The Journal of Physical Chemistry B最新文献_第5页

Discrimination and Translocation of Charged Proteinogenic Amino Acids through a Single-Walled Carbon Nanotube

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-25 DOI: 10.1021/acs.jpcb.4c0869210.1021/acs.jpcb.4c08692

Yingjun Shen, and , Mingming Ding*,

{"title":"Discrimination and Translocation of Charged Proteinogenic Amino Acids through a Single-Walled Carbon Nanotube","authors":"Yingjun Shen,  and , Mingming Ding*, ","doi":"10.1021/acs.jpcb.4c0869210.1021/acs.jpcb.4c08692","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08692https://doi.org/10.1021/acs.jpcb.4c08692","url":null,"abstract":"Nanopore sensing relies on associating the measured current signals with specific features of the target molecules. The diversity of amino acids presents significant challenges in detecting and sequencing peptides and proteins. The hollow and uniform tubular structure of single-walled carbon nanotubes (SWCNTs) makes them ideal candidates for nanopore sensors. Here, we demonstrate by molecular dynamics simulations the discrimination and translocation of charged proteinogenic amino acids through the nanopore sensor formed by inserting a SWCNT into lipid bilayers. Moreover, our analysis suggests that the current blockade is influenced not only by excluded atomic volume but also by noncovalent interactions between amino acids and SWCNT during similar helical translocation. The presence of noncovalent interactions enhances the understanding of current differences in nanopore translocation of molecules with similar excluded atomic volume. This finding provides new perspectives and applications for the optimal design of SWCNT nanopore sensors.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 13","pages":"3502–3513 3502–3513"},"PeriodicalIF":2.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143758786","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

Theoretical Basis for Refractive Index Changes Resulting from Solution Phase Molecular Interaction

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-25 DOI: 10.1021/acs.jpcb.4c0756310.1021/acs.jpcb.4c07563

Michael N. Kammer, Amanda K. Kussrow and Darryl J. Bornhop*,

{"title":"Theoretical Basis for Refractive Index Changes Resulting from Solution Phase Molecular Interaction","authors":"Michael N. Kammer, Amanda K. Kussrow and Darryl J. Bornhop*, ","doi":"10.1021/acs.jpcb.4c0756310.1021/acs.jpcb.4c07563","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07563https://doi.org/10.1021/acs.jpcb.4c07563","url":null,"abstract":"Refractive index (RI) is a fundamental optical property widely used to investigate the physical and chemical characteristics of materials. Here, we build on our previous work to refine the framework for RI sensing in solution-phase chemical and biochemical interactions. Starting from the Clausius–Mossotti relation, we present a first-principles derivation of a relationship for the RI signal resulting from chemical binding. We then demonstrate how the binding-induced conformational and hydration changes of interacting species relate to their estimated change in dielectric and thus the solution-phase change in refractive index (ΔRI). By varying the model parameters, such as solvation shell size and polarizability, we investigate the RI changes for two interactions: Ca2+ with the protein Recoverin and benzenesulfonamide with carbonic anhydrase 2 (CAII). These examples show that our theory predicts that even for small changes in binding-induced polarizability (relative to previous literature values), a quantifiable RI change is produced within the detectable range of RI detectors operating at ca. 10–6 RIU. Empirical observations confirm our theoretical predictions. Surprisingly, theory and experiment yield a decrease in ΔRI for the benzenesulfonamide-CAII interaction. We attribute this observation to shielding of charged residues and water molecule displacement during the binding event. Our approach is generalized, enabling it to be extended to other binding systems, as well as those undergoing nonbinding conformational changes, and facilitates the exploration of diverse biological and chemical processes by solution-phase RI sensing.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 13","pages":"3297–3305 3297–3305"},"PeriodicalIF":2.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpcb.4c07563","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143758889","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}

引用次数: 0

Subcritical Determination of the Frenkel Line in Liquid Nitrogen, the Emergent Final Picture, and a Universal Equation for the Coordination Number of Real Fluids.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-25 DOI: 10.1021/acs.jpcb.5c00018

Ciprian G Pruteanu, Ayobami D Daramola, Marcin Kirsz, Cerian E A Robertson, Luke J Jones, Tianrui Wang, John S Loveday, Graeme J Ackland, Oliver L G Alderman, John E Proctor

