ejaz Ahmed , Rahman Shah Zaib Saleem , Muhammad Arshad
The pursuit of high-performance nonlinear optical (NLO) materials remains central to advancing optical communication, photonic circuitry, and laser-based technologies. In this study, we theoretically designed and evaluated a new class of alkali metal-doped diazadioxa[8]circulene complexes, denoted as M@C8 (M = Li, Na, K), using density functional theory. Metal doping induces profound structural and electronic reorganization, with interaction energies ranging from −0.25 to −11.21 kcal mol−1, affirming both favorable metal binding and thermodynamic stability. Remarkably, these modifications lead to dramatic enhancements in NLO performance. The pristine C8 molecule exhibits a negligible static first hyperpolarizability (β0) of just 0.03 au; however, upon doping, β0 surges to an exceptional 470074.83 au for 3-Li@C8, an increase of nearly 1.57 × 107-fold. Under dynamic conditions (λ = 1064 nm), the first-order hyperpolarizability β(−ω, ω, 0) reaches 104948.80 au for 3-Na@C8, while the hyper-Rayleigh scattering hyperpolarizability (βHRS) peaks at 2837379.65 au for 5-K@C8, showcasing outstanding frequency-dependent NLO activity. Complementary UV–Vis analysis reveals pronounced redshifts in absorption (from 199.39 nm for C8 to 773.60 nm for 6-K@C8), indicating enhanced π-electron delocalization and efficient intramolecular charge transfer. Taken together, these findings position M@C8 complexes as compelling molecular platforms for next-generation NLO materials with exceptional static and dynamic optical responses.
{"title":"Quantum chemical engineering of enhanced nonlinear optical responses in alkali metal-doped diazadioxacirculenes for molecular photonics","authors":"Sabir Ali Siddique , Shanza Fatima , Muhammad Bilal Ahmed Siddique , Ejaz Ahmed , Rahman Shah Zaib Saleem , Muhammad Arshad","doi":"10.1016/j.jmgm.2025.109229","DOIUrl":"10.1016/j.jmgm.2025.109229","url":null,"abstract":"<div><div>The pursuit of high-performance nonlinear optical (NLO) materials remains central to advancing optical communication, photonic circuitry, and laser-based technologies. In this study, we theoretically designed and evaluated a new class of alkali metal-doped diazadioxa[8]circulene complexes, denoted as M@C8 (M = Li, Na, K), using density functional theory. Metal doping induces profound structural and electronic reorganization, with interaction energies ranging from −0.25 to −11.21 kcal mol<sup>−1</sup>, affirming both favorable metal binding and thermodynamic stability. Remarkably, these modifications lead to dramatic enhancements in NLO performance. The pristine C8 molecule exhibits a negligible static first hyperpolarizability (<em>β</em><sub><em>0</em></sub>) of just 0.03 au; however, upon doping, <em>β</em><sub><em>0</em></sub> surges to an exceptional 470074.83 au for 3-Li@C8, an increase of nearly 1.57 × 10<sup>7</sup>-fold. Under dynamic conditions (<em>λ</em> = 1064 nm), the first-order hyperpolarizability <em>β</em>(−ω, ω, 0) reaches 104948.80 au for 3-Na@C8, while the hyper-Rayleigh scattering hyperpolarizability (<em>β</em><sub>HRS</sub>) peaks at 2837379.65 au for 5-K@C8, showcasing outstanding frequency-dependent NLO activity. Complementary UV–Vis analysis reveals pronounced redshifts in absorption (from 199.39 nm for C8 to 773.60 nm for 6-K@C8), indicating enhanced π-electron delocalization and efficient intramolecular charge transfer. Taken together, these findings position M@C8 complexes as compelling molecular platforms for next-generation NLO materials with exceptional static and dynamic optical responses.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109229"},"PeriodicalIF":3.0,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145573755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-18DOI: 10.1016/j.jmgm.2025.109227
Zia ur Rehman , Ayesha Saddiqa , A.F. Abd El-Rehim , Amna Parveen , Heba Y. Zahran , Zeesham Abbas
