The Journal of Physical Chemistry B最新文献

{"title":"Linear and Nonlinear Rheological Investigations of Poly(3-hexylthiophene) H-Aggregated Gel Networks.","authors":"Gopal Lal Dhakar, Sudip Malik","doi":"10.1021/acs.jpcb.4c06835","DOIUrl":"10.1021/acs.jpcb.4c06835","url":null,"abstract":"<p><p>Owing to its facile synthesis and low cost, poly(3-hexylthiophene) (P3HT) has been extensively investigated in the field of organic electronics. Well-defined packing of P3HT chains and getting controlled morphologies, which solely depend on the polarity of the solvent, remain challenging. Herein, the aggregation behaviors of P3HT in organic solvents having different solvent polarities have been investigated to achieve different orderings of P3HT chains (H-type or J-type). The aggregation in the solution phase and the subsequent structural as well as morphological behaviors of P3HT chains have been investigated by absorption, X-ray powder diffraction, and topological studies, respectively. It has been noticed from absorption studies that P3HT forms H-type aggregates in anisole, phenetole, etc., whereas it produces J-type aggregates in toluene. More surprisingly, H-type aggregations of P3HT chains at low concentrations (<i>C</i>_P3HT = 0.001 g/cm³) eventually lead to the formation of the gel network that ceases the flow of the solvents. Contrary to expectations, J-type aggregation in toluene does not produce the gel network at the said concentration. Further, to reveal the viscoelastic and microstructural properties, P3HT gel networks have been thoroughly investigated by small-amplitude oscillatory shear (SAOS) and large-amplitude oscillatory shear (LAOS) with varying concentrations, solvents, and molecular weights of P3HT. With quantitative analysis, the nonlinear rheological characteristics of higher harmonics, strain-stiffening ratio, shear-thinning ratio, dissipation ratio, intracycle transient moduli, and derivative of transient moduli have been evaluated for P3HT networks, which significantly provide the rheological information for the understanding of conducting polymer networks.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12292-12309"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764550","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":"Structural Characterization and Hydration Dynamics of Cross-Linked Collagen and Hyaluronic Acid Scaffolds by Nuclear Magnetic Resonance.","authors":"Pablo A Fernández, Mariana P Cid, Romina Comín, Manuel I Velasco","doi":"10.1021/acs.jpcb.4c06316","DOIUrl":"10.1021/acs.jpcb.4c06316","url":null,"abstract":"<p><p>Understanding a biomaterial's structural and hydration dynamics is essential for its development and applications in tissue regeneration. In this study, collagen-hyaluronic acid (HA) scaffolds were analyzed utilizing Nuclear Magnetic Resonance (NMR) techniques to elucidate how different cross-linking conditions influence the internal architecture and interaction with solvents in these scaffolds. The scaffolds were fabricated using 3D printing and cross-linked with 1,4-butanediol diglycidyl ether (BDDGE), a process known to impact their mechanical properties. We gained insights into the microstructural organization and hydration behavior within the scaffolds when exposed to water and ethanol by employing proton relaxation and diffusion measurements. To better understand the system's performance, static and dynamic experiments were performed. Our results indicate that the degree of cross-linking affects the scaffold's ability to retain water, with higher cross-linking leading to more rigid structures. This also altered the hydration dynamics mainly due to a difference in the diffusion of water within the scaffold. In addition, the anisotropy of the collagen fibers also decreases with the cross-linking. Ethanol, a less polar solvent, provided a contrasting environment that further revealed the structural dependencies on the cross-linking density. The study's findings contribute to a deeper understanding of how the structure and morphology affect the functionality of collagen-HA scaffolds, offering critical information for optimizing their design for specific biomedical applications, such as soft tissue regeneration. Our experiments show how NMR is a valuable tool to provide information on dynamic processes not only in collagen-HA scaffolds but also in many biocompatible polymeric samples. The outcomes of this research provide a foundation for future work aimed at tailoring scaffold properties to enhance their performance in clinical settings, ultimately advancing the field of tissue engineering.