The Journal of Physical Chemistry B最新文献

{"title":"Self-Assembled Oligomers Facilitate Amino Acid-Driven CO₂ Capture at the Air-Aqueous Interface.","authors":"Nitesh Kumar, Vyacheslav S Bryantsev","doi":"10.1021/acs.jpcb.4c05994","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c05994","url":null,"abstract":"<p><p>Direct air capture of CO₂ using amino acid absorbents, such as glycine or sarcosine, is constrained by the relatively slow mass transfer of CO₂ through the air-aqueous interface. Our recent study showed a marked improvement in CO₂ capture by introducing CO₂-permeable oligo-dimethylsiloxane (ODMS-MIM⁺) oligomers with cationic (imidazolium, MIM⁺) headgroups. In this work, we have employed all-atom molecular dynamics simulations in combination with subensemble analysis using network theory to provide a detailed molecular picture of the behavior of CO₂ and the glycinate anions (Gly^-) at the ODMS-MIM⁺ decorated air-aqueous interfaces. We show that the cationic head groups of the surfactants enhance the concentration and lifetime of Gly^- in the interfacial region, while ODMS tails promote the physisorption of CO₂ in the interfacial region. Together, these two factors increase the effective region of contact and the probability of interactions between CO₂ and Gly^- compared to that of the pure air-aqueous interface. The fundamental insights gained in this work establish essential foundations for developing hybrid systems with oligomer-decorated interfaces to maximize the overall CO₂ capture rates.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062532","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":"Accessing Different Protein Conformer Ensembles with Tunable Capillary Vibrating Sharp-Edge Spray Ionization","authors":"Daud Sharif,&nbsp;Vikum K. Dewasurendra,&nbsp;Mst Nigar Sultana,&nbsp;Sultan Mahmud,&nbsp;Chandrima Banerjee,&nbsp;Mohammad Rahman,&nbsp;Peng Li,&nbsp;David E. Clemmer,&nbsp;Matthew B. Johnson* and Stephen J. Valentine*,&nbsp;","doi":"10.1021/acs.jpcb.4c0484210.1021/acs.jpcb.4c04842","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c04842https://doi.org/10.1021/acs.jpcb.4c04842","url":null,"abstract":"<p >Capillary vibrating sharp-edge spray ionization (cVSSI) has been used to control the droplet charging of nebulized microdroplets and monitor effects on protein ion conformation makeup as determined by mass spectrometry (MS). Here it is observed that the application of voltage results in noticeable differences to the charge state distributions (CSDs) of ubiquitin ions. The data can be described most generally in three distinct voltage regions: Under low-voltage conditions (&lt;+200 V, LV regime), low charge states (2+ to 4+ ions) dominate the mass spectra. For midvoltage conditions (+200 to +600 V, MV regime), higher charge states (7+ to 12+ ions) are observed. For high-voltage conditions (&gt;+600 V, HV regime), the “nano-electrospray ionization (nESI)-type distribution” is achieved in which the 6+ and 5+ species are observed as the dominant ions. Analysis of these results suggests that different pathways to progeny nanodroplet production result in the observed ions. For the LV regime, aerodynamic breakup leads to low charge progeny droplets that are selective for the native solution conformation ensemble of ubiquitin (minus multimeric species). In the MV regime, the large droplets persist for longer periods of time, leading to droplet heating and a shift in the conformation ensemble to partially unfolded species. In the HV regime, droplets access progeny nanodroplets faster, leading to native conformation ensemble sampling as indicated by the observed nESI-type CSD. The notable observation of limited multimer formation and adduct ion formation in the LV regime is hypothesized to result from droplet aero breakup resulting in protein and charge carrier partitioning in sampled progeny droplets. The tunable droplet charging afforded by cVSSI presents opportunities to study the effects of the droplet charge, droplet size, and mass spectrometer inlet temperature on the conformer ensemble sampled by the mass spectrometer. Additionally, the approach may provide a tool for rapid comparison of protein stabilities.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 5","pages":"1626–1639 1626–1639"},"PeriodicalIF":2.