Physical Chemistry Chemical Physics最新文献

{"title":"Correlating molecular structure and self-assembly mechanism via Temporal Analysis of Multidimensional Chemical Interactions Space: Application to assemblies of isomeric peptides","authors":"Sangeeta Das, Rumela Adhikary, Snehamay Bagchi, Argha Chakraborty, Avisek Das","doi":"10.1039/d4cp04597a","DOIUrl":"https://doi.org/10.1039/d4cp04597a","url":null,"abstract":"Computational modelling of self-assembly mechanisms is a promising way to establish chemically meaningful relationships between molecular structures of the building blocks and the final outcomes of the spontaneous assemblies. However, such connections are not immediately apparent, due to the presence of complex interplay involving a multitude of intermolecular interactions with complicated temporal variations. In this paper, we propose a method, called Temporal Analysis of Multidimensional Chemical Interaction Space (TAMCIS), which looks at important combinations of interactions, rather than analysing them one at a time. Each molecule was assigned a vector order parameter, with components representing appropriately chosen chemical interactions. The aggregate data was processed with density-based clustering, resulting in \"interaction clusters\". Time dependent partitioning of the molecules among these clusters revealed the mechanism in terms of interactions, thereby making a direct connection to the molecular structures of the building blocks. We applied the method to a comparative study of assembly mechanisms of two isomeric hydrophobic tri-peptides in water, namely tri-L-leucine (LLL) and tri-L-isoleucine (III). Initially, both systems started to aggregate via non-bonded interactions through sidechains. But at later stages, they diverged in the interaction space when hydrogen bonding and electrostatic contacts became important. Overall, a stark difference was observed, LLL assembly grew by a combination of interactions. In contrast, the III primarily utilized one type of hydrogen bonding, leading to $beta$-sheet-like arrangements found in proteins. The TAMCIS provided a clear path for deciphering the origins of emergent complexities in spontaneous self-assemblies from dynamical simulation data.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"108 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143866405","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":"The halogen(I) complex of astatine: a theoretical perspective on structural and bonding properties","authors":"Hao Luo, Ze-Kai Li, Zhuo-Wei Zhang, Lin-Jia Chen, Jing Su","doi":"10.1039/d4cp04903a","DOIUrl":"https://doi.org/10.1039/d4cp04903a","url":null,"abstract":"Halonium ions (X<small>⁺</small>) can interact with two Lewis bases to form linear 3c4e halogen-bonded halogen(<small>I</small>) complexes ([D⋯X⋯D]<small>⁺</small>), which have been found to be useful in organic synthesis and supramolecular chemistry. However, current research is limited to lighter halogens (F, Cl, Br, and I) and does not include the At element owing to the lack of stable isotopes for experimental studies. Herein, we explore the structural and bonding properties of an At-mediated 3c4e halogen(<small>I</small>) complex ([D⋯At⋯D]<small>⁺</small>) and the effects of various Lewis bases, substituents, and halogens using relativistic density functional theory (DFT) and the coupled-cluster approach with single, double and perturbative triple excitation (CCSD(T)) calculations. Theoretical calculation results show that At, similar to other halogens, can form a linear [D⋯At⋯D]<small>⁺</small> structure with equal bond lengths from the halonium ion to two donor atoms. The physical nature of the interaction and electronic structure of the At-mediated 3c4e halogen(<small>I</small>) complex are the same as those of the halogen(<small>I</small>) complexes of light halogens. Interestingly, the positive correlation between the polarizability of the halogen and the interaction between D and [D⋯X]<small>⁺</small> fragments (X = F to At) observed at the scalar relativistic level does not hold when considering spin–orbit coupling effects on the At atom. This work deepens the understanding of the halogen bonds of At, and the stable [D⋯At⋯D]<small>⁺</small> structure offers new insights into At coordination chemistry and the relevant experimental study of radiolabeling of At.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"65 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143862154","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":"The nucleation and growth of methane hydrates in the presence of phenylalanine and tryptophan: A comparative molecular dynamics simulations study","authors":"Aashu Aashu, Shivam Rawat, C. N. Ramachandran","doi":"10.1039/d5cp00972c","DOIUrl":"https://doi.org/10.1039/d5cp00972c","url":null,"abstract":"A series of nanoscale molecular dynamics simulations are carried out at 270 K and 500 bar to explore the nucleation of hydrates using a mixture of water, methane and amino acids. Different concentrations of phenylalanine and tryptophan are used to study the nucleation and growth of methane hydrates. It is found that both amino acids promote the nucleation and growth of methane hydrates at lower