{"title":"Machine learning with new functional structure descriptors for design and screening of ionic liquids in CO2 efficient capture","authors":"Ranran Geng, Wenjuan Deng, Zhiqiang Hu, JianLei Wang, Yuanyuan Zhao, Baichaun Zhou, Guocai Tian","doi":"10.1039/d5cp01972a","DOIUrl":"https://doi.org/10.1039/d5cp01972a","url":null,"abstract":"Carbon dioxide emission reduction, conversion and utilization are the hot and difficult issues in the world. As a new kind of green solvents, ionic liquids (ILs) are widely used in CO2 capture and conversion, but there are various kinds of ILs (more than 1018). How to select and screen the appropriate ILs for CO2 capture is an urgent problem to be solved. Therefore, it is of great significance to establish the Quantitative Structure-Property Relationships (QSPR) of ILs for CO2 capture. From the practical point of view of ILs design and synthesis, a new functional structure descriptor (FSD) based on group contribution method (GC) was constructed. At the same time, the idea of increasing dimension to increase accuracy in traditional machine learning is changed, and the feasibility of reducing the dimension under the condition of ensuring accuracy is examined. A dimensionless molecular descriptor CORE is constructed. Based on these two new molecular descriptors, we discussed the performance of six common ensemble learning models (CatBoost, LightGBM, XGBoost, GBDT, RF and AdaBoost) for CO2 solubility in ILs. It is shown that all ensemble learning models can achieve good performance, but CatBoost model is the most outstanding. The R² of 0.9945 and MAE of 0.0108 for CatBoost-FSD model is achieved, while R² and MAE is 0.9925 and 0.0120 for CatBoost-CORE model, respectively. The interpretability of CatBoost-CORE model is analyzed, and the key features are determined. Based on the CORE descriptor, the best experimental conditions are obtained, and nine kinds of ILs with superior performance are recommended.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"14 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144305474","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}
Geanso M. de Moura, Sérgio Alves de Azevedo, Julio Ricardo Sambrano, Mateus R. Lage, Adenilson O. dos Santos, Stanislav R. Stoyanov, T. Andrade-Filho
{"title":"Optical properties of sarcosine crystal under hydrostatic pressure: a DFT-based computational study","authors":"Geanso M. de Moura, Sérgio Alves de Azevedo, Julio Ricardo Sambrano, Mateus R. Lage, Adenilson O. dos Santos, Stanislav R. Stoyanov, T. Andrade-Filho","doi":"10.1039/d5cp01046b","DOIUrl":"https://doi.org/10.1039/d5cp01046b","url":null,"abstract":"Organic crystals have become attractive for applications as nonlinear optical materials due to their nonlinear susceptibility, optical transparency, and other properties that can be tuned using elevated pressure. We have investigated the optical properties of the zwitterionic crystal of the natural amino acid sarcosine using the first-principles projected augmented plane wave method and the GGA and hybrid exchange-correlation functionals. The molecular crystal of sarcosine is composed of zwitterion organic molecules arranged in an antiparallel fashion by the formation of distinct hydrogen bond chains in the planes (100), (010), and (001). The calculated anisotropic optical properties of sarcosine, including the dielectric constant, absorption, extinction coefficient, refractive index, reflectivity, energy loss function, and optical conductivity, are determined from ambient to 3.7 GPa hydrostatic pressure along crystallographic axes <em>a</em>, <em>b</em>, and <em>c</em>. Sarcosine has an optical anisotropy at ambient and external hydrostatic pressures, characterized by specific peaks in the ultraviolet spectrum. The results show the potential application of the studied system in nonlinear optics, UV detectors, and high-pressure photonic applications.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"1 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144329123","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":"Complex active site structures influence absorption spectrum of Chrimson wild type and mutants","authors":"Katharina Spies, Beatrix M. Bold, Marcus Elstner","doi":"10.1039/d5cp00762c","DOIUrl":"https://doi.org/10.1039/d5cp00762c","url":null,"abstract":"The red light-activated channelrhodopsin Chrimson is widely used in optogenetic applications, including vision and hearing restoration. Despite structural insights from X-ray crystallography and their identification of another red-shifted mutant (S169A), the molecular determinants of its large spectral shift remain incompletely understood. In this study, we