This research uses density functional theory to examine the structural, electronic, optical, mechanical, thermodynamic, thermoelectric, magnetic, and photovoltaic properties of Sn-based AmSnX3 (Am = Rb, Cs; X = Cl, Br, I) perovskites. The tolerance factor (0.71–1.04) and the negative cohesive energy confirm the materials’ structural and thermodynamic stability. The electronic properties show semiconducting behavior, with energy band gaps of 0.42 eV for RbSnBr3 and 1.02 eV for CsSnCl3. The maximum absorption values (7.16 × 104 cm−1 to 8.11 × 104 cm−1) in the visible region indicate efficient light harvesting for solar cell applications. Mechanical properties suggest mechanical stability and ductility. The Debye temperature (146.08–190.78 K) offers insights into heat capacity and thermal behavior at different temperatures. The Seebeck coefficient at room temperature classifies RbSnBr3, RbSnI3, and CsSnCl3 as p-type materials, while RbSnCl3, CsSnBr3, and CsSnI3 are n-type. The calculated power conversion efficiencies, from 12.47 % for CsSnI3 to 29.54 % for CsSnCl3, emphasize the novelty of this work, which combines structural, mechanical, electronic, and optical analyses for the first time to thoroughly evaluate the potential of RbSnX3 and CsSnX3 perovskites in optoelectronic and energy applications.
{"title":"Density functional modelling of lead-free Sn-based AmSnX3 (Am=Rb, Cs; X=Cl, Br, I) perovskites as sustainable materials for optoelectronics and solar cell applications","authors":"Zia ur Rehman , Ayesha Saddiqa , A.F. Abd El-Rehim , Amna Parveen , Heba Y. Zahran , Zeesham Abbas","doi":"10.1016/j.jmgm.2025.109227","DOIUrl":"10.1016/j.jmgm.2025.109227","url":null,"abstract":"<div><div>This research uses density functional theory to examine the structural, electronic, optical, mechanical, thermodynamic, thermoelectric, magnetic, and photovoltaic properties of Sn-based AmSnX<sub>3</sub> (Am = Rb, Cs; X = Cl, Br, I) perovskites. The tolerance factor (0.71–1.04) and the negative cohesive energy confirm the materials’ structural and thermodynamic stability. The electronic properties show semiconducting behavior, with energy band gaps of 0.42 eV for RbSnBr3 and 1.02 eV for CsSnCl<sub>3</sub>. The maximum absorption values (7.16 × 10<sup>4</sup> cm<sup>−1</sup> to 8.11 × 10<sup>4</sup> cm<sup>−1</sup>) in the visible region indicate efficient light harvesting for solar cell applications. Mechanical properties suggest mechanical stability and ductility. The Debye temperature (146.08–190.78 K) offers insights into heat capacity and thermal behavior at different temperatures. The Seebeck coefficient at room temperature classifies RbSnBr<sub>3</sub>, RbSnI<sub>3</sub>, and CsSnCl<sub>3</sub> as p-type materials, while RbSnCl<sub>3</sub>, CsSnBr<sub>3</sub>, and CsSnI<sub>3</sub> are n-type. The calculated power conversion efficiencies, from 12.47 % for CsSnI<sub>3</sub> to 29.54 % for CsSnCl<sub>3</sub>, emphasize the novelty of this work, which combines structural, mechanical, electronic, and optical analyses for the first time to thoroughly evaluate the potential of RbSnX<sub>3</sub> and CsSnX<sub>3</sub> perovskites in optoelectronic and energy applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109227"},"PeriodicalIF":3.0,"publicationDate":"2025-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145573802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pharmaceutical pollutants such as Diclofenac and Naproxen are emerging environmental contaminants due to their persistence and potential biological hazards. In this study, pristine and functionalized Kekulene nanorings (KNRs) were theoretically explored as novel adsorbents using density functional theory (DFT). Various functional groups (–COOH, –NO2, –NO, –N, –O, –S) were introduced to modulate the interaction with drug molecules. Adsorption energy (Ea) calculations confirmed spontaneous physisorption across all systems, with values ranging from −2.473 to −0.441 eV. Notably, the KNR–NO2–N system in aqueous phase exhibited the lowest Ea (−0.441 eV) and shortest recovery time (τ = 2.864 × 10−5 s), making it the most promising candidate for rapid desorption and recyclability. Non-covalent interaction (NCI) analysis revealed that van der Waals forces and weak electrostatic interactions dominate the adsorption mechanism. Natural Bond Orbital (NBO) analysis of the oxygen atom (O6) confirmed variable charge transfer behaviour, reflecting the influence of surface functionalization. HOMO–LUMO analysis showed frontier orbital localization patterns that shifted upon functionalization, especially in Naproxen complexes, indicating enhanced electronic interactions. Compared to benchmark materials such as PTX@rGO and FPV@GN, KNR-based adsorbents demonstrated competitive or superior tunability and desorption potential. These results suggest that functionalized KNRs—particularly KNR–NO2–N—are promising candidates for efficient, reversible pharmaceutical pollutant capture in both gas and aqueous environments.