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpcb.4c04842","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143127481","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":"Predicting Carbonic Anhydrase Binding Affinity: Insights from QM Cluster Models","authors":"Mackenzie Taylor,&nbsp;Haedam Mun and Junming Ho*,&nbsp;","doi":"10.1021/acs.jpcb.4c0639310.1021/acs.jpcb.4c06393","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06393https://doi.org/10.1021/acs.jpcb.4c06393","url":null,"abstract":"<p >A systematic series of QM cluster models has been developed to predict the trend in the carbonic anhydrase binding affinity of a structurally diverse dataset of ligands. Reference DLPNO–CCSD(T)/CBS binding energies were generated for a cluster model and used to evaluate the performance of contemporary density functional theory methods, including Grimme’s “3c” DFT composite methods (r²SCAN-3c and ωB97X-3c). It is demonstrated that when validated QM methods are used, the predictive power of the cluster models improves systematically with the size of the cluster models. This provided valuable insights into the key interactions that need to be modeled quantum mechanically and could inform how the QM region should be defined in hybrid quantum mechanics/molecular mechanics (QM/MM) models. The use of r²SCAN-3c on the largest cluster model composed of 16 residues appears to be an economical approach to predicting binding trends compared with using more robust DFT methods such as ωB97M-V and provides a significant improvement compared with docking.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 5","pages":"1475–1485 1475–1485"},"PeriodicalIF":2.8,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143127640","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":"Directed Evolution's Selective Use of Quantum Tunneling in Designed Enzymes─A Combined Theoretical and Experimental Study.","authors":"Kseniia Korchagina, Sree Ganesh Balasubramani, Jordan Berreur, Emilie F Gerard, Linus O Johannissen, Anthony P Green, Sam Hay, Steven D Schwartz","doi":"10.1021/acs.jpcb.4c08169","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08169","url":null,"abstract":"<p><p>Natural enzymes are powerful catalysts, reducing the apparent activation energy for reactions and enabling chemistry to proceed as much as 10¹⁵ times faster than the corresponding solution reaction. It has been suggested for some time that, in some cases, quantum tunneling can contribute to this rate enhancement by offering pathways through a barrier inaccessible to activated events. A central question of interest to both physical chemists and biochemists is the extent to which evolution introduces mechanisms below the barrier, or tunneling mechanisms. In view of the rapidly expanding chemistries for which artificial enzymes have been created, it is of interest to see how quantum tunneling has been used in these reactions. In this paper, we study the evolution of possible proton tunneling during C-H bond cleavage in enzymes that catalyze the Morita-Baylis-Hillman (MBH) reaction. The enzymes were generated by theoretical design, followed by laboratory evolution. We employ classical and centroid molecular dynamics approaches in path sampling computations to determine whether there is a quantum contribution to lowering the free energy of the proton transfer for various experimentally generated protein and substrate combinations. These data are compared to experiments reporting on the observed kinetic isotope effect (KIE) for the relevant reactions. Our results indicate the modest involvement of tunneling when laboratory evolution has resulted in a system with a higher classical free energy barrier to chemistry (that is, when optimization of processes other than chemistry results in a higher chemical barrier).</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057504","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":"Modulating Enzyme's Conformational Space: Impact of Substrate Binding, Mode Alteration, and Active Site Mutation in DapC, an Aminotransferase Enzyme of Lysine Biosynthetic Pathway.","authors":"Sourav Manna, Sabyashachi Mishra","doi":"10.1021/acs.jpcb.4c06274","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06274","url":null,"abstract":"<p><p>The microbial aminotransferase enzyme DapC is vital for lysine biosynthesis in various Gram-positive bacteria, including <i>Mycobacterium tuberculosis</i>. Characterization of the enzyme's conformational dynamics and identifying the key residues for ligand binding are crucial for the development of effective antimicrobials. This study employs atomistic simulations to explore and categorize the dynamics of DapC in comparison to other classes of aminotransferase. DapC undergoes an open-to-closed conformational change upon substrate binding, characterized by the movement of the N-terminal α2 helix, akin to that observed in the class Ib aspartate aminotransferase from <i>Thermus thermophilus</i>. Based on sequence similarity, essential dynamics, and the absence of the characteristic hinge movement, DapC is classified as a class Ib aminotransferase of type-I pyridoxal-5'-phosphate (PLP)-dependent enzyme. In the open state of DapC, two binding modes of glutamate, namely, canonical and alternate, separated by a dihedral rotation, are equally preferred. The closed state prefers the canonical binding mode, which is favorable for catalysis. In the case where the substrate binds in the alternate mode, a low-barrier dihedral rotation generates the canonical mode for efficient catalysis. The presence of two highly conserved residues, Phe14 and Gln31, stabilizes the closed state of substrate-bound DapC. Mutations of these residues disrupt the crucial hydrophobic interactions with the substrate, causing the enzyme to shift to an open state. While Phe14 has a dominant role, Gln31 is less consequential in regulating the conformational change, while the double mutation leads to a rapid conformation change.