Adam Knirsch , Bruno N. Falcone , Jonathan D. Hirst
{"title":"Practical guidelines for optimising free energy calculations using thermodynamic integration","authors":"Adam Knirsch , Bruno N. Falcone , Jonathan D. Hirst","doi":"10.1016/j.cplett.2025.142395","DOIUrl":"10.1016/j.cplett.2025.142395","url":null,"abstract":"<div><div>Free energy calculations are valuable in structure-based drug design, but their accuracy and reliability remain challenges. We present an automated workflow for estimation of protein–ligand binding affinity built with AMBER20, alchemlyb, and open-source cycle closure algorithm. Evaluated on 178 perturbations across four datasets, the short sub-nanosecond simulations performed comparably or better than prior studies for the MCL1, BACE, and CDK2 datasets, while the TYK2 dataset required a longer equilibration time (<span><math><mrow><mo>∼</mo><mn>2</mn><mspace></mspace><mi>ns</mi></mrow></math></span>). Perturbations with <span><math><mrow><mrow><mo>|</mo><mi>Δ</mi><mi>Δ</mi><mi>G</mi><mo>|</mo></mrow><mo>></mo><mn>2</mn><mo>.</mo><mn>0</mn></mrow></math></span> kcal/mol exhibited higher errors, suggesting such perturbations are unreliable, hence providing a practical guideline for improving thermodynamic integration simulations.</div></div>","PeriodicalId":273,"journal":{"name":"Chemical Physics Letters","volume":"880 ","pages":"Article 142395"},"PeriodicalIF":3.1,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145047304","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}
Narinderjit Singh Sawaran Singh , Maher Ali Rusho , Akmal Abilkasimov , Mutabar Latipova , Ahmed Aldulaimi , Anmar Ghanim Taki , Rafid Jihad Albadr , Waam Mohammed Taher , Aseel Smerat , M.Ramkumar Raja , Saiful Islam
{"title":"Exploring transition metal-based electrocatalysts for carbon dioxide reduction: Towards enhanced product","authors":"Narinderjit Singh Sawaran Singh , Maher Ali Rusho , Akmal Abilkasimov , Mutabar Latipova , Ahmed Aldulaimi , Anmar Ghanim Taki , Rafid Jihad Albadr , Waam Mohammed Taher , Aseel Smerat , M.Ramkumar Raja , Saiful Islam","doi":"10.1016/j.cplett.2025.142410","DOIUrl":"10.1016/j.cplett.2025.142410","url":null,"abstract":"<div><div>The development of advanced electrocatalysts has been considered crucial to capture chemically inert CO<sub>2</sub> and for converting it into valuable products like fuel. It also plays a significant role in addressing the emission of greenhouse gasses and the energy crises in a sustainable manner. However, achieving control over product selectivity at low overpotentials is one the major challenges. This study employed density functional theory to investigate the electrocatalytic potential of different single transition metals (Ni, Co, and Fe) in the electrochemical reduction reaction of CO<sub>2</sub> (hereafter ECO<sub>2</sub>RR). The efficacy of ECO<sub>2</sub>RR was evaluated based on the reaction intermediates (COOH, CHO and CO) when incorporated into BN-biphenyl monolayer (BNML) systems. Interestingly, incorporating Fe into BNML was found to be the most efficient option for ECO<sub>2</sub>RR, resulting in the production of CH<sub>4</sub> with a remarkably low limiting potential (−0.31 V). In the hydrogen evolution reaction (HER), CO<sub>2</sub> showed a higher affinity for the activation site on Fe-BNML compared to H<sub>2</sub>, indicating differences in adsorption energy (−0.92 vs. -0.40 eV). Additionally, Fe-BNML effectively suppressed HER during the ECO<sub>2</sub>RR process, with a HER limiting potential of −0.40 V. The findings can pave the way for developing low-potential electrocatalysts with improved selectivity and activity for CO<sub>2</sub> reduction.</div></div>","PeriodicalId":273,"journal":{"name":"Chemical Physics Letters","volume":"880 ","pages":"Article 142410"},"PeriodicalIF":3.1,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145047555","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}
