The Journal of Physical Chemistry B最新文献_第4页

MD Multi-Sector Selector: Recursive Extraction and Refinement of Molecular Dynamics Based Sectors Yields Two Sectors in p53 Tumor Suppressor Protein.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-02 DOI: 10.1021/acs.jpcb.4c08495

Christopher A Chiu, Sean Stetson, Kelly M Thayer

{"title":"MD Multi-Sector Selector: Recursive Extraction and Refinement of Molecular Dynamics Based Sectors Yields Two Sectors in p53 Tumor Suppressor Protein.","authors":"Christopher A Chiu, Sean Stetson, Kelly M Thayer","doi":"10.1021/acs.jpcb.4c08495","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08495","url":null,"abstract":"Allosteric signaling in proteins allows perturbations at one locale to modulate activity at an orthosteric distant site. This may explain how distal mutations disrupt protein activity and offer pathways for the development of allosteric therapeutics, a novel class of restorative compounds to reactivate native function. Despite the ubiquitous presence of allosteric control in nature and the promises that it holds for treating currently untreatable diseases, quantitative theory of the mechanism of allostery is lacking. Working to fill this critical gap, we have developed a novel method to identify groups of covarying residues which the sector hypothesis suggests are capable of transmitting allosteric signals in proteins. A major problem with sectors computed from covariance measures is the selection relies upon a full covariance matrix rather than on the covariance among the residues posited to be in the sector. We demonstrate a novel method which constructs sectors on the basis of cohesion within the residues in the sector to eliminate the incongruity between the sector idea and the way it is calculated. Furthermore, the refinement can be iteratively applied, enabling the extraction of more than one sector in a well-defined, systematic manner. In this study, we report on the development of MD multi-sector selector and its application to allosteric signaling in the tumor suppressor protein p53. We consider the implications of our findings on our long-term goal of allosterically reactivating mutant p53 as a means of curing cancer, and critically assess the broader applicability of MD multi-sector selector across diverse fields.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770753","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}

引用次数: 0

Neural Network-Based Molecular Dynamics Simulation of Water Assisted by Active Learning.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-02 DOI: 10.1021/acs.jpcb.4c06633

Dan Zhao, Yao Huang, Hujun Shen

{"title":"Neural Network-Based Molecular Dynamics Simulation of Water Assisted by Active Learning.","authors":"Dan Zhao, Yao Huang, Hujun Shen","doi":"10.1021/acs.jpcb.4c06633","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06633","url":null,"abstract":"In our study, we combined classical molecular dynamics (MD) simulations with the simulated annealing (SA) method to explore the conformational landscape of water molecules. By using the K-means clustering method, we processed the MD simulation data to extract representative samples of water molecular structures used to train a deep potential (DP) model. Our DeePMD method showed accuracy in predicting water structural properties compared to DFT-MD results. Meanwhile, this approach achieves a balanced prediction of water density and self-diffusion coefficients compared with earlier DeePMD simulations. These results highlight the essential role of representative sampling techniques in training the DP model. Furthermore, we demonstrated the effectiveness of combining the DeePMD simulation with the centroid molecular dynamics (CMD) approach, which incorporates nuclear quantum effects (NQEs). This approach successfully reproduced the shoulder feature at 3250 cm-1 in the Raman spectra for the O-H stretch. Incorporating the path integral method into the DeePMD simulations underscores the importance of considering NQEs in understanding water molecules' structural and dynamic behaviors.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770754","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}

引用次数: 0

Structures and Ion Transport Properties of Hydrate-Melt Electrolytes: A Machine-Learning Potential Molecular Dynamics Study.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-02 DOI: 10.1021/acs.jpcb.4c07559

