Halogenation is a widely used strategy in drug design, not only to improve ADME properties but also because halogens can engage in halogen bonds (XBs) with biological targets. To predict protein--ligand binding free energies (ΔGbind), paramount in drug discovery, MM-PBSA remains a popular intermediate approach between less accurate docking and more rigorous free-energy methods. However, the use of extra-points of charge (EPs) to describe halogen anisotropy and enable XB sampling in MM-PBSA calculations is still uncommon. Optimized halogen radii (ropt) for PBSA calculations, which are compatible with EPs and reproduce hydration free energies with good accuracy, were recently developed. Yet, their impact on protein--ligand binding free energy calculations has not been systematically assessed. Here, we evaluate the performance of ropt in estimating ΔGbind values for three sets of halogenated inhibitors of casein kinase-2 with available experimental binding data. We compared three EP models and standard RESP charges (no EPs), while also analyzing the effect of the internal dielectric constant ( εin) and sampling time. Our results show that direct use of the X-ray structures generally leads to poor correlations, whereas relaxation through MM minimization, particularly with εin, yields substantially improved agreement with experiment. Incorporating configurational sampling via MD further enhances the correlations, though Pearson coefficients varied notably with both sampling length and PBSA setup. Interestingly, longer MD sampling did not consistently improve correlations, highlighting the sensitivity of MM-PBSA to the simulation conditions. Nonetheless, optimized radii (ropt) provided slight but systematic improvements, while inclusion of halogen anisotropy through EPs considerably increased correlations in two of the three ligand sets studied. The choice of εin strongly influenced the quality of predictions: the use of EPs was sufficient to mimic polarizability in systems with multiple halogens, but for ligands with fewer halogens, a higher εin proved beneficial. To our knowledge, this is the first comprehensive benchmark of MM-PBSA calculations using EP-based simulations, and our findings provide practical guidelines on how to best combine EPs, optimized radii, dielectric constants, and sampling strategies for an improved description of halogen bonding in protein--ligand complexes.
{"title":"Impact of the Halogen PB Radii in the Estimation of Protein-Ligand Binding Energies Using MM-PBSA Calculations","authors":"Andreia Fortuna, Paulo J. Costa","doi":"10.1039/d5cp03537f","DOIUrl":"https://doi.org/10.1039/d5cp03537f","url":null,"abstract":"Halogenation is a widely used strategy in drug design, not only to improve ADME properties but also because halogens can engage in halogen bonds (XBs) with biological targets. To predict protein--ligand binding free energies (ΔG<small><sub>bind</sub></small>), paramount in drug discovery, MM-PBSA remains a popular intermediate approach between less accurate docking and more rigorous free-energy methods. However, the use of extra-points of charge (EPs) to describe halogen anisotropy and enable XB sampling in MM-PBSA calculations is still uncommon. Optimized halogen radii (r<small><sub>opt</sub></small>) for PBSA calculations, which are compatible with EPs and reproduce hydration free energies with good accuracy, were recently developed. Yet, their impact on protein--ligand binding free energy calculations has not been systematically assessed. Here, we evaluate the performance of r<small><sub>opt</sub></small> in estimating ΔG<small><sub>bind</sub></small> values for three sets of halogenated inhibitors of casein kinase-2 with available experimental binding data. We compared three EP models and standard RESP charges (no EPs), while also analyzing the effect of the internal dielectric constant ( ε<small><sub>in</sub></small>) and sampling time. Our results show that direct use of the X-ray structures generally leads to poor correlations, whereas relaxation through MM minimization, particularly with ε<small><sub>in</sub></small>, yields substantially improved agreement with experiment. Incorporating configurational sampling via MD further enhances the correlations, though Pearson coefficients varied notably with both sampling length and PBSA setup. Interestingly, longer MD sampling did not consistently improve correlations, highlighting the sensitivity of MM-PBSA to the simulation conditions. Nonetheless, optimized radii (r<small><sub>opt</sub></small>) provided slight but systematic improvements, while inclusion of halogen anisotropy through EPs considerably increased correlations in two of the three ligand sets studied. The choice of ε<small><sub>in</sub></small> strongly influenced the quality of predictions: the use of EPs was sufficient to mimic polarizability in systems with multiple halogens, but for ligands with fewer halogens, a higher ε<small><sub>in</sub></small> proved beneficial. To our knowledge, this is the first comprehensive benchmark of MM-PBSA calculations using EP-based simulations, and our findings provide practical guidelines on how to best combine EPs, optimized radii, dielectric constants, and sampling strategies for an improved description of halogen bonding in protein--ligand complexes.