The Journal of Physical Chemistry B最新文献

{"title":"Microscopic Insights into Hydrate Cage Decomposition and CO2 Release of CO2+ TBAB Double Hydrate in Cold Energy Discharge","authors":"Kairan Yang,&nbsp;Zixu Han and Peng Zhang*,&nbsp;","doi":"10.1021/acs.jpcb.5c03829","DOIUrl":"10.1021/acs.jpcb.5c03829","url":null,"abstract":"<p >Semiclathrate tetrabutylammonium bromide (TBAB) hydrate can incorporate gas CO₂ to form CO₂ + TBAB double hydrate, which is an ideal gas and energy storage material due to its high energy density and favorable phase change conditions for refrigeration applications. In this study, the dissociation behaviors and underlying mechanism of this CO₂ + TBAB double hydrate at the microscale for energy release are studied through molecular dynamic simulations under thermal-driven conditions (283 K–301 K). The results indicate that two distinct hydrate cages (CO₂ 5¹² cages and TBAB semiclathrate cages) decompose in a stepwise manner during dissociation and exhibit distinct features. For the TBAB semiclathrate cage, the TBA⁺ ions initially adsorb on the hydrate surface as cages collapse and ultimately diffuse to the liquid phase. This phenomenon is attributed to the strong interaction between TBA⁺ ions and the hydrate cages strengthens the stability of the TBAB semiclathrate cage and empty the 5¹² cage after CO₂ release. For the CO₂ 5¹² cage, the cages deform and decompose upon the release of the encaged CO₂ molecules. The temperature dependence on the dissociation rate of the CO₂ + TBAB double hydrate could be described using the Arrhenius formula, with the activation energy determined to be 61.53 kJ mol^–1. A reduction in the 5¹² cage occupancy greatly diminishes hydrate stability and promotes the hydrate dissociation rate. Furthermore, the regulation of the CO₂ molecule on hydrate dissociation is realized through affecting the reformation of the 5¹² cage. The increase of the CO₂ molecule concentration in the liquid phase shows an inhibitory effect on the release of the CO₂ molecule from the hydrate cage because the possibility of reformation of the 5¹² cage at the hydrate surface increases, providing microscopic insights into the dissociation behavior of hydrate induced by depressurization at the macroscopic scale.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 36","pages":"9229–9239"},"PeriodicalIF":2.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Adaptive Force Matching Potential for Alanine Developed with Møller–Plesset Perturbation Theory and Smooth Fourier Transform Correction Map","authors":"Ying Yuan,&nbsp; and ,&nbsp;Feng Wang*,&nbsp;","doi":"10.1021/acs.jpcb.5c04529","DOIUrl":"10.1021/acs.jpcb.5c04529","url":null,"abstract":"<p >Developing accurate force fields for biomolecules remains a significant challenge due to the subtle energetic differences between various conformational states. We present a novel force field model for polyalanine, ALAMP2_25, developed using adaptive force matching (AFM) with Møller–Plesset perturbation theory at the second order (MP2) as the reference method. By fitting smaller model compounds and transferring parameters to larger peptides, we overcome the limitations of traditional AFM approaches and enable the use of more accurate electronic structure methods. The ALAMP2_25 model incorporates a new correction scheme, Smooth Fourier Transform-based φ, ψ correction map (SFT-CMAP), which efficiently describes φ, ψ coupling with reduced overfitting. Our model demonstrates good agreement with experimental <i>J</i>-coupling data for hydrated polyalanine and shows improved transferability to <i>N</i>-methylated cyclic alanine when compared to previously reported DFT based models. The developed framework provides a pathway for creating accurate force fields for a broader range of amino acids and biomolecules, enabling first-principles-based simulations of complex biological systems with applications in protein folding, ligand binding, and drug design.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 36","pages":"9165–9174"},"PeriodicalIF":2.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c04529","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep Eutectic Solvent Interaction with Graphene Oxide: A Combined Experimental and Molecular Dynamics Characterization","authors":"Simone Di Muzio,&nbsp;Fabio Ramondo and Giulia Fioravanti*,&nbsp;","doi":"10.1021/acs.jpcb.5c03461","DOIUrl":"10.1021/acs.jpcb.5c03461","url":null,"abstract":"<p >The interaction between graphene oxide (GO) and deep eutectic solvents (DESs) plays a crucial role in the design of functional materials for a wide range of applications. In this study, we present a combined experimental and computational investigation aimed at elucidating the structural and molecular organization of GO–DES systems using ethaline and reline as model deep eutectic