Yukihiro Okuno

{"title":"Structures and Ion Transport Properties of Hydrate-Melt Electrolytes: A Machine-Learning Potential Molecular Dynamics Study.","authors":"Yukihiro Okuno","doi":"10.1021/acs.jpcb.4c07559","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07559","url":null,"abstract":"High-concentration aqueous electrolytes (hydrate-melts) have attracted significant attention for lithium-ion batteries due to their nonflammability and low toxicity. In these electrolytes, the static and dynamic structures of the solvent play a crucial role in determining various properties, such as the ionic conductivity, of the system. To clarify the solvent structure and ion diffusion mechanism, we conducted molecular dynamics simulations using a machine learning potential for Li and Na hydrate-melts. By analyzing the dynamical interaction between ions and their coordinating molecules, we found the ligand exchange of H2O molecules coordinated to cations occurs frequently. As a result, it is considered that the kinetic energy of H2O is transferred to cations and drives the diffusion of cations in the hydrate-melts. This ion transport mechanism is different from the conventionally understood vehicle-type or hopping-type ion transport mechanism. The comparison of Na hydrate-melts and Li hydrate-melts shows the higher diffusion of Na relative to Li. It was suggested that there exists an optimal value for the strength of interaction between cations and H2O molecules, which influences ion diffusion, and that the interaction for Na is close to this optimal value compared to that of the Li.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762646","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}

引用次数: 0

Understanding the Aggregation of Lanthanum(III) Nitrate Clusters in Pure Methanol: A Molecular Dynamics Investigation.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-02 DOI: 10.1021/acs.jpcb.4c08316

Erwann Guillam, Magali Duvail, Lara Žiberna, Jean-François Dufrêche

{"title":"Understanding the Aggregation of Lanthanum(III) Nitrate Clusters in Pure Methanol: A Molecular Dynamics Investigation.","authors":"Erwann Guillam, Magali Duvail, Lara Žiberna, Jean-François Dufrêche","doi":"10.1021/acs.jpcb.4c08316","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08316","url":null,"abstract":"A detailed analysis of the structure and speciation of La3+ clusters in the 0.1 mol L-1 La(NO3)3 salt methanol (MeOH) solution has been performed by means of molecular dynamics (MD) simulations. The time distribution and NO3-/MeOH ligand composition of these clusters have been computed using graph theory techniques. These analyses revealed the formation of branched-like polynuclear clusters in the solution, the predominant clusters being the 3, 7, and 8 La3+ clusters. In these clusters, the La3+ cations are bound by \"monodentate\" nitrate bridges. Moreover, the mechanism of aggregation of the La3+ clusters has been examined with the development of a 3-step model. Finally, the origin of the aggregation process has been identified by estimating the binding constant for the ion pair La3+-NO3- using the Bjerrum theory of dilute solutions, with pK° = 5.32 at 25 °C. The low value of the dielectric constant of methanol promotes the binding of the ion pair La3+-NO3- and the nitrato-bridging polymerization, resulting in the formation of clusters.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770755","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}

引用次数: 0

Stimuli-Responsive Peptide Liquid Crystals for Tandem Measurements of Residual Chemical Shift Anisotropy and Residual Dipole Coupling in One Sample.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-04-01 DOI: 10.1021/acs.jpcb.4c08005

Jin-Hao He, Yan-Ling Yang, Ai-Qing Zhang, Si-Yong Qin

{"title":"Stimuli-Responsive Peptide Liquid Crystals for Tandem Measurements of Residual Chemical Shift Anisotropy and Residual Dipole Coupling in One Sample.","authors":"Jin-Hao He, Yan-Ling Yang, Ai-Qing Zhang, Si-Yong Qin","doi":"10.1021/acs.jpcb.4c08005","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08005","url":null,"abstract":"The combined use of residual chemical shift anisotropy (RCSA) and residual dipolar coupling/residual dipole coupling (RDC) could provide highly complementary information about the structure and relative configuration of unknown organic molecules for their elucidation. However, tandem RCSA and RDC measurements in one sample remain a formidable challenge due to their varied testing requirements. Herein, a stimuli-responsive supramolecular liquid crystal self-assembled from an amphiphilic oligopeptide of C19H39-CONH-VVVVKKK-CONH2 was constructed, which underwent a phasic transformation from anisotropy to isotropy when subjected to a thermal treatment. Both the anisotropic and isotropic phases exhibited good stability, facilitating tandem measurements of 13C-{1H}-RCSA and (13C-1H)-RDC in one sample with no need for special instruments or correction procedures. We expect that the joint use of RCSAs and RDCs will significantly improve data accuracy and utility for structural and configurational determination of small organic molecules and even biomacromolecules.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762622","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}

引用次数: 0

Cluster Structure and Ordering in the Nucleation and Growth of Binary Molecular Mixtures.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-31 DOI: 10.1021/acs.jpcb.5c00430