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"1 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147478236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
David Parker, Dominic J. Black, Robert Pal, Mark A Fox, Xinyi Wen
The nature of dynamic quenching of the europium or terbum excited states in Δ and Λ stereoisomeric cationic complexes by S and R Trolox has been studied by emission and CPL spectroscopy and DFT computations. Non-linear Stern-Volmer quenching kinetics were observed and the stereoselective behaviour was interpreted in terms of an exciplex model, where the binding constant for exciplex formation, Kex , and the rate constant for exciplex decay, k3 , determine overall quenching efficiency. Dynamic quenching was most efficient with R Trolox for the Δ Eu and Tb complexes in three systems. Ground state DFT calculations revealed that the Δ complex with S Trolox was 10 kJ mol-1 lower in energy than with R Trolox, yet was quenched less efficiently, suggesting that the origins of the observed chiral quenching behaviour are not associated with the relative stabilities of each exciplex, but with their relative rates of decay.
{"title":"Dynamic chiral quenching of europium and terbium excited states","authors":"David Parker, Dominic J. Black, Robert Pal, Mark A Fox, Xinyi Wen","doi":"10.1039/d5cp04880j","DOIUrl":"https://doi.org/10.1039/d5cp04880j","url":null,"abstract":"The nature of dynamic quenching of the europium or terbum excited states in Δ and Λ stereoisomeric cationic complexes by S and R Trolox has been studied by emission and CPL spectroscopy and DFT computations. Non-linear Stern-Volmer quenching kinetics were observed and the stereoselective behaviour was interpreted in terms of an exciplex model, where the binding constant for exciplex formation, Kex , and the rate constant for exciplex decay, k3 , determine overall quenching efficiency. Dynamic quenching was most efficient with R Trolox for the Δ Eu and Tb complexes in three systems. Ground state DFT calculations revealed that the Δ complex with S Trolox was 10 kJ mol-1 lower in energy than with R Trolox, yet was quenched less efficiently, suggesting that the origins of the observed chiral quenching behaviour are not associated with the relative stabilities of each exciplex, but with their relative rates of decay.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"27 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147465966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Carbonless biomolecular design, in which carbon atoms are systematically replaced by boron and nitrogen under an isoelectronicity constraint, offers a route to carbon free analogues that retain the structural logic of familiar biochemistry. The concept is applied to amino acids and peptides, using glycine, histidine, lysine, and the tripeptide Gly–His–Lys (GHK) as a representative system. DFT(ωB97XD)/aug-cc-pVDZ calculations with aqueous PCM solvation, supported by CREST conformer sampling at the GFN2-xTB/ALPB level, identify unique low energy carbonless building blocks, cGly, cHis, and cLys, defined as carbonless analogues of Gly, His, and Lys among all isoelectronic BN constitutional isomers. These residues enable construction of cGHK, defined as the carbonless analogue of GHK, whose conformational landscape is predicted to be broader than that of GHK under physiological aqueous conditions, consistent with enhanced conformational plasticity. Cu(II) complexation is modeled with an experimentally supported 3N1O motif including one explicit water ligand, and an isodesmic ligand exchange thermodynamic cycle based on ensemble Gibbs free energies indicates stronger stabilization of Cu(II) by cGHK than by GHK (∆Gexch=−6.24 kcal/mol at 298 K), with only a minor ensemble correction. The results demonstrate the feasibility of carbonless amino acids and peptides and show that BN substitution can tune conformational behavior and metal binding thermodynamics in carbon free bioinspired scaffolds.