present a computational analysis of wild type Chrimson and several mutants within a QM/MM approach. A key finding is the pronounced flexibility of the active site, where multiple conformations interconvert on the nano-second scale. We also highlight the role of residue S169, whose hydrogen bonding influences the torsional flexibility of the nearby counterion E165, thus affecting the prevalence of distinct structural motifs at the active site. The comparison of experimental and QM/MM MD-sampled absorption spectra supports the validity of our computational models. A direct hydrogen bond between counterions is identified as one of the key factors contributing to the red-shifted absorption spectrum, with increased occurrence observed in the red-shifted S169A mutant.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"93 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144305471","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":"Pre-trained Language Models for Protein and Molecular Design","authors":"Erdong Zhang, Calvin Yu-Chian Chen, Zilin Pan, Zequan Yao, Tiejun Dong, Guan-Xing Chen, Tingwen Deng, Shiwei Chen","doi":"10.1039/d5cp00785b","DOIUrl":"https://doi.org/10.1039/d5cp00785b","url":null,"abstract":"Pre-trained Language Models (PLMs) have recently emerged as a powerful tool, showcasing exceptional performance not just in natural language understanding but also in the realm of biological research. The advantage of PLMs lies in their ability to leverage the structural similarity between biological sequences and natural language. PLMs offer novel solutions for protein research and drug design applications. By pre-training on extensive unlabeled biological sequences and then fine-tuning for specific tasks, PLMs have delivered remarkable results. To summarize the growing landscape of PLMs in biological research, this paper integrates exemplary PLMs and common datasets, demonstrating the potential and application prospects of PLMs in prediction and generation tasks.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"10 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144296229","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}
Xiuchen Han,Qi Yang,Shuning Wang,Xinyue Zhang,Dongmeng Chen,Peiwen Xiao,Wenjing Fang,Bing Liu
{"title":"The orientation design of high-polarity ligand dipole CF3-PEA for enhancing the surface stability and optoelectronic properties of the FAPbI3 perovskite.","authors":"Xiuchen Han,Qi Yang,Shuning Wang,Xinyue Zhang,Dongmeng Chen,Peiwen Xiao,Wenjing Fang,Bing Liu","doi":"10.1039/d5cp00612k","DOIUrl":"https://doi.org/10.1039/d5cp00612k","url":null,"abstract":"Ligand dipoles are introduced onto perovskite surfaces to enhance the optoelectronic properties and stability of organic-inorganic hybrid perovskite solar cells (PSCs), achieving diverse spatial distributions and orientational variations due to their interaction. However, the impacts of ligand dipole orientation on the performance of PSCs remain unclear. In this work, we investigate the adsorption of high-polarity ligand dipole 4-trifluoromethyl-phenethylammonium (CF3-PEA) with orientation design on the PbI2-terminated surface of the formamidinium perovskite (FAPbI3), revealing the impact of CF3-PEA orientation on the atomic structure, stability, and optoelectronic properties of the FAPbI3 surface. The results indicate that on the FAPbI3 surface along with the (001) crystal plane, the optimal crystal orientation of CF3-PEA is [2, 4, -1], where the strong -NH3/π⋯I interaction results in the parallel alignment of CF3-PEA with the FAPbI3 surface. Under the optimal [2, 4, -1] orientation, the surface adsorption system exhibits the lowest relative total energy difference (0 eV), formation energy (-0.746 eV) and adsorption energy (-4.14 eV) among all adsorption systems, with the formation energy being 1.54 times those of bare FAPbI3, revealing its highest stability. Moreover, the adsorption of CF3-PEA with [2, 4, -1] orientation results in a decrease of the work function from 6.764 eV of bare FAPbI3 to 6.743 eV due to the strong -NH3/π⋯I interaction with significant charge transfer. Furthermore, the appearance of sub-bandgap states in density of states leads to an obvious redshift in the light absorption coefficient attributed to structural distortions, which indicates that the optoelectronic properties of FAPbI3 are improved. This work provides insights into optimizing the performance of PSCs by regulating the orientation of ligand dipoles.