Joseph Gregory Z Cabinta, Earl Adrian D R Hans, Roosevelt T Tabag, Johnrob Y Bantang, Ricky B Nellas

{"title":"Cluster Structure and Ordering in the Nucleation and Growth of Binary Molecular Mixtures.","authors":"Joseph Gregory Z Cabinta, Earl Adrian D R Hans, Roosevelt T Tabag, Johnrob Y Bantang, Ricky B Nellas","doi":"10.1021/acs.jpcb.5c00430","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00430","url":null,"abstract":"A complete understanding of aerosol formation remains elusive due to the microscopic scale and transient occurrence of nucleation. This process is further complicated by the multicomponent nature of atmospheric nucleating systems in which the properties of conucleating compounds influence the affinity of molecules to cluster. Molecular dynamics simulations were performed to investigate homogeneous vapor-liquid nucleation and growth of six binary mixtures composed of water, n-nonane, 1-butanol, and methanol. Structural analyses were performed to understand the dynamic configurations generated from binary nuclei. Geometric structure analysis revealed that clusters were found to be more spherical with increasing cluster size, while composition analysis revealed that more miscible species had less mole fraction variability from an equimolar composition. Radial density profiling and cluster snapshots revealed structural features that were dependent on the miscibility of the nucleating pairs. Homogeneous mixing was observed in n-nonane/1-butanol and water-methanol due to their miscibility. Meanwhile, systems with partial miscibility (water/1-butanol, water/methanol, 1-butanol/methanol, n-nonane/methanol), exhibited preferential ordering into core-shell structures. In water/n-nonane, simultaneous unary nucleation was observed, leading to lens-on-sphere configuration. Microstructure analysis also revealed internal fragmentation within core-shell motifs of water/1-butanol and 1-butanol/methanol. These findings have serious implications in nucleation theories, which lead to valuable insights for the nucleation of naturally occurring multicomponent systems in the atmosphere.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750079","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}

引用次数: 0

Thermodynamics of Isomers and Solubility Prediction in Multicomponent Sugar Solutions.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-31 DOI: 10.1021/acs.jpcb.4c08616

Silvio Trespi, Shina Roshanfekr, Marco Mazzotti

引用次数: 0

Aggregation-Induced Excitation-Energy Quenching in Fucoxanthin Chlorophyll a/c-Binding Proteins from the Diatom Phaeodactylum tricornutum.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-29 DOI: 10.1021/acs.jpcb.4c06894

Yoshifumi Ueno, Ou-Yang Li, Jian-Ren Shen, Tatsuya Tomo, Seiji Akimoto, Ryo Nagao

{"title":"Aggregation-Induced Excitation-Energy Quenching in Fucoxanthin Chlorophyll a/c-Binding Proteins from the Diatom Phaeodactylum tricornutum.","authors":"Yoshifumi Ueno, Ou-Yang Li, Jian-Ren Shen, Tatsuya Tomo, Seiji Akimoto, Ryo Nagao","doi":"10.1021/acs.jpcb.4c06894","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06894","url":null,"abstract":"Light-harvesting complexes (LHCs) are vital for photosynthesis, capturing light energy and transferring it to photosystems I and II. In diatoms, fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) function as unique LHCs. In this study, we examined the spectral properties of untreated and aggregated FCP complexes (Untreated-FCP and Aggregated-FCP, respectively) from the diatom Phaeodactylum tricornutum. Fluorescence quantum yields and excitation-energy transfer pathways were evaluated using absolute fluorescence spectroscopy and fluorescence decay-associated (FDA) spectra. Aggregation of FCPs significantly enhanced excitation-energy quenching, with a marked decrease in fluorescence quantum yield from 37.6% in Untreated-FCP to 4.8% in Aggregated-FCP. The FDA spectra of Aggregated-FCP showed prominent fluorescence decays with relatively high amplitudes with time constants of 310 ps and 1.6 ns, reflecting distinct alterations in excitation-energy transfer among Chls upon aggregation. These changes were accompanied by long-wavelength shifts and broadening of the fluorescence-emission spectra, characteristics typically observed in aggregated LHCs in land plants. Our results suggest that the structural rearrangement of pigment molecules, driven by changes in Chl-Chl and Chl-Car interactions, underlies the observed excitation-energy quenching upon aggregation. This study provides key insights into the quenching mechanisms of diatom FCPs, offering broader implications for understanding energy regulation in photosynthetic systems.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741761","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}