solvents. These two DESs are among the most widely studied and well-characterized, making them ideal benchmarks for probing GO–liquid interactions. We synthesized GO and performed a detailed characterization via X-ray photoelectron spectroscopy (XPS), obtaining precise information about the type and distribution of oxygen-containing functional groups. Based on these experimental data, we developed a realistic molecular model of GO, providing a reliable and reproducible framework for atomistic simulations. Infrared and Raman spectroscopies reveal specific changes in vibrational modes upon GO–DES interaction, while differential scanning calorimetry (DSC) indicates modifications in thermal behavior. Classical molecular dynamics (MD) simulations show the formation of hydrogen-bond networks between the DES components and GO surface functionalities. Our results demonstrate a reciprocal structural influence between GO and DES at the molecular level and establish a validated computational protocol for the study of these hybrid systems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 36","pages":"9206–9218"},"PeriodicalIF":2.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c03461","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal Nucleation Kinetics and Mechanism: Influence of Interaction Potential","authors":"Porhouy Minh,&nbsp;Steven W. Hall,&nbsp;Ryan S. DeFever and Sapna Sarupria*,&nbsp;","doi":"10.1021/acs.jpcb.5c04269","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04269","url":null,"abstract":"<p >Modulating liquid-to-solid transitions and the resulting crystalline structure for tailored properties is much desired. Colloidal systems are exemplary to this end, but the fundamental knowledge gaps in relating the influence of intermolecular interactions to crystallization behavior continue to hinder progress. In this study, we address this knowledge gap by studying nucleation and growth in systems with modified Lennard-Jones potential. Specifically, we study the commonly used 12-6 potential and a softer 7-6 potential. The thermodynamic state point for the study is chosen such that both systems are investigated at the same level of supercooling and pressure. Under these conditions, we find that the nucleation rate for both systems is comparable. Interestingly, the nucleation pathways and resulting crystal structures are different. In the 12-6 system, nucleation and growth occur predominantly through the FCC structure. Softening the potential alters the critical nucleus composition and introduces two distinct nucleation pathways. One pathway predominantly leads to the nucleus with a body-centered cubic (BCC) structure, while the other favors the face-centered cubic (FCC) arrangement. Our study illustrates that polymorph selection can be achieved through modifications to intermolecular interactions without impacting nucleation kinetics. The results have significant implications in designing approaches for polymorph selection and modulating self-assembly mechanisms.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 35","pages":"8976–8990"},"PeriodicalIF":2.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144931465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Probing the Role of Telopeptides in Collagen Fibrillogenesis by Second Harmonic Scattering","authors":"Joshua de Lizaraga,&nbsp;Marta Martin,&nbsp;Estelle Salmon,&nbsp;Thierry Cloitre,&nbsp;Csilla Gergely* and Christian Jonin*,&nbsp;","doi":"10.1021/acs.jpcb.5c02016","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02016","url":null,"abstract":"<p >Collagen, the primary structural protein in the extracellular matrix, plays a critical role in tissue architecture and mechanical integrity. This study investigates the structural and nonlinear optical properties of atelocollagen (Acol) and telocollagen (Tcol) in response to pH variations by using second harmonic scattering (SHS), polarization-resolved SHS (P-SHS), and atomic force microscopy (AFM). AFM imaging revealed distinct morphological differences, with Acol forming wavy, non-cross-linked, and randomly arranged fibers, while Tcol exhibited a more interconnected, mesh-like fibrillar network. SHS and P-SHS measurements further confirmed these differences, indicating significant variations in hyperpolarizability and depolarization ratio (DR) between Acol and Tcol. The results suggest that telopeptides play a crucial role in collagen fibrillogenesis, influencing the molecular symmetry and optical responses. The observed differences in nonlinear optical properties highlight the potential of SHS as a powerful tool for characterizing collagen self-assembly mechanisms. These findings contribute to a broader understanding of collagen organization in biological and biomaterial contexts, with implications for tissue engineering, fibrosis research, and regenerative medicine. Future work should explore how external factors, such as ionic strength and cross-linking agents, further modulate collagen fibril formation and its mechanical properties.