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"103 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295828","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":"On the structure of hybrid water-in-salt electrolytes.","authors":"Raúl Lois-Cuns,Antía Santiago-Alonso,Martín Otero-Lema,Juan J Parajó,Josefa Salgado,Hadrián Montes-Campos,Trinidad Méndez-Morales,Luis M Varela","doi":"10.1039/d5cp00680e","DOIUrl":"https://doi.org/10.1039/d5cp00680e","url":null,"abstract":"Water-in-salt electrolytes are promising candidates for next-generation lithium-ion batteries due to their enhanced safety and cost-effectiveness. However, optimizing the performance of hybrid aqueous/non-aqueous water-in-salt electrolytes remains a challenge. This work investigates the structural characteristics of mixtures of a LiTFSI water-in-salt based electrolyte (21 m) with several common solvents (e.g. carbonates, dimethyl sulfoxide, acetonitrile) using molecular dynamics simulations combined with experimental measurements. Our analysis reveals a correlation between the ability of a given cosolvent to solvate lithium cations and its Lewis basicity. A strong Lewis basicity favours the formation of free water cluster aggregates in the system, which reduces the electrochemical performance of the electrolyte. Moreover, the relative permittivity of the cosolvents also plays an important role in modifying the ionic interaction.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"6 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295847","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}
Einaras Sipavičius, Lukas Mikalauskas, Vytautas Klimavičius, Kęstutis Aidas
{"title":"Intermolecular organization in aqueous mixtures of choline lysinate studied by NMR and molecular dynamics/quantum mechanics","authors":"Einaras Sipavičius, Lukas Mikalauskas, Vytautas Klimavičius, Kęstutis Aidas","doi":"10.1039/d5cp00861a","DOIUrl":"https://doi.org/10.1039/d5cp00861a","url":null,"abstract":"Aiming to scrutinize intermolecular organization in aqueous mixtures of choline lysinate, [Cho][Lys], ionic liquid (IL), the dependences of the <small><sup>1</sup></small>H NMR chemical shifts and diffusion coefficients on their composition were measured. To rationalize experimental findings, extensive molecular dynamics (MD) simulations and linear response quantum mechanics/molecular mechanics (QM/MM) computations of NMR shielding constants were performed. Analysis of MD trajectories reveals that extent of intermolecular contacts between cations and anions intensifies with the increasing content of the IL in the mixture. Moreover, the tendency of choline cations and the side chains of lysinate anions to self-aggregate was observed as well, leading to the formation of a continuous, highly polar domain composed of choline cations and the carboxylate groups of lysinate anions, as well as a less polar domain formed by the side chains of the anions in IL-rich mixtures. Under these circumstances, isolated water pockets are found to be situated at the interface of the polar and nonpolar ionic domains. The dependences of the measured diffusion coefficients on the composition of the mixture reveals the existence of two dynamical regimes – fast and slow regimes below and above molar fraction of the IL of 11%, respectively. Results of MD simulations suggest that – at this specific molar composition of aqueous [Cho][Lys] mixture – continuous water network ceases giving way to the continuous structure of ionic domains being formed. The QM/MM results for the <small><sup>1</sup></small>H NMR chemical shifts of aqueous IL mixtures generally agree well with experimental findings and corroborate structural results. The prominent upfield shift of the NMR signal of protons in fast exchange with the rising content of the IL was successfully rationalized.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"34 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144305478","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}
Mantu Kumar Sah, Soumya Mukherjee, Satrajit Adhikari, Satyam Ravi
{"title":"Construction of First Principle Based Adiabatic and Diabatic Hamiltonian for TiO68- unit of BaTiO3 Crystal: Photoemission Spectra and Ferroelectricity","authors":"Mantu Kumar Sah, Soumya Mukherjee, Satrajit Adhikari, Satyam Ravi","doi":"10.1039/d5cp01761k","DOIUrl":"https://doi.org/10.1039/d5cp01761k","url":null,"abstract":"The ferroelectric property of BaTiO<small><sub>3</sub></small> crystal arises from the strong Pseudo Jahn-Teller (PJT) interactions between the non-degenerate ground electronic state, <small><sup>1</sup></small>A<small><sub>1g</sub></small> and the degenerate <small><sup>1</sup></small>T<small><sub>1u</sub></small> symmetry states through the nuclear distortions of t<small><sub>1u</sub></small> modes in TiO<small><sub>6</sub></small><small><sup>8-</sup></small> unit. In a d<small><sup>0</sup></small> electronic