{"title":"Carbonless Amino Acids and a Carbonless GHK Peptide","authors":"Piotr Skurski, Iwona Anusiewicz","doi":"10.1039/d6cp00567e","DOIUrl":"https://doi.org/10.1039/d6cp00567e","url":null,"abstract":"Carbonless biomolecular design, in which carbon atoms are systematically replaced by boron and nitrogen under an isoelectronicity constraint, offers a route to carbon free analogues that retain the structural logic of familiar biochemistry. The concept is applied to amino acids and peptides, using glycine, histidine, lysine, and the tripeptide Gly–His–Lys (GHK) as a representative system. DFT(ωB97XD)/aug-cc-pVDZ calculations with aqueous PCM solvation, supported by CREST conformer sampling at the GFN2-xTB/ALPB level, identify unique low energy carbonless building blocks, cGly, cHis, and cLys, defined as carbonless analogues of Gly, His, and Lys among all isoelectronic BN constitutional isomers. These residues enable construction of cGHK, defined as the carbonless analogue of GHK, whose conformational landscape is predicted to be broader than that of GHK under physiological aqueous conditions, consistent with enhanced conformational plasticity. Cu(II) complexation is modeled with an experimentally supported 3N1O motif including one explicit water ligand, and an isodesmic ligand exchange thermodynamic cycle based on ensemble Gibbs free energies indicates stronger stabilization of Cu(II) by cGHK than by GHK (∆G<small><sub>exch</sub></small><small><sub></sub></small>=−6.24 kcal/mol at 298 K), with only a minor ensemble correction. The results demonstrate the feasibility of carbonless amino acids and peptides and show that BN substitution can tune conformational behavior and metal binding thermodynamics in carbon free bioinspired scaffolds.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"44 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147465967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ethylene is a fundamental petrochemical feedstock, and efficient, low-carbon ethane-to-ethylene processes are gaining increasing importance. This paper reviews major process routes, including steam cracking dehydrogenation, catalytic dehydrogenation, oxidative dehydrogenation, chemical looping, photocatalysis, electrocatalysis, and membrane reaction technologies. It focuses on discussing the oxygen regulation mechanisms within ethane chemical looping technologies. The key conclusion is that the performance of chemical looping oxidative dehydrogenation is primarily governed by oxygen chemistry, where ethylene selectivity reflects the kinetic competition between the target dehydrogenation reaction and secondary olefin oxidation reactions, which is determined by the carrier oxygen supply and reaction reactivity. High selectivity therefore requires constraining oxygen reactivity within a narrow, dynamically tunable window rather than maximizing oxygen participation. Moreover, the review also distills oxygen-carrier design principles linking oxygen capacity, lattice-oxygen mobility, and reactive oxygen species, and summarizes compositional and structural strategies (e.g., doping and phase/interface engineering) to balance redox stability with selectivity. To provide theoretical guidance for constructing high-performance oxygen carriers for oxidation dehydrogenation in the ethane chemical looping.