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 35","pages":"9020–9029"},"PeriodicalIF":2.9,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144931430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chain Formation and Addition Drive the Debye Relaxation of Methanol","authors":"Rebecca A. Bone*,&nbsp;Moses K. J. Chung,&nbsp;Jay W. Ponder and Kathleen Schwarz*,&nbsp;","doi":"10.1021/acs.jpcb.5c04122","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04122","url":null,"abstract":"<p >The Debye relaxation in alcohols has generally been attributed to “collective motion” driven by hydrogen bonding, but the molecular mechanism of relaxation has yet to be conclusively identified. Taking methanol as a model alcohol, we apply an oscillating electric field in molecular dynamics simulations to directly evaluate the molecular motions and identify the mechanism. Methanol forms short-lived chains of hydrogen-bonded molecules through the hydroxyl group. We find that the hydroxyl group rotates in response to the field with a frequency dependence that tracks the Debye peak, implicating these chains in the Debye relaxation. Focusing on the hydroxyl OH rotation, we consider the events (e.g., diffusion of chains, birth, growth) over the lifetime of chains that could contribute to this frequency dependence. We find that molecular participation in chains is responsible for the OH alignment relative to the field: molecules align incrementally, ″clicking in″ during chain formation and during molecular addition to existing chains.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 35","pages":"8946–8951"},"PeriodicalIF":2.9,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c04122","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144931468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidation of the Molecular Interaction Network Underlying Full-Length FUS Conformational Transitions and Its Phase Separation Using Atomistic Simulations","authors":"Shuo-Lin Weng*,&nbsp;Priyesh Mohanty and Jeetain Mittal*,&nbsp;","doi":"10.1021/acs.jpcb.5c02911","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02911","url":null,"abstract":"<p >Fused in Sarcoma (FUS) is a multidomain nucleic acid binding protein which orchestrates cellular functions such as gene expression, transcription, and DNA repair through liquid–liquid phase separation (LLPS). While crucial to understanding cellular processes, an atomic-level view of the molecular-level interactions associated with full-length (FL) FUS LLPS remains challenging due to its low solubility <i>in vitro</i>. Here, using all-atom (AA) molecular dynamics (MD) simulations, we examined the conformational dynamics and interactions of FL FUS in both dilute and condensed phases. Comparing two modern force fields (FFs)─Amber ff03ws and ff99SBws-STQ, we found that monomer simulation ensembles generated by both FFs exhibited qualitatively similar intramolecular interaction profiles dominated by intrinsically disordered regions (IDRs). While the two folded domains minimally participated in intramolecular interactions, their stabilities significantly influenced the chain dimension and led to discrepancies compared to experimental data for both FFs. We observed that the Amber ff99SBws-STQ coupled with parameters adopted from the Zinc Amber force field (ZAFF) maintained stable folded domains and improved estimates of the chain dimensions. Finally, a microsecond-time scale simulation of FL FUS condensate revealed an extensive network of electrostatic interactions which are strongly correlated with those that modulate the dilute phase conformations. Overall, insights from our AAMD simulations illuminate the interplay between folded domain stability and IDR interactions in modulating protein conformation and phase separation.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 35","pages":"8843–8857"},"PeriodicalIF":2.9,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c02911","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144931551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Atomistic Insights into Fluorinated/Chlorinated Ether-Based LHCEs on Lithium Metal: Decomposition Mechanisms via Multiscale Simulations","authors":"Fuming Du*,&nbsp;Haibin Wang,&nbsp;Jiwei Chen,&nbsp;Hao Huang,&nbsp;Tuo Ye,&nbsp;Shiyun Duan,&nbsp;Ruizhi Zhang,&nbsp;Jianjun Liu and Hailong Hu,&nbsp;","doi":"10.1021/acs.jpcb.5c02963","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02963","url":null,"abstract":"<p >The interfacial stability of localized high-concentration electrolytes (LHCEs) with fluorinated (F2DEE) or chlorinated (Cl2DEE) ether solvents critically controls lithium