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12143-12153"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764573","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":"Recent Advances in Simulation Software and Force Fields: Their Importance in Theoretical and Computational Chemistry and Biophysics","authors":"Christophe Chipot*,&nbsp;","doi":"10.1021/acs.jpcb.4c0623110.1021/acs.jpcb.4c06231","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06231https://doi.org/10.1021/acs.jpcb.4c06231","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"128 49","pages":"12023–12026 12023–12026"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142850256","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":"Exploring the Allosteric Response of Fascin to Its Inhibitor.","authors":"Jinmei Pan, Kai Chen, Lirui Lin, Li-Yan Xu, En-Min Li, Geng Dong","doi":"10.1021/acs.jpcb.4c04813","DOIUrl":"10.1021/acs.jpcb.4c04813","url":null,"abstract":"<p><p>Fascin is a major actin-binding protein (ABP) for stabilizing filopodia to support efficient adhesion and migration of cancer cells. Fascin is also highly expressed in metastatic tumors. Disrupting the actin-binding site (ABS) on fascin constitutes a critical approach to hindering tumor metastasis. The G2 series of small molecules was formulated with the specific purpose of obstructing the binding pocket of fascin. The determination of inhibitor-induced structural dynamics in fascin is crucial for a comprehensive of its biological functions and the strategic development of pharmacological interventions. In this study, we utilized both equilibrium and dynamical-nonequilibrium molecular dynamics (D-NEMD) to elucidate the molecular mechanisms responsible for transmitting structural changes when removing the G2 inhibitor, in both the wild type (WT) and its variants. Our findings indicate that when G2 is removed, structural dynamics in fascin originate from the G2 binding pocket of fascin and propagate signals through the conformational transformation that spans all four β-trefoil domains. Although different mutant variants demonstrated comparable conformational networks, they showed varying response times. However, the signaling pathways in mutants remained consistent in comparison to the WT fascin. This study provides valuable insights into the structural features and communication pathways of fascin and provides avenues for the development of targeted inhibitors with promising prospects in cancer therapy.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12050-12058"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764499","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":"Complexation of Actinyl Ions with DHOA and TBP in an Ionic Liquid and a Molecular Solvent: How Similar or Different Are They?","authors":"Dharmendra B Sharma, Mridusmita Sarma, Seraj A Ansari, Sk Musharaf Ali, Prasanta K Mohapatra","doi":"10.1021/acs.jpcb.4c06791","DOIUrl":"10.1021/acs.jpcb.4c06791","url":null,"abstract":"<p><p>Complexation thermodynamics of uranyl ions with well-known reprocessing ligands like tributyl phosphate (TBP) and dihexyl octanamide (DHOA) was studied in an ionic liquid (IL) versus a molecular solvent. Whereas 1-butyl-3-methylimidazolium bis(trifluoromethyl sulfonyl)imide (Bumim·Tf₂N) was used as an IL due to its favorable viscosity, acetonitrile was the choice of molecular solvent due to its poor coordinating nature. Optical spectroscopy studies revealed that UO₂²⁺ ions formed species of the types ML₁ and ML₂ with both TBP and DHOA, in a stepwise manner. The formation constants (log β) of UO₂²⁺ with DHOA in the IL were determined as 3.58 ± 0.03 and 6.54 ± 0.10, while those with TBP were obtained as 3.42 ± 0.05 and 6.38 ± 0.08, respectively. In the case of acetonitrile, on the other hand, these β values were significantly lower than those observed in the IL medium, which was supported by the DFT calculations. Calorimetric titrations of the UO₂²⁺ ions with DHOA and TBP confirmed that the complex formation reactions were thermodynamically more favored in the ionic liquid medium than the molecular solvent. The nature of binding through FTIR investigations and DFT calculations suggested that the complexes formed in the IL medium were cationic in nature of the types [UO₂(H₂O)₃(TBP)₂]²⁺ and [UO₂(H₂O)₃(DHOA)₂]²⁺, but neutral complexes were formed in the molecular solvent of the types [UO₂(NO₃)₂(TBP)₂] and [UO₂(NO₃)₂(DHOA)₂].