{"title":"Pathways for Ethane Conversion to Ethylene and Regulation of Lattice Oxygen in Ethane Chemical looping Oxygen Carriers: A Review","authors":"Tao Li, Yuelun Li, Zeshan Wang, Jiahao Zheng, Chunqiang Lu, Kongzhai Li, Dong Tian","doi":"10.1039/d6cp00498a","DOIUrl":"https://doi.org/10.1039/d6cp00498a","url":null,"abstract":"Ethylene is a fundamental petrochemical feedstock, and efficient, low-carbon ethane-to-ethylene processes are gaining increasing importance. This paper reviews major process routes, including steam cracking dehydrogenation, catalytic dehydrogenation, oxidative dehydrogenation, chemical looping, photocatalysis, electrocatalysis, and membrane reaction technologies. It focuses on discussing the oxygen regulation mechanisms within ethane chemical looping technologies. The key conclusion is that the performance of chemical looping oxidative dehydrogenation is primarily governed by oxygen chemistry, where ethylene selectivity reflects the kinetic competition between the target dehydrogenation reaction and secondary olefin oxidation reactions, which is determined by the carrier oxygen supply and reaction reactivity. High selectivity therefore requires constraining oxygen reactivity within a narrow, dynamically tunable window rather than maximizing oxygen participation. Moreover, the review also distills oxygen-carrier design principles linking oxygen capacity, lattice-oxygen mobility, and reactive oxygen species, and summarizes compositional and structural strategies (e.g., doping and phase/interface engineering) to balance redox stability with selectivity. To provide theoretical guidance for constructing high-performance oxygen carriers for oxidation dehydrogenation in the ethane chemical looping.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"84 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147466022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Graphene is inherently prone to forming ripples and curved regions, both with and without defects, which modify its local geometry and, consequently, its electronic structure. Such curvature effects become particularly important when graphene serves as a support for atomically dispersed single-atom catalytic sites (M-N-C), which are key motifs for small-molecule activation. These sites can be regarded as defect structures within a two-dimensional (2D) framework; however, the role of curvature as a vector descriptor-capturing both the magnitude and the direction (sign) of curvature-remains largely unexplored in reactivity analysis. Here, we investigate how the sign of curvature impacts the stability, electronic structure, and adsorption properties of M-N-C sites using first-principles density functional theory (DFT) calculations encompassing 3d, 4d, and 5d transition-metal centers. We find that curvature modulates the thermodynamic stability of single-atom sites, with larger metal centers being preferentially stabilized in regions of higher curvature. Furthermore, curvature modulates key aspects of chemical bonding, including covalency and ionicity, as demonstrated using H adsorption as a model case. Curvature serves as a control parameter for tuning the M-H bonding strength, with the effect being most pronounced for early transition metals. CO2 activation is then examined as a representative example of small-molecule activation under curvature, revealing that the nature of curvature can drastically modify the activation mechanism at a given metal center. Notably, curvature enhances CO2 adsorption and activation even for metals that are inactive on flat surfaces. Because ripples are intrinsic to 2D materials and can also be engineered through external stimuli or mechanochemical deformation, these findings demonstrate that exploiting curvature as a vector descriptor in chemical space enables new forms of reactivity inaccessible on planar surfaces.