configuration of Ti<small><sup>4+</sup></small> ion, the PJT interaction leads to a stabilization effect, which has been explored using Beyond Born-Oppenheimer (BBO) theory. The <small><sup>1</sup></small>T<small><sub>1u</sub></small> excited states form a three-state degeneracy, exhibiting feeble Jahn-Teller (JT) distortions over the t<small><sub>2g</sub></small> planes. For the first time, we compute <em>ab initio</em> adiabatic potential energy surfaces (PESs) and non-adiabatic coupling terms (NACTs), and thereafter, diabatic PESs and couplings for the perovskite unit, TiO<small><sub>6</sub></small><small><sup>8-</sup></small>. Using a Time-Dependent Discrete Variable Representation (TDDVR) approach, the theoretical photoemission spectra exhibit good agreement with the experimental ones. Moreover, the experimental observation on order parameter associated with ferroelectric properties of BaTiO<small><sub>3</sub></small> crystal show close resemblance with present and other theoretical predictions.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"31 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144296230","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":"Recent advances in CeO2 based abrasives for chemical mechanical polishing.","authors":"Yongxin Wang,Yunhui Shi,Jiabao Cheng,Yao Xu,Yizhan Wang,Jiawei Qiu","doi":"10.1039/d5cp00778j","DOIUrl":"https://doi.org/10.1039/d5cp00778j","url":null,"abstract":"Chemical mechanical polishing (CMP) is a critical technique that combines chemical etching and mechanical grinding to achieve atomic-level surface planarization and eliminate subsurface damage in various materials, playing a key role in wafer thinning and smoothing. CeO2 abrasives, owing to their unique electronic structure and moderate chemical reactivity, exhibit excellent properties such as high polishing rate, reactivity, and selectivity. With advancements in manufacturing processes and the growing demand for ultra-flat surfaces, the preparation and application of CeO2-based abrasives in CMP have emerged as key research areas. This review paper provides an overview of the synthesis methods for typical CeO2-based abrasives and their applications. Additionally, the application of CeO2-based abrasives in CMP slurries is discussed, focusing on their use in polishing silicon-based materials and other non-silicon-based materials. Finally, the common challenges associated with CeO2-based abrasives in CMP are summarized, and future directions and potential advancements in this field are prospected.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"43 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295825","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}
Xin-Xin Liu,Jia-Jia Ma,Guo Li,Ling-Ya Peng,Qiu Fang,Wei-Hai Fang,Ganglong Cui
{"title":"Photodimerization of norbornenes and cyclohexenes catalyzed by Cu(I) complexes: mechanistic similarities and differences.","authors":"Xin-Xin Liu,Jia-Jia Ma,Guo Li,Ling-Ya Peng,Qiu Fang,Wei-Hai Fang,Ganglong Cui","doi":"10.1039/d5cp01567g","DOIUrl":"https://doi.org/10.1039/d5cp01567g","url":null,"abstract":"The Cu(I)-photocatalyzed cycloaddition reaction has become an important way to construct four-membered ring products. A recent experiment reported the photocycloaddition of norbornenes (nb) and cyclohexenes (ch) catalyzed by CuOTf. However, the atomic level details remain lacking. Herein, using high-level electronic structure methods, the initial photophysics and subsequent dimerization reaction of two Cu complexes ([Cu(nb)2]+ and [Cu(ch)2]+) were explored. For both species, the 1MLCT state is initially populated and there are two triplet states (3MLCT and 3LC). Notably, in [Cu(ch)2]+, an additional 1LC state appears near 1MLCT rendering 1MLCT short-lived and difficult to detect experimentally as a result of an ultrafast internal conversion to 1LC. Through direct and 3MLCT-mediated intersystem crossing, the lowest 3LC state is populated. The most striking difference of the 3LC structures of [Cu(ch)2]+ and [Cu(nb)2]+ is that one cyclohexene of the former undergoes a half-chair-to-chair conformational change while the latter does not. From the precursor 3LC, two successive but nonadiabatic reactions form two C-C bonds in the 3LC and S0 states, respectively. The current work provides the first efforts to understand the atomistic details of the Cu-catalyzed dimerization of norbornenes and cyclohexenes and paves a way for rationally designing superior photocatalysts for olefins dimerization.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"228 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295826","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}