{"title":"Tailoring adsorption properties of Kekulene nanoring via functionalization for pharmaceutical pollutant removal","authors":"Hazem Abdelsalam , Mohamed Abdel Rafea , Mahmoud A.S. Sakr , Qinfang Zhang","doi":"10.1016/j.jmgm.2025.109231","DOIUrl":"10.1016/j.jmgm.2025.109231","url":null,"abstract":"<div><div>Pharmaceutical pollutants such as Diclofenac and Naproxen are emerging environmental contaminants due to their persistence and potential biological hazards. In this study, pristine and functionalized Kekulene nanorings (KNRs) were theoretically explored as novel adsorbents using density functional theory (DFT). Various functional groups (–COOH, –NO<sub>2</sub>, –NO, –N, –O, –S) were introduced to modulate the interaction with drug molecules. Adsorption energy (E<sub>a</sub>) calculations confirmed spontaneous physisorption across all systems, with values ranging from −2.473 to −0.441 eV. Notably, the KNR–NO<sub>2</sub>–N system in aqueous phase exhibited the lowest E<sub>a</sub> (−0.441 eV) and shortest recovery time (τ = 2.864 × 10<sup>−5</sup> s), making it the most promising candidate for rapid desorption and recyclability. Non-covalent interaction (NCI) analysis revealed that van der Waals forces and weak electrostatic interactions dominate the adsorption mechanism. Natural Bond Orbital (NBO) analysis of the oxygen atom (O6) confirmed variable charge transfer behaviour, reflecting the influence of surface functionalization. HOMO–LUMO analysis showed frontier orbital localization patterns that shifted upon functionalization, especially in Naproxen complexes, indicating enhanced electronic interactions. Compared to benchmark materials such as PTX@rGO and FPV@GN, KNR-based adsorbents demonstrated competitive or superior tunability and desorption potential. These results suggest that functionalized KNRs—particularly KNR–NO<sub>2</sub>–N—are promising candidates for efficient, reversible pharmaceutical pollutant capture in both gas and aqueous environments.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109231"},"PeriodicalIF":3.0,"publicationDate":"2025-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145564241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-17DOI: 10.1016/j.jmgm.2025.109223
Alexander Trachtenberg, Barak Akabayov
The rapidly growing number of protein structures in the Protein Data Bank (PDB) offers opportunities to derive biological insights from proteins with common features. Taking advantage of this “big data” resource, we developed an automated open-source Python script designated “Vanalyzer” that performs statistical analysis on vanadate-binding sites across the PDB. Vanalyzer evaluates the structural properties of proteins containing vanadium-based oxyanions by comparing binding interfaces and geometries across a diverse array of proteins. Additionally, it allows a focused analysis on specific enzyme classes, facilitating direct comparisons between them. The newly developed tool will contribute to the understanding of vanadate recognition within protein binding sites and will serve as a valuable, up-to-date resource for analyzing both current and newly submitted vanadate structures in the PDB.