{"title":"Generalizable Mechanochemical Impact of Curvature Governing Stability and Reactivity at Catalytic Sites on Rippled Supports","authors":"Sayan Banerjee, Sampad Mandal","doi":"10.1039/d5cp04759e","DOIUrl":"https://doi.org/10.1039/d5cp04759e","url":null,"abstract":"Graphene is inherently prone to forming ripples and curved regions, both with and without defects, which modify its local geometry and, consequently, its electronic structure. Such curvature effects become particularly important when graphene serves as a support for atomically dispersed single-atom catalytic sites (M-N-C), which are key motifs for small-molecule activation. These sites can be regarded as defect structures within a two-dimensional (2D) framework; however, the role of curvature as a vector descriptor-capturing both the magnitude and the direction (sign) of curvature-remains largely unexplored in reactivity analysis. Here, we investigate how the sign of curvature impacts the stability, electronic structure, and adsorption properties of M-N-C sites using first-principles density functional theory (DFT) calculations encompassing 3d, 4d, and 5d transition-metal centers. We find that curvature modulates the thermodynamic stability of single-atom sites, with larger metal centers being preferentially stabilized in regions of higher curvature. Furthermore, curvature modulates key aspects of chemical bonding, including covalency and ionicity, as demonstrated using H adsorption as a model case. Curvature serves as a control parameter for tuning the M-H bonding strength, with the effect being most pronounced for early transition metals. CO2 activation is then examined as a representative example of small-molecule activation under curvature, revealing that the nature of curvature can drastically modify the activation mechanism at a given metal center. Notably, curvature enhances CO2 adsorption and activation even for metals that are inactive on flat surfaces. Because ripples are intrinsic to 2D materials and can also be engineered through external stimuli or mechanochemical deformation, these findings demonstrate that exploiting curvature as a vector descriptor in chemical space enables new forms of reactivity inaccessible on planar surfaces.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"9 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147466027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evgeny Katz, Gunay Hasanova, Sabina Omarova, Nailya Abdullayeva, Afat Mammadova, Mehmet Firat Baran:, Abdulkadir Levent, Mehmet Tevfik Adican, Aziz Eftekhari, T. Kavetskyy, Ondrej Šauša, Oleh Smutok, Rovshan Khalilov
The biological green synthesis of silver nanoparticles (AgNPs) has attracted considerable attention due to its sustainability and potential applications in biomedical and technological fields. In this study, AgNPs synthesized using Artemisia lerchiana Weber extract were systematically compared and characterized by energy-dispersive X-ray spectroscopy, X-ray diffraction, and thermogravimetric–differential thermal analyses. The electrochemical performance of A. lerchiana–derived AgNP-based electrode materials was investigated using cyclic voltammetry (CV), galvanostatic charge–discharge (GCD), and electrochemical impedance spectroscopy (EIS) in a 1 M Na₂SO₄ aqueous electrolyte. The CV results showed that the electrodes exhibited predominantly capacitive behavior with notable pseudocapacitive contributions, achieving a maximum specific capacitance of 239.07 F·g⁻¹ at a scan rate of 5 mV·s⁻¹. GCD tests confirmed excellent charge–discharge reversibility, with the highest capacitance value recorded at a current density of 0.07 A·g⁻¹, reaching 322.14 F·g⁻¹. Long-term cycling over 5000 charge–discharge cycles showed minimal degradation and preserved capacitive properties, indicating high electrochemical durability. EIS analysis revealed low charge-transfer resistance and favorable ion-diffusion kinetics, reflecting the high electrical conductivity and ion-accessible architecture of the A. lerchiana AgNP composite. These results demonstrate that A. lerchiana–derived AgNP electrodes combine high energy-storage capacity, fast charge–discharge capability, and long-term stability, making them promising candidates for advanced supercapacitor applications.