{"title":"Mass spectrometric observation of a dipole-bound dimer anion [H2⋯H2O]− produced under atmospheric pressure Corona discharge: Formation mechanism and hyperconjugative stability","authors":"Mitsuo Takayama, Kanako Sekimoto","doi":"10.1016/j.cplett.2025.142396","DOIUrl":"10.1016/j.cplett.2025.142396","url":null,"abstract":"<div><div>The formation of a hydrogen-included dipole-bound dimer anion, [H<sub>2</sub>⋯H<sub>2</sub>O]<sup>−</sup>, has been reported using a corona discharge mass spectrometer. Quantum chemical calculations suggested the hypothesis that the anion forms through an energetically favorable reaction, H<sup>−</sup> + H∙ + H<sub>2</sub>O → [H<sub>2</sub>⋯H<sub>2</sub>O]<sup>−</sup>. The calculated dipole moments of the [H<sub>2</sub>⋯H<sub>2</sub>O] complex range from 2.04 to 2.06 D, which may enable an electron to bind to the complex. A novel finding is that the Rydberg orbitals of the anion's NBO acceptor contribute to stabilizing the [H<sub>2</sub>⋯H<sub>2</sub>O]<sup>−</sup> anion by at least 15.37 kcal/mol (0.66 eV) through hyperconjugation.</div></div>","PeriodicalId":273,"journal":{"name":"Chemical Physics Letters","volume":"880 ","pages":"Article 142396"},"PeriodicalIF":3.1,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145097223","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}
Narinderjit Singh Sawaran Singh , Thanaa Amir Ahmed , Ahmed Aldulaimi , Anmar Ghanim Taki , Rafid Jihad Albadr , Waam Mohammed Taher , Mariem Alwan , Hiba Mushtaq , Mohammed Akbar , Amir Ibrahim Ali Arabi , Saiful Islam
{"title":"Selective detection of NH₃ over H2S, HCl, CO2, and NO2 using boron-doped T-graphene nanocages: A DFT study","authors":"Narinderjit Singh Sawaran Singh , Thanaa Amir Ahmed , Ahmed Aldulaimi , Anmar Ghanim Taki , Rafid Jihad Albadr , Waam Mohammed Taher , Mariem Alwan , Hiba Mushtaq , Mohammed Akbar , Amir Ibrahim Ali Arabi , Saiful Islam","doi":"10.1016/j.cplett.2025.142412","DOIUrl":"10.1016/j.cplett.2025.142412","url":null,"abstract":"<div><div>We employed density functional theory (DFT) to develop a boron-doped T-graphene nanocage (BTG) as a sensor for NH<sub>3</sub> detection. Boron doping introduces an electron-deficient site that enhances adsorption energy (<em>E</em><sub>ads</sub> = −17.9 kcal/mol) and reduces the energy gap (<em>E</em><sub>g</sub>) by 12.6 %. The BTG demonstrates strong electrical conductivity and confirms charge transfer from NH<sub>3</sub> to boron. Furthermore, it exhibits exceptional selectivity against interference from CO<sub>2</sub>, H<sub>2</sub>S, HCl, and NO<sub>2</sub>, along with a rapid recovery time of 13.2 s under visible light. This makes it a promising candidate for gas sensing in ambient conditions.</div></div>","PeriodicalId":273,"journal":{"name":"Chemical Physics Letters","volume":"880 ","pages":"Article 142412"},"PeriodicalIF":3.1,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145020773","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}
{"title":"Plasma-assisted catalysis for graphene pre-nucleation: the role of high-index nickel nanocrystal surfaces","authors":"Tursunpulat Juraboev , Feruz Khaydarov , Quan-Zhi Zhang , Aamir Shahzad , Umedjon Khalilov","doi":"10.1016/j.cplett.2025.142411","DOIUrl":"10.1016/j.cplett.2025.142411","url":null,"abstract":"<div><div>The reactivity of high-index Ni nanocrystal surfaces is critical for catalytic carbon nanostructure synthesis. We used reactive molecular dynamics to probe C<sub>2</sub> and C<sub>2</sub>H radical interactions with Ni(111), Ni(210), and Ni(331) surfaces under acetylene plasma conditions. While high-index surfaces showed enhanced reactivity, the Ni(331) facet proved superior, promoting both rapid pre-nucleation and the subsequent growth of a high-quality crystalline layer. This performance stems from an optimal balance of low carbon-diffusion barriers and suppressed C<sub>2</sub> dissociation, yielding the lowest activation energies for C<sub>4</sub> chain and C<sub>6</sub> ring formation. These findings establish engineered surface faceting as a promising route toward superior catalysts.</div></div>","PeriodicalId":273,"journal":{"name":"Chemical Physics Letters","volume":"880 ","pages":"Article 142411"},"PeriodicalIF":3.1,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145020776","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}