引用次数: 0

Pterin–Thymidine Adducts: From Their Photochemical Synthesis to Their Photosensitizing Properties

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-25 DOI: 10.1021/acs.jpcb.5c0018510.1021/acs.jpcb.5c00185

Gricelda Godoy-Ortega, Gemma M. Rodríguez-Muñiz, Virginie Lhiaubet-Vallet, Carolina Lorente* and Andrés H. Thomas*,

{"title":"Pterin–Thymidine Adducts: From Their Photochemical Synthesis to Their Photosensitizing Properties","authors":"Gricelda Godoy-Ortega, Gemma M. Rodríguez-Muñiz, Virginie Lhiaubet-Vallet, Carolina Lorente* and Andrés H. Thomas*, ","doi":"10.1021/acs.jpcb.5c0018510.1021/acs.jpcb.5c00185","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00185https://doi.org/10.1021/acs.jpcb.5c00185","url":null,"abstract":"Pterin (Ptr) is the model compound of aromatic pterins, which are efficient photosensitizers present in human skin and are able to oxidize biomolecules upon UVA irradiation. Photosensitization involves chemical alteration of a biomolecule as a result of the initial absorption of radiation by another chemical species, the photosensitizer. Under anaerobic conditions, Ptr reacts with thymine (T) to form photoadducts (T-Ptr). In this work, we present a method to prepare and purify T-Ptr adducts, using 2′-deoxythymidine 5′-monophosphate (dTMP) and single stranded oligonucleotide 5′-d(TTTTT)-3′ (dT5), and investigate their photosensitizing properties. Interestingly, the Ptr moiety, when attached to T, retains its photophysical properties. The adduct dTMP-Ptr, upon excitation, forms singlet and triplet excited states, the latter being capable of transferring energy to dissolved O2 and generating singlet oxygen, with an efficiency similar to Ptr. In air-equilibrated solutions, both dTMP-Ptr and dT5-Ptr adducts can photosensitize the oxidation of tryptophan and 2′-deoxyguanosine 5′-monophosphate, two of the main targets of photosensitization in biological systems, with efficiencies close to that of free Ptr. The mechanisms involved in the oxidation of biomolecules can be either type I (electron transfer) or type II (singlet oxygen).","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 13","pages":"3334–3344 3334–3344"},"PeriodicalIF":2.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143758915","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

Tuning Excited-State Charge Transfer Character in Cofacial Core-Substituted Perylenediimide Dimers

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-25 DOI: 10.1021/acs.jpcb.5c0061710.1021/acs.jpcb.5c00617

Samuel B. Tyndall, Jonathan R. Palmer, Nikolai A. Tcyrulnikov, Ryan M. Young and Michael R. Wasielewski*,

{"title":"Tuning Excited-State Charge Transfer Character in Cofacial Core-Substituted Perylenediimide Dimers","authors":"Samuel B. Tyndall, Jonathan R. Palmer, Nikolai A. Tcyrulnikov, Ryan M. Young and Michael R. Wasielewski*, ","doi":"10.1021/acs.jpcb.5c0061710.1021/acs.jpcb.5c00617","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00617https://doi.org/10.1021/acs.jpcb.5c00617","url":null,"abstract":"Understanding the interplay between excimer formation and symmetry-breaking charge separation is important for optimizing charge separation in organic photovoltaic materials. To explore this connection, we synthesized four 1,6,7,12-tetrakis(p-X-phenoxy)perylene-(3,4:9,10)-bisdicarboximide cofacially stacked dimers, where X = MeO, tert-butyl, Br, and CF3. Steady-state spectroscopy reveals H-type aggregation and excimer formation in all four dimers, while transient absorption spectroscopy shows relatively small changes in their excited-state absorptions. However, time-resolved fluorescence (TRF) spectroscopy shows that relaxation occurs from an initial Frenkel exciton-dominated excimer state to one in which charge transfer (CT) character contributes. Relaxation to the lower-lying state with CT character is attributed to a combination of structural and charge distribution changes elicited by varying the substituents. This study illustrates how subtle changes in charge distribution and structure can combine to influence the excited state dynamics that influence charge separation in molecular dimers.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 13","pages":"3454–3463 3454–3463"},"PeriodicalIF":2.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143758788","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