纳米银纳米颗粒的生物绿色合成因其可持续性和在生物医学和技术领域的潜在应用而受到广泛关注。本研究采用能量色散x射线光谱、x射线衍射、热重差热分析等方法对青蒿提取物合成的AgNPs进行了系统比较和表征。采用循环伏安法（CV）、恒流充放电法（GCD）和电化学阻抗谱法（EIS）在1 M Na₂SO₄水溶液中研究了龙井草衍生的agnp基电极材料的电化学性能。CV结果表明，电极表现出主要的电容行为，并有明显的赝电容贡献，在扫描速率为5 mV·s的情况下，最大比电容为239.07 F·g⁻¹。GCD测试证实了极好的充放电可逆性，在0.07 a·g⁻¹的电流密度下记录的最高电容值达到322.14 F·g⁻¹。长期循环超过5000次充放电循环显示最小的退化和保持电容性能，表明高电化学耐久性。EIS分析显示，该复合材料具有较低的电荷转移电阻和良好的离子扩散动力学，反映了该复合材料的高导电性和离子可达性结构。这些结果表明，A. lerchiana衍生的AgNP电极具有高储能能力，快速充放电能力和长期稳定性，使其成为先进超级电容器应用的有希望的候选者。
{"title":"Bioinspired silver nanoparticles from Artemisia lerchiana as durable electrodes for next-generation supercapacitors","authors":"Evgeny Katz, Gunay Hasanova, Sabina Omarova, Nailya Abdullayeva, Afat Mammadova, Mehmet Firat Baran:, Abdulkadir Levent, Mehmet Tevfik Adican, Aziz Eftekhari, T. Kavetskyy, Ondrej Šauša, Oleh Smutok, Rovshan Khalilov","doi":"10.1039/d5cp05057j","DOIUrl":"https://doi.org/10.1039/d5cp05057j","url":null,"abstract":"The biological green synthesis of silver nanoparticles (AgNPs) has attracted considerable attention due to its sustainability and potential applications in biomedical and technological fields. In this study, AgNPs synthesized using Artemisia lerchiana Weber extract were systematically compared and characterized by energy-dispersive X-ray spectroscopy, X-ray diffraction, and thermogravimetric–differential thermal analyses. The electrochemical performance of A. lerchiana–derived AgNP-based electrode materials was investigated using cyclic voltammetry (CV), galvanostatic charge–discharge (GCD), and electrochemical impedance spectroscopy (EIS) in a 1 M Na₂SO₄ aqueous electrolyte. The CV results showed that the electrodes exhibited predominantly capacitive behavior with notable pseudocapacitive contributions, achieving a maximum specific capacitance of 239.07 F·g⁻¹ at a scan rate of 5 mV·s⁻¹. GCD tests confirmed excellent charge–discharge reversibility, with the highest capacitance value recorded at a current density of 0.07 A·g⁻¹, reaching 322.14 F·g⁻¹. Long-term cycling over 5000 charge–discharge cycles showed minimal degradation and preserved capacitive properties, indicating high electrochemical durability. EIS analysis revealed low charge-transfer resistance and favorable ion-diffusion kinetics, reflecting the high electrical conductivity and ion-accessible architecture of the A. lerchiana AgNP composite. These results demonstrate that A. lerchiana–derived AgNP electrodes combine high energy-storage capacity, fast charge–discharge capability, and long-term stability, making them promising candidates for advanced supercapacitor applications.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"7 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147466020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Computational screening of metal-organic frameworks (MOFs) relies on crystallographic inputs that are commonly treated as “computation-ready”. In practice, however, conventional CIF preprocessing often applies fixed-parameter treatments, overlooking the structural details described in the original reports. To address this, we introduce SmartCIF, a context-aware literature-integrated framework that redefines CIF preprocessing as an explicit assumption-driven procedure. SmartCIF couples topology-based structural analysis with natural-language reasoning over the original publications to make chemically informed decisions about retaining or removing all kind of CIF parts according to the user’s computational objectives. Benchmarking across 321 MOFs against reported BET surface areas and CO2/N2 adsorption data demonstrates that SmartCIF reconciles geometric accessibility with chemical fidelity, avoiding both pore-blocking and over-opened nonphysical results base on the original publications. These results establish that CIF preprocessing is inherently application-dependent and that treating preprocessing assumptions as explicit, controllable variables is essential for reproducible interpretable high-throughput screening. This assumption-aware paradigm embodied by SmartCIF generalizes existing computation-ready resources and provides a flexible foundation for large-scale simulations beyond adsorption.