{"title":"Vanalyzer: an open-source tool for automated statistical analysis and continuous updating of vanadate-binding sites in the Protein Data Bank","authors":"Alexander Trachtenberg, Barak Akabayov","doi":"10.1016/j.jmgm.2025.109223","DOIUrl":"10.1016/j.jmgm.2025.109223","url":null,"abstract":"<div><div>The rapidly growing number of protein structures in the Protein Data Bank (PDB) offers opportunities to derive biological insights from proteins with common features. Taking advantage of this “big data” resource, we developed an automated open-source Python script designated “Vanalyzer” that performs statistical analysis on vanadate-binding sites across the PDB. Vanalyzer evaluates the structural properties of proteins containing vanadium-based oxyanions by comparing binding interfaces and geometries across a diverse array of proteins. Additionally, it allows a focused analysis on specific enzyme classes, facilitating direct comparisons between them. The newly developed tool will contribute to the understanding of vanadate recognition within protein binding sites and will serve as a valuable, up-to-date resource for analyzing both current and newly submitted vanadate structures in the PDB.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109223"},"PeriodicalIF":3.0,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145564194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-17DOI: 10.1016/j.jmgm.2025.109226
Erick Bahena-Culhuac , Rodolfo Daniel Ávila-Avilés , Martiniano Bello
Histone deacetylase 3 (HDAC3) is a key epigenetic regulator implicated in breast cancer progression and represents a promising therapeutic target. Here, we investigated 14 HDAC3–ligand complexes using molecular dynamics (MD) simulations and binding free energy calculations (MM/GBSA) to identify the determinants of inhibitor binding. Key residues consistently engaged across ligands included Gly132, His134–135, Phe144, Asp170, His172, Phe200, Asp259, Leu266, Gly296, Tyr298, and the catalytic Zn2+ ion. Among the compounds, domatinostat and entinostat exhibited the strongest affinities (ΔGbind ≈ −70 kcal/mol), in reasonable agreement with experimental data (r = 0.60). Both ligands also showed small Highest Occupied Molecular Orbital–Lowest Unoccupied Molecular Orbital (HOMO–LUMO) gaps, high softness, and elevated electrophilicity indices, providing chemical cues for the design of next-generation HDAC3 inhibitors. Notably, ligand binding stabilized regions surrounding Phe200 and Asn370, restricting the conformational flexibility required for enzymatic activation. This supports an allosteric inhibition mechanism in which ligands lock HDAC3 into inactive conformations. Collectively, these findings offer mechanistic insights into HDAC3 regulation and highlight structural hot spots for the rational design of selective inhibitors with potential applications in targeted breast cancer therapy.
{"title":"Targeting HDAC3 dynamics: Allosteric role of Phe200 in inhibitor binding and breast cancer therapy","authors":"Erick Bahena-Culhuac , Rodolfo Daniel Ávila-Avilés , Martiniano Bello","doi":"10.1016/j.jmgm.2025.109226","DOIUrl":"10.1016/j.jmgm.2025.109226","url":null,"abstract":"<div><div>Histone deacetylase 3 (HDAC3) is a key epigenetic regulator implicated in breast cancer progression and represents a promising therapeutic target. Here, we investigated 14 HDAC3–ligand complexes using molecular dynamics (MD) simulations and binding free energy calculations (MM/GBSA) to identify the determinants of inhibitor binding. Key residues consistently engaged across ligands included Gly132, His134–135, Phe144, Asp170, His172, Phe200, Asp259, Leu266, Gly296, Tyr298, and the catalytic Zn<sup>2+</sup> ion. Among the compounds, domatinostat and entinostat exhibited the strongest affinities (ΔGbind ≈ −70 kcal/mol), in reasonable agreement with experimental data (r = 0.60). Both ligands also showed small Highest Occupied Molecular Orbital–Lowest Unoccupied Molecular Orbital (HOMO–LUMO) gaps, high softness, and elevated electrophilicity indices, providing chemical cues for the design of next-generation HDAC3 inhibitors. Notably, ligand binding stabilized regions surrounding Phe200 and Asn370, restricting the conformational flexibility required for enzymatic activation. This supports an allosteric inhibition mechanism in which ligands lock HDAC3 into inactive conformations. Collectively, these findings offer mechanistic insights into HDAC3 regulation and highlight structural hot spots for the rational design of selective inhibitors with potential applications in targeted breast cancer therapy.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"142 ","pages":"Article 109226"},"PeriodicalIF":3.0,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145573742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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