Catalytic Effects of Water-Solvated Metal Cations in Epoxy-Amine Curing through Hydrogen Bonds and Metal–Ligand Interactions

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-25 DOI: 10.1021/acs.jpcb.4c0587410.1021/acs.jpcb.4c05874

Dipak Prasad, and , Nilanjan Mitra*,

引用次数: 0

Theoretical Basis for Refractive Index Changes Resulting from Solution Phase Molecular Interaction.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-25 DOI: 10.1021/acs.jpcb.4c07563

Michael N Kammer, Amanda K Kussrow, Darryl J Bornhop

{"title":"Theoretical Basis for Refractive Index Changes Resulting from Solution Phase Molecular Interaction.","authors":"Michael N Kammer, Amanda K Kussrow, Darryl J Bornhop","doi":"10.1021/acs.jpcb.4c07563","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07563","url":null,"abstract":"Refractive index (RI) is a fundamental optical property widely used to investigate the physical and chemical characteristics of materials. Here, we build on our previous work to refine the framework for RI sensing in solution-phase chemical and biochemical interactions. Starting from the Clausius-Mossotti relation, we present a first-principles derivation of a relationship for the RI signal resulting from chemical binding. We then demonstrate how the binding-induced conformational and hydration changes of interacting species relate to their estimated change in dielectric and thus the solution-phase change in refractive index (ΔRI). By varying the model parameters, such as solvation shell size and polarizability, we investigate the RI changes for two interactions: Ca2+ with the protein Recoverin and benzenesulfonamide with carbonic anhydrase 2 (CAII). These examples show that our theory predicts that even for small changes in binding-induced polarizability (relative to previous literature values), a quantifiable RI change is produced within the detectable range of RI detectors operating at ca. 10-6 RIU. Empirical observations confirm our theoretical predictions. Surprisingly, theory and experiment yield a decrease in ΔRI for the benzenesulfonamide-CAII interaction. We attribute this observation to shielding of charged residues and water molecule displacement during the binding event. Our approach is generalized, enabling it to be extended to other binding systems, as well as those undergoing nonbinding conformational changes, and facilitates the exploration of diverse biological and chemical processes by solution-phase RI sensing.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699133","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

Subcritical Determination of the Frenkel Line in Liquid Nitrogen, the Emergent Final Picture, and a Universal Equation for the Coordination Number of Real Fluids

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-25 DOI: 10.1021/acs.jpcb.5c0001810.1021/acs.jpcb.5c00018

Ciprian G. Pruteanu*, Ayobami D. Daramola, Marcin Kirsz, Cerian E. A. Robertson, Luke J. Jones, Tianrui Wang, John S. Loveday, Graeme J. Ackland*, Oliver L. G. Alderman and John E. Proctor*,

{"title":"Subcritical Determination of the Frenkel Line in Liquid Nitrogen, the Emergent Final Picture, and a Universal Equation for the Coordination Number of Real Fluids","authors":"Ciprian G. Pruteanu*, Ayobami D. Daramola, Marcin Kirsz, Cerian E. A. Robertson, Luke J. Jones, Tianrui Wang, John S. Loveday, Graeme J. Ackland*, Oliver L. G. Alderman and John E. Proctor*, ","doi":"10.1021/acs.jpcb.5c0001810.1021/acs.jpcb.5c00018","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00018https://doi.org/10.1021/acs.jpcb.5c00018","url":null,"abstract":"We performed a series of neutron scattering experiments on deeply subcritical liquid nitrogen at 90 K (0.7TC). Our findings, when taken together with our previous results at 160 K (1.27TC) and 300 K (2.4TC), allow the Frenkel line phenomenon to be characterized in a reliable and consistent manner over an extremely broad temperature range, extending into the subcritical regime. Through an analysis of local order, we show how the fluid structure changes as the Frenkel line is crossed and present a new method for identifying the line. Our determination of coordination numbers shows a remarkable data collapse when plotted against density. This allows us to produce a universal relationship relating the coordination number to the density of a simple fluid, dictated by molecular/atomic size and its density on the melt line.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 13","pages":"3420–3427 3420–3427"},"PeriodicalIF":2.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpcb.5c00018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143758909","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}

引用次数: 0

How Does an Anti-Cancer Peptide Passively Permeate the Plasma Membrane of a Cancer Cell and Not a Normal Cell?