{"title":"SmartCIF: A Context-Aware Multi-Agent System for Automated Preprocessing and Curation of MOF CIFs","authors":"qixiang zhang, Chen Zhang, Liwei Wang","doi":"10.1039/d6cp00100a","DOIUrl":"https://doi.org/10.1039/d6cp00100a","url":null,"abstract":"Computational screening of metal-organic frameworks (MOFs) relies on crystallographic inputs that are commonly treated as “computation-ready”. In practice, however, conventional CIF preprocessing often applies fixed-parameter treatments, overlooking the structural details described in the original reports. To address this, we introduce SmartCIF, a context-aware literature-integrated framework that redefines CIF preprocessing as an explicit assumption-driven procedure. SmartCIF couples topology-based structural analysis with natural-language reasoning over the original publications to make chemically informed decisions about retaining or removing all kind of CIF parts according to the user’s computational objectives. Benchmarking across 321 MOFs against reported BET surface areas and CO2/N2 adsorption data demonstrates that SmartCIF reconciles geometric accessibility with chemical fidelity, avoiding both pore-blocking and over-opened nonphysical results base on the original publications. These results establish that CIF preprocessing is inherently application-dependent and that treating preprocessing assumptions as explicit, controllable variables is essential for reproducible interpretable high-throughput screening. This assumption-aware paradigm embodied by SmartCIF generalizes existing computation-ready resources and provides a flexible foundation for large-scale simulations beyond adsorption.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"16 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147448431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lasse Stausberg,Frank Heberling,Johannes Lützenkirchen
Mineral surfaces in contact with aqueous solutions develop an electric double layer (EDL) through surface (de-)protonation reactions and adsorption of ions, diffusion, and electrostatic forces, resulting in a Stern- and a diffuse layer of ions. Most current models used for surface speciation calculations do not consider changes in surface chemistry caused by charge regulation effects, i.e. effects of interacting EDLs of surfaces in close proximity. Charge regulation modeling requires equilibrium calculation of every involved surface simultaneously, while also solving the Poisson-Boltzmann equation (PBE) to quantify electrostatic interaction. Since analytical solutions of the PBE for complex geometries do not exist it becomes necessary to solve such problems numerically. A Python code is presented that combines a general chemical speciation code, Three Plane Surface Complexation Model, and a Finite Element solution of the PBE on two-dimensional domains. The Finite Element PBE solver is benchmarked against analytical solutions and the speciation code is benchmarked against a PHREEQC model as well as an existing 1D charge regulation code. A test case involving charge regulation in a corner of two perpendicular surfaces is modeled. Charge regulation modeling on a nanoscale enables simulations of the electrostatic environment and surface chemistry in nano-confined systems and interactions of nanoparticles. This may also improve simulations of environmental and biological systems, cementitious materials and modeling of the electrostatic environment and sorption on nanoporous clay materials. Such information can be vital for the in depth understanding of natural and engineered barrier systems of nuclear waste repositories or other environmental scenarios.
{"title":"Charge regulation and surface complexation modeling in nanoscale 2D geometries: benchmarking and test cases of a novel code (CRESCENDO).","authors":"Lasse Stausberg,Frank Heberling,Johannes Lützenkirchen","doi":"10.1039/d6cp00143b","DOIUrl":"https://doi.org/10.1039/d6cp00143b","url":null,"abstract":"Mineral surfaces in contact with aqueous solutions develop an electric double layer (EDL) through surface (de-)protonation reactions and adsorption of ions, diffusion, and electrostatic forces, resulting in a Stern- and a diffuse layer of ions. Most current models used for surface speciation calculations do not consider changes in surface chemistry caused by charge regulation effects, i.e. effects of interacting EDLs of surfaces in close proximity. Charge regulation modeling requires equilibrium calculation of every involved surface simultaneously, while also solving the Poisson-Boltzmann equation (PBE) to quantify electrostatic interaction. Since analytical solutions of the PBE for complex geometries do not exist it becomes necessary to solve such problems numerically. A Python code is presented that combines a general chemical speciation code, Three Plane Surface Complexation Model, and a Finite Element solution of the PBE on two-dimensional domains. The Finite Element PBE solver is benchmarked against analytical solutions and the speciation code is benchmarked against a PHREEQC model as well as an existing 1D charge regulation code. A test case involving charge regulation in a corner of two perpendicular surfaces is modeled. Charge regulation modeling on a nanoscale enables simulations of the electrostatic environment and surface chemistry in nano-confined systems and interactions of nanoparticles. This may also improve simulations of environmental and biological systems, cementitious materials and modeling of the electrostatic environment and sorption on nanoporous clay materials. Such information can be vital for the in depth understanding of natural and engineered barrier systems of nuclear waste repositories or other environmental scenarios.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"8 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147439540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nikolaj Klinkby,Anne P Rasmussen,Anders G S Lauridsen,Mordechai Sheves,Lars H Andersen
Retinal protonated Schiff base (RPSB) is the active chromophore in opsin proteins, including rhodopsin for vision. Yet, the spectral consequences of geometric constraints imposed by the protein environment remain insufficiently characterised. We report on gas-phase action-absorption spectra of six retinal analogues with defined steric modifications, recorded in an electrostatic ion-storage ring after cooling in a cryogenic ion trap. Analogues bearing out-of-plane distortions or a shortened π-conjugated polyene chain exhibit pronounced blue-shifts in their absorption maxima. We further present the spectrum of a cryogenically cooled RPSB photofragment of mass 248 amu, whose absorption band near 370 nm matches that of a synthesised β-ionone protonated Schiff base, consistent with substantial truncation of the polyene system. These results isolate the intrinsic spectral signatures of constrained RPSB geometries and provide a framework for understanding protein-induced tuning in opsins.