Qiaoyan Cheng , Mi Zhong , Dai-He Fan , Zheng-Tang Liu
{"title":"First-principles study on the electronic structure and optical properties of metal elements (X = Ge, Sn, Pb, Sb, Bi) doped cubic CuI","authors":"Qiaoyan Cheng , Mi Zhong , Dai-He Fan , Zheng-Tang Liu","doi":"10.1016/j.cplett.2025.142409","DOIUrl":"10.1016/j.cplett.2025.142409","url":null,"abstract":"<div><div>This first principles study dopes CuI with Ge, Sn, Pb, Sb, and Bi. Doping causes volume expansion. Stability depends on atomic size matching. Ge, Sn, and Pb create deep donor levels. Sb and Bi create shallow donor levels. All dopants give n-type conductivity. This makes CuI a transparent conductor. Pb bonding is ionic. Sb and Bi bonding is neutral. Ge, Sn, Pb boost low energy absorption. Their optical properties match pure CuI above 2.2 to 2.4 eV. Sb and Bi change low energy optics greatly. Sb and Bi are best for n-type use. Ge, Sn, Pb are good for optoelectronics.</div></div>","PeriodicalId":273,"journal":{"name":"Chemical Physics Letters","volume":"880 ","pages":"Article 142409"},"PeriodicalIF":3.1,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145047300","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}
{"title":"Cadmium mediated aggregation of spherical-planar and spherical-spherical aromatic lead-based clusters towards extended cluster materials","authors":"Peter L. Rodríguez-Kessler , Alvaro Muñoz-Castro","doi":"10.1016/j.cplett.2025.142394","DOIUrl":"10.1016/j.cplett.2025.142394","url":null,"abstract":"<div><div>Spherical and planar aromatic structures are relevant building units for forming cluster-based materials. [Pb<sub>9</sub>CdCdPb<sub>9</sub>]<sup>6−</sup> and [Pb<sub>9</sub>CdPh]<sup>3−</sup> species, appears as prototypical aggregates combining spherical-spherical and spherical-planar aromatic units, based on the spherical aromatic [Pb<sub>9</sub>]<sup>4−</sup> Zintl-ion cluster and planar aromatic -Ph. Our results expose the inherent aromatic characteristics of the parent units to be retained at the overall aggregate, featuring the interplay between enabled shielding cones from adjacent aromatic states. For [Pb<sub>9</sub>CdCdPb<sub>9</sub>]<sup>6−</sup>, a sizably enhance of the common shielding regions is obtained. Thus, further explorative synthesis efforts can be rationally designed and conceived from well-defined spherical and planar aromatic units in the quest for novel materials based on Zintl-ions clusters.</div></div>","PeriodicalId":273,"journal":{"name":"Chemical Physics Letters","volume":"880 ","pages":"Article 142394"},"PeriodicalIF":3.1,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145047302","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}
Maik Budde , Dihya Sadi , Nelson de Oliveira , Sophie Bois , Mathéo Tardat , Carolina A. Garcia-Soto , Garrett A. Curley , Edmond Baratte , Olivier Guaitella
{"title":"In-situ quantitative measurements of methyl radicals in oxygen-containing reactive environments by VUV absorption spectroscopy using synchrotron radiation","authors":"Maik Budde , Dihya Sadi , Nelson de Oliveira , Sophie Bois , Mathéo Tardat , Carolina A. Garcia-Soto , Garrett A. Curley , Edmond Baratte , Olivier Guaitella","doi":"10.1016/j.cplett.2025.142388","DOIUrl":"10.1016/j.cplett.2025.142388","url":null,"abstract":"<div><div>Absolute methyl radical number densities are measured in-situ in a low-temperature discharge in methane and oxygen diluted in argon/helium, using vacuum ultraviolet synchrotron radiation absorption spectroscopy. Instead of the methyl absorption band around 216<!