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057506","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":"Directed Evolution’s Selective Use of Quantum Tunneling in Designed Enzymes─A Combined Theoretical and Experimental Study","authors":"Kseniia Korchagina,&nbsp;Sree Ganesh Balasubramani,&nbsp;Jordan Berreur,&nbsp;Emilie F. Gerard,&nbsp;Linus O. Johannissen,&nbsp;Anthony P. Green,&nbsp;Sam Hay and Steven D. Schwartz*,&nbsp;","doi":"10.1021/acs.jpcb.4c0816910.1021/acs.jpcb.4c08169","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08169https://doi.org/10.1021/acs.jpcb.4c08169","url":null,"abstract":"<p >Natural enzymes are powerful catalysts, reducing the apparent activation energy for reactions and enabling chemistry to proceed as much as 10¹⁵ times faster than the corresponding solution reaction. It has been suggested for some time that, in some cases, quantum tunneling can contribute to this rate enhancement by offering pathways through a barrier inaccessible to activated events. A central question of interest to both physical chemists and biochemists is the extent to which evolution introduces mechanisms below the barrier, or tunneling mechanisms. In view of the rapidly expanding chemistries for which artificial enzymes have been created, it is of interest to see how quantum tunneling has been used in these reactions. In this paper, we study the evolution of possible proton tunneling during C–H bond cleavage in enzymes that catalyze the Morita–Baylis–Hillman (MBH) reaction. The enzymes were generated by theoretical design, followed by laboratory evolution. We employ classical and centroid molecular dynamics approaches in path sampling computations to determine whether there is a quantum contribution to lowering the free energy of the proton transfer for various experimentally generated protein and substrate combinations. These data are compared to experiments reporting on the observed kinetic isotope effect (KIE) for the relevant reactions. Our results indicate the modest involvement of tunneling when laboratory evolution has resulted in a system with a higher classical free energy barrier to chemistry (that is, when optimization of processes other than chemistry results in a higher chemical barrier).</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 5","pages":"1555–1562 1555–1562"},"PeriodicalIF":2.8,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143127726","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":"Predicting Carbonic Anhydrase Binding Affinity: Insights from QM Cluster Models.","authors":"Mackenzie Taylor, Haedam Mun, Junming Ho","doi":"10.1021/acs.jpcb.4c06393","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06393","url":null,"abstract":"<p><p>A systematic series of QM cluster models has been developed to predict the trend in the carbonic anhydrase binding affinity of a structurally diverse dataset of ligands. Reference DLPNO-CCSD(T)/CBS binding energies were generated for a cluster model and used to evaluate the performance of contemporary density functional theory methods, including Grimme's \"3c\" DFT composite methods (r²SCAN-3c and ωB97X-3c). It is demonstrated that when validated QM methods are used, the predictive power of the cluster models improves systematically with the size of the cluster models. This provided valuable insights into the key interactions that need to be modeled quantum mechanically and could inform how the QM region should be defined in hybrid quantum mechanics/molecular mechanics (QM/MM) models. The use of r²SCAN-3c on the largest cluster model composed of 16 residues appears to be an economical approach to predicting binding trends compared with using more robust DFT methods such as ωB97M-V and provides a significant improvement compared with docking.