{"title":"Spectroscopy of cryogenic protonated Schiff-base retinal derivatives.","authors":"Nikolaj Klinkby,Anne P Rasmussen,Anders G S Lauridsen,Mordechai Sheves,Lars H Andersen","doi":"10.1039/d6cp00364h","DOIUrl":"https://doi.org/10.1039/d6cp00364h","url":null,"abstract":"Retinal protonated Schiff base (RPSB) is the active chromophore in opsin proteins, including rhodopsin for vision. Yet, the spectral consequences of geometric constraints imposed by the protein environment remain insufficiently characterised. We report on gas-phase action-absorption spectra of six retinal analogues with defined steric modifications, recorded in an electrostatic ion-storage ring after cooling in a cryogenic ion trap. Analogues bearing out-of-plane distortions or a shortened π-conjugated polyene chain exhibit pronounced blue-shifts in their absorption maxima. We further present the spectrum of a cryogenically cooled RPSB photofragment of mass 248 amu, whose absorption band near 370 nm matches that of a synthesised β-ionone protonated Schiff base, consistent with substantial truncation of the polyene system. These results isolate the intrinsic spectral signatures of constrained RPSB geometries and provide a framework for understanding protein-induced tuning in opsins.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"76 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147439537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We present a molecular dynamics study revealing that dielectric loss in liquid water in GHz region arises not from isolated molecular rotations, but from collective dipolar correlations spanning more than tens of molecules. By introducing a distance-dependent dipole correlation function, we quantify the spatial extent and temporal evolution of orientational fluctuations contributing to dielectric relaxation. Three distinct peaks identified in the dipole vector correlation at 0.25 nm, 0.53 nm, and 0.75 nm-corresponding to coordinated reorientation among approximately 70 water molecules-indicate a strong link between molecular structure and dielectric behaviour. These findings provide a microscopic basis for understanding dielectric absorption and offer new insights into the design of water-based dielectric systems.
{"title":"Understanding Dielectric Loss in Water via Distance-Dependent Dipole Correlation Functions","authors":"Miki Nakano, Shigenori Tanaka","doi":"10.1039/d5cp03962b","DOIUrl":"https://doi.org/10.1039/d5cp03962b","url":null,"abstract":"We present a molecular dynamics study revealing that dielectric loss in liquid water in GHz region arises not from isolated molecular rotations, but from collective dipolar correlations spanning more than tens of molecules. By introducing a distance-dependent dipole correlation function, we quantify the spatial extent and temporal evolution of orientational fluctuations contributing to dielectric relaxation. Three distinct peaks identified in the dipole vector correlation at 0.25 nm, 0.53 nm, and 0.75 nm-corresponding to coordinated reorientation among approximately 70 water molecules-indicate a strong link between molecular structure and dielectric behaviour. These findings provide a microscopic basis for understanding dielectric absorption and offer new insights into the design of water-based dielectric systems.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"31 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147447853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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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