</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12179-12188"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764563","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":"Recent Advances in Simulation Software and Force Fields: Their Importance in Theoretical and Computational Chemistry and Biophysics.","authors":"Christophe Chipot","doi":"10.1021/acs.jpcb.4c06231","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06231","url":null,"abstract":"","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"128 49","pages":"12023-12026"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811436","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":"The Impact of Nanocarbon Powder on the Characteristics of a Gel Propellant System with a High Concentration of Aluminum.","authors":"Jiyuan Chen, Hui Zhao, Weifeng Li, Haifeng Liu","doi":"10.1021/acs.jpcb.4c04430","DOIUrl":"10.1021/acs.jpcb.4c04430","url":null,"abstract":"<p><p>The addition of aluminum particles to a gel propellant has garnered attention through its potential for enhancing fuel properties. In order to enhance the energy performance of gel propellants, it is imperative to prepare gel propellants with high concentrations of aluminum. However, high-concentration aluminum-containing gels encounter two challenges. First, the combustion process leads to the agglomeration of aluminum particles, resulting in incomplete combustion. Additionally, elevated concentrations of aluminum particles increase the viscosity of the gel, impeding its atomization process and, subsequently, affecting combustion efficiency. These aforementioned issues pose practical obstacles for the application of high-concentration aluminum-containing gel propellants. In this research, a high-concentration aluminum-containing gel formulation was supplemented with nanocarbon powder. By investigating the impact of nanocarbon on various properties of the gel, its potential for addressing the above issues was analyzed. The investigation into the combustion performance of aluminum-containing gel blended with carbon powder revealed that the addition of 10 wt % nanocarbon powder to the gel system leads to a significant increase in the volumetric calorific value of the gel propellant by 21.21%. This enhancement not only improves the energy performance but also addresses the issue of incomplete combustion associated with aluminum. The rheology experiments conducted on gels demonstrate that the addition of nanocarbon powder results in an increased viscosity of the gel at lower shear rates, thereby enhancing its ability to withstand external disturbances during storage. Furthermore, this incorporation also enhances the gel's shear thinning properties, leading to a significant reduction in viscosity at higher shear rates and facilitating easier atomization of the gel system. In summary, the incorporation of nanocarbon powder can optimize the storage, atomization, and combustion processes of the gel, offering a straightforward and efficient approach to enhance the practical performance of metallized gel propellants.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12197-12208"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708617","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":"Understanding the Directed Evolution of a Natural-like Efficient Artificial Metalloenzyme.","authors":"Anagh Mukherjee, Subhendu Roy","doi":"10.1021/acs.jpcb.4c06994","DOIUrl":"10.1021/acs.jpcb.4c06994","url":null,"abstract":"<p><p>The artificial metalloenzyme containing iridium in place of iron along with four directed evolution mutations C317G, T213G, L69V, and V254L in a natural cytochrome P450 presents an important milestone in merging the extraordinary efficiency of biocatalysts with the versatility of small molecule chemical catalysts in catalyzing a new-to-nature carbene insertion reaction. This is a show-stopper enzyme, as it exhibits a catalytic efficiency similar to that of natural enzymes. Despite this remarkable discovery, there is no mechanistic and structural understanding as to why it displays extraordinary efficiency after the incorporation of the four active site mutations by directed evolution methods, which so far has been intractable to any experimental methods. In this study, we have deciphered how directed evolution mutations gradually alter the protein conformational ensemble to populate a catalytically active conformation to boost a multistep catalysis in a natural-like artificial metalloenzyme using large-scale molecular dynamics simulations, rigorous quantum chemical (QM), and multiscale quantum chemical/molecular mechanics (QM/MM) calculations. It reveals how evolution precisely positions the cofactor-substrate in an unusual but effective orientation within a reshaped active site in the catalytically active conformation stabilized by C-H···π interactions from more