metal battery performance. However, atomistic mechanisms driving their solid electrolyte interphase (SEI) formation remain unclear. We systematically compare the decomposition pathways of 1LiFSI-1.6F2DEE-3TTE and 1LiFSI-1.6Cl2DEE-3TTE on Li metal using multiscale simulations: classical molecular dynamics (CMD), ab initio molecular dynamics (AIMD), and density functional theory (DFT). CMD simulations show unique electric double layer (EDL) reorganization under charging; both LHCEs retain FSI^– anions within 6 Å of the Li anode, contrasting with conventional low-concentration electrolytes. This spatial selectivity enables AIMD simulations with two configurations (FSI^–-near and FSI^–-far interfaces). Results reveal that FSI^– reduction (with solvent participation) dominates over TTE dissociation, with calculated SEI fragment ratios (F/Cl/S) matching the experimental XPS trend. Electronic structure analysis via projected density of states, bond evolution, and Bader charge transfer clarifies decomposition sequences. DFT identifies key dehalogenation differences: F2DEE requires 0.11 eV energy barrier for defluorination, while Cl2DEE undergoes spontaneous barrierless dechlorination. This explains higher organic carbon content in Cl2DEE-derived SEI observed experimentally. Our work establishes a multiscale framework correlating solvation evolution, EDL dynamics, and SEI mechanisms, providing atomistic design guidelines for stable high-voltage lithium battery electrolytes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 35","pages":"8919–8932"},"PeriodicalIF":2.9,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144931546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Analytical Theory for the Ion-Specific Surface Tension of Nonaqueous Electrolyte Solutions","authors":"Tiejun Xiao*,&nbsp;Yun Zhou and Yi Liu,&nbsp;","doi":"10.1021/acs.jpcb.5c04212","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04212","url":null,"abstract":"<p >Analytical prediction of the ion-specific surface tension of nonaqueous electrolyte solutions remains an open challenge. In a previous work [<i>J. Chem. Theory Comput.</i> <b>2024,</b> <i>20,</i> 10158–10166], we have developed an analytical theory for the surface tension of aqueous electrolyte solutions by mapping an aqueous electrolyte solution to a restricted primitive model (RPM). In this work, we extend this prescription to nonaqueous solutions by also mapping a nonaqueous solution to a RPM. Our theory is applied to several 1:1 nonaqueous electrolyte solutions and compared with experimental data. Without introducing any adjustable parameters, our theory leads to a good prediction of surface tension increments of several nonaqueous solutions with a salt concentration up to 1 mol/L.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 35","pages":"8970–8975"},"PeriodicalIF":2.9,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144931498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cation Code: Designing Bis(trifluoromethylsulfonyl)imide-Based Ionic Liquids for Electrochemical Applications","authors":"Pranav J. Thacker,&nbsp;Jiaying Jin,&nbsp;Jon-Marc McGregor,&nbsp;Louise M. Cañada,&nbsp;Joaquin Resasco and Joan F. Brennecke*,&nbsp;","doi":"10.1021/acs.jpcb.5c04559","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04559","url":null,"abstract":"<p >The choice of the core cation structure can have significant effects on the suitability of a bis(trifluoromethylsulfonyl)imide ([Tf₂N]⁻)-based room temperature ionic liquid (RTIL) for a particular electrochemical application. While bulkier aliphatic cations (such as ammonium, phosphonium, piperidinium and pyrrolidinium) exhibit wider electrochemical windows (ECWs &gt; 6 V) than sulfur containing cations and many aromatic cations, they are more viscous and, subsequently, have lower molar conductivities. Among RTILs with wide ECWs, pyrrolidiniums have the best molar conductivities (0.81 S cm² mol^–1 for butylmethylpyrrolidinium [Tf₂N] at 298.15 K). Triethylsulfonium [Tf₂N] has the highest molar conductivity of the RTILs tested, followed by three ILs with aromatic cations (dialkylimidazolium, dialkyl-3-triazolium, and pyridinium). Triethylsulfonium [Tf₂N] and butylpyridinium [Tf₂N] also have high degrees of dissociation (0.67 and 0.71, respectively). Superbase derived RTILs are largely unsuitable, due to high melting points, small ECWs and low molar conductivity. While pyrrolidinium and imidazolium ILs are popular choices for electrochemical applications, pyridinium and, especially, triethylsulfonium, ILs have been largely overlooked as RTIL candidates for electrochemical applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 35","pages":"9005–9019"},"PeriodicalIF":2.9,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144931425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}