concentrations. The formation of different types of rings, partially and fully formed cages formed between water molecules are analyzed. Hydrogen bond analysis revealed a decrease in the number of hydrogen bonds formed between water molecules in the presence of amino acids. Each molecule of phenylalanine and tryptophan forms five to six hydrogen bonds with water molecules. The formation of hydrate cages is analyzed using the F4 structural order parameter that indicated the co-existence of the hydrate cages as well as the liquid phase. The analysis of the radial distribution function (RDF) obtained for different concentrations of phenylalanine and tryptophan confirmed the encapsulation of methane molecules inside various water cages. The studies revealed that, at high concentrations of phenylalanine and tryptophan, the amino acids act as an inhibitor delaying both the nucleation and the growth of the hydrates. The formation of the cages and the encapsulation of methane molecules are further supported using the mean square displacement of methane molecules.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"67 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143862152","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":"Unraveling the Influence of Excluded Volume on Orientational Relaxation Dynamics in Dendrimers","authors":"Shelly Bhardwaj, Amit Kumar","doi":"10.1039/d5cp00804b","DOIUrl":"https://doi.org/10.1039/d5cp00804b","url":null,"abstract":"This study investigates the orientational relaxation dynamics of flexible dendrimers while incorporating excluded volume interactions among non-bonded monomers using the optimized Rouse-Zimm formalism. Excluded volume effects are modeled as an effective co-volume between adjacent non-bonded monomers through a delta function pseudopotential, while hydrodynamic interactions are accounted for using the preaveraged Oseen tensor. This work examines ( P_2^{(i)}(t) ) as a function of dendrimer generation and the strength of excluded volume interactions between nearest non-bonded monomers. The theoretical framework builds upon the work of [Kumar and Biswas (Phys. Chem. Chem. Phys., 2013, 15, 20294)], which analyzed orientational relaxation in semiflexible dendrimers but did not consider excluded volume interactions. The temporal decay of ( P_2^{(i)}(t) ) at varying excluded volume parameters, ( v_theta ) and ( v_psi ), shows trends consistent with experimental observations under different temperatures.~cite{yimer2012static} The spectral density, ( J(omega) ), obtained via the Fourier cosine transform of ( P_2^{(i)}(t) ), is significantly influenced by excluded volume interactions. In the high-frequency regime, ( J(omega) ) decreases with increasing frequency, exhibiting a crossover pattern as excluded volume interactions vary in the intermediate frequency range. The area under the spectral density curve increases as the excluded volume parameters ( v_theta ) and ( v_psi ) decrease. The reduced spin-lattice relaxation rate, ( [1/T_{1H}] ), follows a power-law scaling in the intermediate frequency regime, with exponents dependent on dendrimer generation and the strength of excluded volume interactions. Notably, for generation ( G = 5 ), the calculated scaling exponent at ( v_theta = 0.24 ) and ( v_psi = 2.12 ) aligns precisely with experimental data,~cite{yimer2012static} validating the theoretical model. The spin-spin relaxation rate, ( left[ frac{1}{T_{2H}} right] ), exhibits a distinct trend influenced by excluded volume interactions. In the intermediate frequency regime, its scaling behavior is closely linked to structural constraints and segmental motion, deviating from ( left[ frac{1}{T_{1H}} right] ) at lower correlation times due to enhanced low-frequency contributions. However, for generation ( G=5 ), ( left[ frac{1}{T_{2H}} right] ) follows a similar trend to ( left[ frac{1}{T_{1H}} right] ) and aligns well with experimental observations.~cite{yimer2012static}","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"9 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143862559","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":"Transition Metal Embedded Boron Doped Graphene for Reduction of CO2 to HCOOH","authors":"Sudatta Giri, Purushothaman Manivannan, Debolina Misra","doi":"10.1039/d5cp01427a","DOIUrl":"https://doi.org/10.1039/d5cp01427a","url":null,"abstract":"Electro-chemical conversion of carbon dioxide stands out as an excellent strategy to alleviate the greenhouse effect. Lately, single atom catalysts have gained notable attention as emerging candidates for CO<small>₂</small> reduction reaction, owing to their remarkable cost-efficiency and unprecedented atomic utilization. Applying density functional theory (DFT), our work examines the first couple of proton coupled electron transfer steps of CO<small>₂</small>RR, on 3d transition metal-doped B-Gr and compares the activity observed with previously studied supports. Since CO<small>₂</small> activation is the 1st step of CO<small>₂</small>RR, we thoroughly investigated the capability of the TM SAs in effectively activating CO<small>₂</small> in both dry phase and in presence of water. According to our calculation, except Ti, Cu and Zn, all other TM@B-Gr