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051079","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":"Complementary Peptide Interactions Support the Ultra-Rigidity of Polymers of De Novo Designed Click-Functionalized Bundlemers.","authors":"Dai-Bei Yang, Tianren Zhang, Jacquelyn E Blum, Christopher J Kloxin, Darrin J Pochan, Jeffery G Saven","doi":"10.1021/acs.jpcb.4c06403","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06403","url":null,"abstract":"<p><p>Computationally designed 29-residue peptides yield tetra-α-helical bundles with <i>D</i>₂ symmetry. The \"bundlemers\" can be bifunctionally linked via thiol-maleimide cross-links at their N-termini, yielding supramolecular polymers with unusually large, micrometer-scale persistence lengths. To provide a molecularly resolved understanding of these systems, all-atom molecular modeling and simulations of linked bundlemers in explicit solvent are presented. A search over relative orientations of the bundlemers identifies a structure, wherein at the bundlemer-bundlemer interface, interior hydrophobic residues are in contact, and α-helices are aligned with a pseudocontiguous α-helix that spans the interface. Calculation of a potential of mean force confirms that the structure in which the bundlemers are in contact and colinearly aligned is a stable minimum. Analyses of hydrogen bonds and hydrophobic complementarity highlight the complementary interactions at the interface. The molecular insight provided reveals the molecular origins of bundlemer alignment within the supramolecular polymers.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051076","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":"Ion–Ion Structural Correlation and Dynamics of Water in Aqueous NaCl Solutions with a Wide Range of Concentrations","authors":"Khushika,&nbsp; and ,&nbsp;Pritam Kumar Jana*,&nbsp;","doi":"10.1021/acs.jpcb.4c0525210.1021/acs.jpcb.4c05252","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c05252https://doi.org/10.1021/acs.jpcb.4c05252","url":null,"abstract":"<p >The behavior of water in concentrated ionic solutions, including supersaturated conditions, is crucial for numerous material and energy conversion processes and fundamental research. All electrolytes whether they “structure-make” or “structure-break” the water structure lead to slower water motion. This study investigates the structure and dynamics of aqueous NaCl solutions across a wide range of concentrations. On the structural side, the primary focus is on ion–ion correlations. In terms of dynamics, we demonstrate that the slowing down of water dynamics continues even beyond the saturated state. We identify three distinct types of dynamics at large concentrations: ballistic, trapped, and diffusive. The van Hove correlation function exhibits no signs of relaxation within a time interval where particle motion is effectively halted. The system displays dynamical heterogeneities, confirmed by evaluating non-Gaussian parameters for the self-part of the van Hove function and identifying the mobile particles. These particles form clusters, with the largest sizes occurring when the non-Gaussian parameters are at their maximum. Additionally, we discuss the relaxation times associated with these systems using the incoherent intermediate scattering function and establish a connection with the mode-coupling theory.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 5","pages":"1675–1688 1675–1688"},"PeriodicalIF":2.8,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143127719","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":"Molecular Dynamics Insights into Water Transport Mechanisms in Polyamide Membranes: Influence of Cross-Linking Degree.","authors":"Chi Zhang, Guangle Bu, Lida Meng, Dan Lu, Sirui Tong, Zhikan Yao, Danjun Zheng, Lin Zhang","doi":"10.1021/acs.jpcb.4c06566","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06566","url":null,"abstract":"<p><p>Polyamide (PA) membranes are widely utilized in desalination and water treatment applications, yet the mechanisms underlying water transport within these amorphous polymer materials remain insufficiently understood. To gain more insight into these problems on a microscopic scale, we employ molecular dynamics (MD) simulations to analyze the relationship between the structural properties and the water permeation behavior of PA membranes. Two distinct atomistic models of PA membranes are developed by controlling their degrees of cross-linking (DC). We then conducted a comparative analysis on their microscopic structural properties and configurations of water inside the membranes and investigated how these differences lead to different water diffusion coefficients. Our results reveal that the membrane with a lower DC exhibits higher polymer mobility and a more orderly microscopic structure, allowing the formation of pores that can hold larger water clusters as well as more transient passages between pores, both contributing to an increased water diffusion coefficient. From these observations, we can conclude that water permeability within PA membranes is governed by both the morphology of semirigid pores and the oscillatory movements of the polymer chains. Overall, these findings contribute to a deeper understanding of the intricate mechanisms governing water permeation in PA membranes and may inform the design of more efficient membranes for reverse osmosis and other water treatment technologies.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051078","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}