ordered mutated L69V and V254L residues to achieve preferential transition state stabilization compared to the ground state. This work essentially tracks down in atomistic detail the shift in the conformational ensemble of the highly active conformation from the less efficient single mutant to the most efficient quadruple mutant and offers valuable insights for designing better enzymes. The active conformation correctly reproduces the experimental barrier height and also accounts for the catalytic effect, which is in good agreement with experimental observations. Moreover, this conformation features an unusual bonding interaction in a metal-carbene species that preferentially stabilizes the rate-determining formation of an iridium porphyrin carbene intermediate to render the observed high catalytic rate acceleration. Our study provides crucial insights into the underlying rationale for directed evolution, reports the major catalytic role of nonelectrostatic interactions in enzyme catalysis different from the electrostatic model, and suggests a crucial principle toward designing enzymes with natural efficiency.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12122-12132"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714887","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":"Stabilization Mechanism of Initiator Transfer RNA in the Small Ribosomal Subunit from Coarse-Grained Molecular Simulations.","authors":"Yoshiharu Mori, Shigenori Tanaka","doi":"10.1021/acs.jpcb.4c04966","DOIUrl":"10.1021/acs.jpcb.4c04966","url":null,"abstract":"<p><p>Proteins play a variety of roles in biological phenomena in cells. Proteins are synthesized by the ribosome, which is a large molecular complex composed of proteins and nucleic acids. Among the many molecules involved in the process of protein synthesis, tRNA is one of the essential molecules. In this study, coarse-grained molecular dynamics simulations were performed to understand how the tRNA molecule is stabilized in the ribosome, and the free energy along the dissociation path of the tRNA was calculated. We found that some ribosomal proteins, which are components of the ribosome, are involved in the stabilization of the tRNA. The positively charged amino acid residues in the C-terminal region of the ribosomal proteins are particularly important for stabilization. These findings contribute to our understanding of the molecular evolution of protein synthesis in terms of the ribosome, which is a universal component of life.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12059-12065"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142737822","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":"Structure-Property Correlation in Ba/Sr-Ca-Mg-Zn-Si-Al-O Glass: Elucidation by Experimental and Molecular Dynamics Simulation Study.","authors":"Sushanta Kumar Mohapatra, Indrajit Tah, Margit Fabian, Saswata Chakraborty, Prince Sen, Krishna K Dey, Manasi Ghosh, H S Maharana, Annapurna Kalyandurg","doi":"10.1021/acs.jpcb.4c04652","DOIUrl":"10.1021/acs.jpcb.4c04652","url":null,"abstract":"<p><p>Broad band transmitting glasses from visible to mid-infrared with good mechanical strength, chemical durability, glass-forming ability, and thermal stability are preferred for optics and laser technology applications. Generally, low phonon energy glasses possess an extended transmission cutoff toward mid-infrared, but at the same time, retention of other desired properties is challenging for the researchers. In this work, we have shown that mixed alkaline earth (Ba/Sr) would have the potential to improve overall glass properties while retaining its low phonon energy when CaO is partially substituted by BaO/SrO in calcium magnesium zinc silica-aluminate (CMZSA) glass. Quantitative structure analysis of its role in glass properties has been carried out using molecular dynamics (MD) simulation and experimental techniques. This study reveals that Al and Si mainly attained fourfold coordination, while Zn and Mg majorly existed in Al-O-Zn/Mg triclusters. The Ba²⁺ ions play almost equal roles as charge compensators and network modifiers, while Sr²⁺ ions play a larger role in charge compensation. As a result, the SrO-added glass leads to the highest bridging oxygens as compared to others and corroborates with improved optical, thermal, and mechanical properties. Hence, the SrO-added glass shows the most stable network connection and improved overall glass properties.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12209-12226"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142737823","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}