systems are able to activate the CO<small>₂</small> molecule. CO<small>₂</small> activation on selected SACs is further attributed to the transfer of charges from the TM SA to the CO<small>₂</small> molecule, as revealed by our Bader charge calculations. In addition, the Gibbs free energy changes for all the reaction intermediates have been calculated to determine the most preferred pathway of the reaction. Our results indicate the preference for OCHO over COOH in the first protonation step, indicating the production of HCOOH as the preferred end product. The same trend has also been observed in presence of H<small>₂</small>O. Our DFT based analysis presented in this work, unravels the crucial role a support plays in determining the activity of a single atom catalyst and paves a way forward to the efficient design of 2D catalyst for CO<small>₂</small> reduction reaction.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"63 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143862157","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":"A near-infrared luminescent organic radical with switchable emission and SOMO-HOMO inversion via protonation/deprotonation process","authors":"Obolda Ablikim, Parida Hazretomar, Mehrigul Abdulahat, Fudong Ma, Ayixiemuguli Tuersun, Zhaoze Ding, Zhuoyang Hu","doi":"10.1039/d5cp00399g","DOIUrl":"https://doi.org/10.1039/d5cp00399g","url":null,"abstract":"We synthesized a novel NIR-emissive (785 nm) D-A•-type triphenylmethyl radical TTM-EMICz using a rigidly structured and large-conjugated donor 6-butylindolo[3,2-b]carbazole (ICz) unit. Studies showed that the non-Aufbau electronic structure and PL spectra of the radical can be regulated by the protonation process, in which the PL spectra of the radical can be adjusted to the visible region. Furthermore, the protonated radical TTM-EMICz shows emission centered at 610 nm and 633 nm with PLQY of 4.5 % and 14.9 % in cyclohexane and toluene, with excited state CT properties. The photostability investigation indicated that radical TTM-EMICz has 350 times higher photostability in cyclohexane compared to the well-known carbazole-capped radical TTM-1Cz. This is the first reported near-infrared organic radical with two-state-emissive characteristics (non-Aufbau and Aufbau electronic states), which can be adjusted by protonation/deprotonation process.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"17 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143862159","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":"A molecular titration strategy: utilizing built-in electric field to detect lithium diffusion coefficient in LiFePO4","authors":"Juezhi Yu, Zexin Lin, Zhihao Deng, Xianrun Cao, Lu Guo, FeiFei Zhang, Sheng Liu, Gangfeng Ouyang","doi":"10.1039/d5cp00481k","DOIUrl":"https://doi.org/10.1039/d5cp00481k","url":null,"abstract":"Electrometric titration techniques have long been used to detect the Li+ diffusion coefficient of electrode materials. However, the influence of electrode additives, cell assembly methods, especially, inaccurate assessments of the reaction area often led to unreliable results. Here, we propose a molecular titration technique (MTT) to detect lithium diffusion coefficient (DLi) in LiFePO4. This MTT alleviates the tedious electrode preparation procedure, circumvents the influence of additives, amends the real reaction area errors, and shortens the testing time, making the testing more precise and efficient than the traditional titration techniques. In detail, [Fe(CN)6]3- solution is added into LiFePO4 solid dropwise, while potential change rate (rp) of the solution is recorded. Thereafter, a built-in electric field (BIEF) electron transferring model is established and the relationship between DLi and rp is formulated with Huggins-Weppner equation. Eventually, the de-lithiation diffusion coefficient of Li1-xFePO4 (1≤x≤0) is tested to be 1~8×10-15 cm2/s based on the recorded data and established formulations.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"7 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143862156","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":"Exploring the Binding Free Energy Landscape of Intrinsically Disordered Protein-Protein Interactions: Insights into the AF9-BCOR Complex implicated in Leukemia","authors":"Shilpa Sharma, Arjun Saha","doi":"10.1039/d5cp01009h","DOIUrl":"https://doi.org/10.1039/d5cp01009h","url":null,"abstract":"Chromosomal rearrangements involving the Mixed-Lineage Leukemia (MLL) gene are implicated in acute leukemias with poor prognosis. In MLL-rearranged leukemias, the aberrant recruitment of transcriptional and epigenetic modifier complexes is driven primarily by the MLL-AF9 fusion protein. AF9 typically inhibits transcription by recruiting BCL-6 corepressor (BCOR); however, the direct fusion of AF9 with MLL results in a loss of context dependence in AF9 recruitment and causes oncogenic transformation of hematopoietic cells. Notably, the E531R mutation in AF9, which disrupts the binding between the MLL-AF9 fusion protein and BCOR, abrogates the leukemogenic potential in a mouse model, underscoring its significance as a therapeutic target in leukemia. AF9 and BCOR interact through their intrinsically