引用次数: 0

Ternary Potassium Single Cation Ionic Liquid Electrolyte for Potassium Secondary Batteries.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-28 DOI: 10.1021/acs.jpcb.4c08105

Hiroki Yamamoto, Keigo Kubota, Jinkwang Hwang, Kazuhiko Matsumoto, Rika Hagiwara

{"title":"Ternary Potassium Single Cation Ionic Liquid Electrolyte for Potassium Secondary Batteries.","authors":"Hiroki Yamamoto, Keigo Kubota, Jinkwang Hwang, Kazuhiko Matsumoto, Rika Hagiwara","doi":"10.1021/acs.jpcb.4c08105","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08105","url":null,"abstract":"Potassium single cation ionic liquids (K-SCILs), which solely contain K+ as the cationic species, realize exceptionally high K+ concentrations and exhibit unique physicochemical and electrochemical properties. However, K-SCILs tend to have high melting points due to the smaller size of K+ than those of bulky organic cations, resulting in high operating temperatures for battery applications. In this study, a K-SCIL with a melting point below that of K metal (64 °C) was developed by evolving a binary system to a ternary one. The resulting K-SCIL, K[FSA]0.33[FTA]0.33[TfO]0.33 (FSA-: bis(fluorosulfonyl)amide, FTA-: (fluorosulfonyl)(trifluoromethanesulfonyl)amide, and TfO-: trifluoromethanesulfonate), has a low melting point of 50 °C with a high K+ concentration of 9.3 mol dm-3 at 55 °C. It allows the safe handling of K metal and exhibits improved solid K metal deposition/dissolution compared to a conventional organic electrolyte. The K-SCIL does not involve the formation of a K+ concentration gradient near the electrode surface, which is demonstrated by the applicability of large currents exceeding a limiting current density assumed by calculation. Furthermore, stable K+ intercalation/deintercalation into/from graphite was successfully demonstrated at 55 °C, highlighting the potential of this K-SCIL for advanced potassium battery applications.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727125","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}

引用次数: 0

Structure of Novel Phosphonium-Based Ionic Liquids with S and O Substitutions from Experiments and a Mixed Quantum-Classical Approach.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-27 DOI: 10.1021/acs.jpcb.5c00129

Raphael Ogbodo, Gobin Raj Acharya, Ho Martin Yuen, Nicole Zmich, Furong Wang, Hideaki Shirota, Sharon I Lall-Ramnarine, James F Wishart, Andrew J Nieuwkoop, Claudio J Margulis

{"title":"Structure of Novel Phosphonium-Based Ionic Liquids with S and O Substitutions from Experiments and a Mixed Quantum-Classical Approach.","authors":"Raphael Ogbodo, Gobin Raj Acharya, Ho Martin Yuen, Nicole Zmich, Furong Wang, Hideaki Shirota, Sharon I Lall-Ramnarine, James F Wishart, Andrew J Nieuwkoop, Claudio J Margulis","doi":"10.1021/acs.jpcb.5c00129","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00129","url":null,"abstract":"This article presents experimental characterization information and synchrotron X-ray scattering measurements on a set of novel O- and S-substituted phosphonium-based ionic liquids (ILs) all coupled with the bis(fluorosulfonyl)imide (FSI-) anion. The ILs include the ethoxyethyltriethylphosphonium (P222(2O2)+) and triethyl[2-(ethylthio)ethyl]phosphonium (P222(2S2)+) cations, and we contrast results on these with those for unsubstituted triethylpentylphosphonium (P2225+). The article also introduces a physics-based protocol that combines classical force field studies on larger simulation boxes with classical and first-principles studies on smaller boxes. The method produces significantly improved S(q) functions in the regime which in prior publications we have associated with inter- and intraionic adjacency correlations. By understanding which shorter-range structural changes improve S(q) in the q-regime of interest, we are also able to pinpoint specific deficiencies in the classical force field model. The approach we take should be quite general and could help study other complex liquids on different length scales.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727108","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}

引用次数: 0