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-24 DOI: 10.1021/acs.jpcb.5c00680

Alfredo E Cardenas, Ehud Neumann, Yang Sung Sohn, Taylor Hays, Rachel Nechushtai, Lauren J Webb, Ron Elber

{"title":"How Does an Anti-Cancer Peptide Passively Permeate the Plasma Membrane of a Cancer Cell and Not a Normal Cell?","authors":"Alfredo E Cardenas, Ehud Neumann, Yang Sung Sohn, Taylor Hays, Rachel Nechushtai, Lauren J Webb, Ron Elber","doi":"10.1021/acs.jpcb.5c00680","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00680","url":null,"abstract":"Passive and targeted delivery of peptides to cells and organelles is a fundamental biophysical process controlled by membranes surrounding biological compartments. Embedded proteins, phospholipid composition, and solution conditions contribute to targeted transport. An anticancer peptide, NAF-144-67, permeates to cancer cells but not to normal cells. The mechanism of this selectivity is of significant interest. However, the complexity of biomembranes makes pinpointing passive targeting mechanisms difficult. To dissect contributions to selective transport by membrane components, we constructed simplified phospholipid vesicles as plasma membrane (PM) models of cancer and normal cells and investigated NAF-144-67 permeation computationally and experimentally. We use atomically detailed simulations with enhanced sampling techniques to study kinetics and thermodynamics of the interaction. Experimentally, we study the interaction of the peptide with large and giant unilamellar vesicles. The large vesicles were investigated with fluorescence spectroscopy and the giant vesicles with confocal microscopy. Peptide permeation across a model of cancer PM is more efficient than permeation across a PM model of normal cells. The investigations agree on the mechanism of selectivity, which consists of three steps: (i) early electrostatic attraction of the peptide to the negatively charged membrane, (ii) the penetration of the peptide hydrophobic N-terminal segment into the lipid bilayer, and (iii) exploiting short-range electrostatic forces to create a defect in the membrane and complete the permeation process. The first step is kinetically less efficient in a normal membrane with fewer negatively charged phospholipids. The model of a normal membrane is less receptive to defect creation in the third step.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690512","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

Molecular Dynamics Investigation into the Stability of KRas and CRaf Multimeric Complexes

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-24 DOI: 10.1021/acs.jpcb.4c0876710.1021/acs.jpcb.4c08767

Chongli Geng, Juan Zeng, Xianming Deng*, Fei Xia* and Xin Xu*,

{"title":"Molecular Dynamics Investigation into the Stability of KRas and CRaf Multimeric Complexes","authors":"Chongli Geng, Juan Zeng, Xianming Deng*, Fei Xia* and Xin Xu*, ","doi":"10.1021/acs.jpcb.4c0876710.1021/acs.jpcb.4c08767","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08767https://doi.org/10.1021/acs.jpcb.4c08767","url":null,"abstract":"In the Ras/Raf/MAPK signaling pathway, Ras and Raf proteins interact synergistically to form a tetrameric complex. NMR experiments have demonstrated that Ras dimerizes in solution and binds stably to Raf, forming Ras·Raf complexes. In this study, we constructed the ternary and quaternary complexes of KRas and CRaf based on crystal structures, denoted as (KRas)2·CRaf and (KRas)2·(CRaf)2, respectively. Molecular dynamics (MD) simulations were performed to investigate the stability of these complexes, while hydrogen bonds as well as salt bridges formed at the protein–protein interaction interfaces were analyzed based on simulation trajectories. The results revealed that the KRas·CRaf complex is more stable in explicit solvent compared with the KRas dimer. Formation of the stable quaternary complex (KRas)2·(CRaf)2 might be attributed to the association of two binary KRas·CRaf complexes. Additionally, MD simulations of the KRasG12D·CRaf complex revealed a stable and extended binding site at the KRas–CRaf interaction interface. This binding site was identified as a potential therapeutic target to block abnormal signal transmission in the pathway.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 13","pages":"3306–3316 3306–3316"},"PeriodicalIF":2.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143758831","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