disordered regions (IDRs), which undergo conformational folding upon complex formation. Understanding this conformational transition is critical for guiding drug discovery efforts but interactions mediated by IDRs remain challenging to study due to their dynamic nature. We propose a hybrid method by combining conventional and Replica Exchange Molecular Dynamics (REMD) simulations, to investigate the binding free energy landscape (BFEL) of wild type (WT) and mutant (MT) AF9-BCOR complexes. REMD simulations of WT AF9 alone revealed a significant loss of β-sheets and mutation accelerated the rate of β-sheet disappearance due to the formation of non-native contacts. FEL of WT AF9-BCOR complex exhibited several local minima, highlighting C-terminal BCOR interactions as potential target for therapeutic intervention. Mutation disrupted the native interactions in AF9-BCOR complex and showed poor binding affinity. Our study uncovers the interaction dynamics of AF9-BCOR and introduces an innovative approach for mapping protein-protein interaction energy landscapes, offering valuable insights to advance targeted drug design.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"219 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143862153","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":"The role of iron in the electronic configuration of mixed nickel iron oxides for the oxygen evolution reaction","authors":"Christopher Gort, Gustavo T. Feliciano, Alexander A. Auer, Bernhard Kaiser, W. Jaegermann, Jan Philipp Hofmann","doi":"10.1039/d5cp00386e","DOIUrl":"https://doi.org/10.1039/d5cp00386e","url":null,"abstract":"Nickel-based oxides are among the best performing catalysts for the alkaline O2 evolution reaction (OER). It has long been recognized that iron enhances the catalytic activity of nickel-based catalysts, though only recently intensive research has been done on the interplay between the two transition metals, leading to the excellent performance, surpassing that of either pure metal. It is still not clear how the electronic configuration in mixed metal compounds changes to enhance their catalytic activity for the OER. We carried out a systematic study of the electronic configuration of thin film mixed metal oxides Ni(1-x)FexOyHz with varying contents x of iron. In this investigation we employed X-ray absorption and resonant valence photoelectron spectroscopy (XAS and resPES) to gain knowledge on the changes induced in the electronic structure by introduction of iron, both before and after electrochemical activation. Based on density functional calculations we found iron species to induce a highly oxidizing environment that facilitates generation of oxo species on iron and neighboring nickel sites. The reduced electron density around Ni-O bonds creates in-gap states near the Fermi level. The magnitude of these in-gap states scales linearly with the OER performance and thus can be used as an activity descriptor. Contrary to literature we see the in-gap states even before electrochemical activation and conclude that they are a consequence of Ni-O-Fe motifs present already before anodization. Beyond 50% metal content the number of Ni-O-Fe motifs is decreasing again, resulting in an interval of 10-30% iron metal content to be optimal for the OER.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"24 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143862155","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":"Green recovery of solid electrolytes from all-solid-state lithium-ion batteries by low-melting mixture solvents with tunable physical properties","authors":"Yu Chen, Xueqing Zhang, Chenyang Wang, Zhuojia Shi, Xihou Wang, Jiayi Dong, Yanlong Wang, Minghui Feng","doi":"10.1039/d4cp04684f","DOIUrl":"https://doi.org/10.1039/d4cp04684f","url":null,"abstract":"All-solid-state lithium-ion batteries (ASSLIBs) are anticipated to be the next generation of high-performance lithium batteries due to their enhanced safety and high energy density. However, the widespread application of ASSLIBs will lead to a significant increase in spent batteries, resulting in environmental pollution and resource depletion. Therefore, the development of environmentally friendly recycling methods for ASSLIBs is both urgent and critical. Low-melting mixture solvents (LoMMSs) are proposed by Professor Yu's research group at Tsinghua University in 2023 to facilitate the advancement of green solvents and green chemistry. Here, we utilized LoMMSs to leach metals from solid-state electrolytes (SSEs) of ASSILBs and apply the 55 anti-solvents method to recover metal ions from leachate. Results show that the leaching efficiency of Li is up to 92.5 % at the mild temperature of 80 oC within 24 h. The high Li leaching efficiency is ascribed to the coordination interaction. Furthermore, the Li leaching efficiency in large-scale applications shows minimal deviation from the optimal efficiency. This research provides valuable insights into the development of efficient, green, and mild recycling methods for SSEs in ASSLIBs.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"11 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857479","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}