--> <!-->nm, the exploitation of the more sensitive band at 150<!--> <!-->nm is demonstrated. Densities as low as (1.6 ± 0.2) × 10<sup>13</sup> <!-->cm<sup>-2</sup> are detected. With oxygen admixture, the expected monotonous decrease of CH<sub>3</sub> density is not observed, but a distinct maximum at a few percent of oxygen, separating a regime dominated by the electron kinetics for low percentages from an oxidation-dominated regime at higher admixtures.</div></div>","PeriodicalId":273,"journal":{"name":"Chemical Physics Letters","volume":"879 ","pages":"Article 142388"},"PeriodicalIF":3.1,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145011063","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}
Weijing Hu , Haizhao Li , Fangjie Liu , Qingjie Wang , Weiwei Shang , Shaojie Du , Guanlun Guo
{"title":"Effects of oxygen and water on initial Sr segregation in La0.6Sr0.4Co0.2Fe0.8O3-δ cathodes: A first principle study","authors":"Weijing Hu , Haizhao Li , Fangjie Liu , Qingjie Wang , Weiwei Shang , Shaojie Du , Guanlun Guo","doi":"10.1016/j.cplett.2025.142390","DOIUrl":"10.1016/j.cplett.2025.142390","url":null,"abstract":"<div><div>First principle method was employed to investigate Sr segregation on La<sub>0.6</sub>Sr<sub>0.4</sub>Co<sub>0.2</sub>Fe<sub>0.8</sub>O<sub>3-δ</sub> (LSCF) cathodes with effects of water and oxygen. Water and oxygen are directly dissociated on LSCF surfaces. Surface oxygen vacancy and water or oxygen molecules accelerate Sr segregation rates comparing to that on pure LSCF surface energetically. Water and oxygen show positive effects on Sr segregation in comparison to oxygen on LSCF surfaces in terms of finally formed Sr contained particles. The most plausible path for Sr segregation may be on water and oxygen contained LSCF surfaces combined energies of formed Sr-contained particles and relative energies between each step.</div></div>","PeriodicalId":273,"journal":{"name":"Chemical Physics Letters","volume":"879 ","pages":"Article 142390"},"PeriodicalIF":3.1,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145005309","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}
{"title":"Interfacially enhanced visible-light photocatalysis for tetracycline degradation with Bi2Se3/g-C3N4 nanocomposite","authors":"Mingli Chen , Han Xu , Zhan Wang","doi":"10.1016/j.cplett.2025.142399","DOIUrl":"10.1016/j.cplett.2025.142399","url":null,"abstract":"<div><div>Tetracycline (TC) contamination in water bodies poses a serious environmental and health risk, underscoring the need for effective remediation strategies. Herein, this work explores a novel approach to TC remediation using a 2D/2D Bi<sub>2</sub>Se<sub>3</sub>/g-C<sub>3</sub>N<sub>4</sub> nanosheet nanocomposite as a visible-light-driven photocatalyst. The key innovation lies in the 2D/2D Bi<sub>2</sub>Se<sub>3</sub>/g-C<sub>3</sub>N<sub>4</sub> heterostructure, designed to enhance charge separation and reactive oxygen species generation. Optimized nanocomposites (5 % Bi<sub>2</sub>Se<sub>3</sub>/g-C<sub>3</sub>N<sub>4</sub>) achieve 86.11 % TC degradation within 90 min, demonstrating substantially superior performance compared to g-C<sub>3</sub>N<sub>4</sub> and Bi<sub>2</sub>Se<sub>3</sub> components. Photoelectrochemical and photoluminescence analyses reveal that the enhanced activity stems from efficient interfacial charge transfer, minimizing electron-hole recombination. This study showcases that Bi<sub>2</sub>Se<sub>3</sub>/g-C<sub>3</sub>N<sub>4</sub> nanocomposites offer a promising strategy for the photocatalytic removal of antibiotic pollutants from water.</div></div>","PeriodicalId":273,"journal":{"name":"Chemical Physics Letters","volume":"879 ","pages":"Article 142399"},"PeriodicalIF":3.1,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145004902","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}