Michael P. Liesen, Ryan L. Hayes, Charles L. Brooks III, Jonah Z. Vilseck
{"title":"Multiple Molecule λ-Dynamics: Probing Drug Resistance with Concurrent Protein and Ligand Perturbations","authors":"Michael P. Liesen, Ryan L. Hayes, Charles L. Brooks III, Jonah Z. Vilseck","doi":"10.1021/acs.jpclett.5c00467","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c00467","url":null,"abstract":"Though commonly used in drug discovery, alchemical free energy calculations have not been extensively used to explore issues of drug resistance caused by missense mutations to a drug target. Unlike traditional methods, λ-dynamics (λD) can evaluate multiple modifications within a single simulation; however, perturbations on more than one molecule, e.g., in a ligand and receptor, have not been performed previously. In an approach referred to as Multiple Molecule λ-Dynamics (MMλD), simultaneous ligand and protein perturbations are performed in a single simulation to sample a small series of ligands bound to native and T315I mutant Abl kinases, a protein target in chronic myelogenous leukemia associated with drug resistance. MMλD agreement with conventional λD calculations and experiments is high, with mean unsigned errors of 0.21 and 0.94 kcal/mol, respectively. Protein sequence specific ligand conformational sampling is also identified. Collectively, this work demonstrates that MMλD is a valuable tool for drug resistance drug discovery.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"64 2 1","pages":""},"PeriodicalIF":6.475,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144278913","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}
Gestél C Kuyler, Elaine Barnard, Randy D Cunningham, Sinothando Sibariboyi, Luke White, Ilanie Wessels, Michael-Phillip Smith, Bennie Motloung, Bert Klumperman
{"title":"Amphiphilic Copolymers and Their Role in the Study of Membrane Proteins.","authors":"Gestél C Kuyler, Elaine Barnard, Randy D Cunningham, Sinothando Sibariboyi, Luke White, Ilanie Wessels, Michael-Phillip Smith, Bennie Motloung, Bert Klumperman","doi":"10.1021/acs.jpclett.5c00680","DOIUrl":"10.1021/acs.jpclett.5c00680","url":null,"abstract":"<p><p>Amphiphilic copolymers have revolutionized the study of membrane proteins (MPs), where MPs are known to be critical targets in pharmaceutical development due to their roles in various physiological processes. Traditionally, MP extraction has relied on detergents, which often compromise the protein integrity. Advancements over the past 15 years include the use of poly(styrene-<i>co</i>-maleic acid) (SMA) to form nanoscale SMALPs (styrene maleic acid lipid particles), enabling detergent-free MP extraction. SMALPs preserve the native environment of MPs, facilitating their detailed analysis through a wide range of biophysical techniques. Despite their advantages, SMA-based technologies face challenges such as sensitivity to divalent cations and instability under low pH conditions. Ongoing research focuses on developing next-generation polymers with enhanced properties, utilizing controlled polymerization techniques to obtain narrow molecular weight distributions and chain-end functionality. This paper explores various SMA derivatives and alternative polymer systems like poly(diisobutylene-<i>alt</i>-maleic acid) (DIBMA) and polymethacrylates, offering potential solutions to current limitations and expanding the toolkit for MP research and application.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":" ","pages":"5784-5799"},"PeriodicalIF":4.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12169657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207217","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}
Christian Brennan, Kiyoung Jo, Chih-Feng Wang, Alan G. Joly, Brian T. O’Callahan, William Edward Farias, Alexander Donald Bielicki, Alem Teklu, Leilei Shi, Qian Zhang, Narayanan Kuthirummal, Ming Hu, Rongying Jin and Yu Gong*,
{"title":"Cavity-Assisted Coherent Phonon Generation and Control in a WSe2/Au Structure","authors":"Christian Brennan, Kiyoung Jo, Chih-Feng Wang, Alan G. Joly, Brian T. O’Callahan, William Edward Farias, Alexander Donald Bielicki, Alem Teklu, Leilei Shi, Qian Zhang, Narayanan Kuthirummal, Ming Hu, Rongying Jin and Yu Gong*, ","doi":"10.1021/acs.jpclett.5c0119010.1021/acs.jpclett.5c01190","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c01190https://doi.org/10.1021/acs.jpclett.5c01190","url":null,"abstract":"<p >Coherent phonons in the Terahertz (THz) regime have gained attention as potential candidates for next-generation high-speed, low-energy information carriers in atomically thin phononic or phonon-integrated on-chip devices. Nevertheless, achieving efficient control of the phonon generation dynamics over THz coherent phonons continues to pose a considerable challenge. In this work, we explore THz coherent phonon generation in exfoliated van der Waals (vdW) flakes of WSe<sub>2</sub> on Au (WSe<sub>2</sub>/Au) and Si (WSe<sub>2</sub>/Si) by using time-resolved pump–probe spectroscopy. The generation of THz coherent phonons was studied as a function of the WSe<sub>2</sub> layer thickness and laser wavelength. Notably, a significant enhancement in THz coherent phonon generation was observed in the WSe<sub>2</sub>/Au structure, but only within a specific range of WSe<sub>2</sub> thicknesses and laser wavelengths. The results from numerical simulations, which consider a self-hybridized optical cavity depending on WSe<sub>2</sub> thickness and optical reflectance and Raman spectroscopy measurements, all align well with the time-domain observations of THz coherent phonon generation. We propose that the observed enhancement in THz coherent phonon generation is strongly influenced by light–matter interactions in the WSe<sub>2</sub> cavity, a mechanism that may be applicable to a broader range of vdW materials. These findings offer promising insights for the development of THz phononic or phonon-integrated devices.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"16 24","pages":"6226–6233 6226–6233"},"PeriodicalIF":4.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144312374","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":"Cavity-Mediated Collective Resonant Suppression of Local Molecular Vibrations","authors":"Vasil Rokaj, Ilia Tutunnikov, H. R. Sadeghpour","doi":"10.1021/acs.jpclett.5c01124","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c01124","url":null,"abstract":"Recent advances in polaritonic chemistry suggest that chemical reactions can be controlled via collective vibrational strong coupling (VSC) in a cavity. In this fully analytical work, we demonstrate that the collective vibrations of a molecular ensemble under VSC execute a beating with a period inversely proportional to the collective vacuum Rabi splitting. Significantly, this collective beating is imprinted on the local dynamics and resonantly suppresses individual molecular vibrations when a fraction of molecules is vibrationally excited, as in activated complexes formed in chemical reactions. This emergent beating occurs on significantly longer time scales than the individual molecular vibration or the cavity field oscillation period, peaking at the cavity-molecule resonance, consistent with polaritonic chemistry experiments. The cavity mediates an energy exchange between excited and ground-state molecules, affecting the dynamics of the entire ensemble. These findings suggest that the dynamics in polaritonic chemical reactions may not be in full equilibrium. In the ultrastrong coupling regime, we find that the local vibrations are modified by the cavity even at short time scales. Notably, these dynamical effects also extend to isotropic molecular ensembles in our model. Our analytical model offers insights into how collective VSC can dampen local molecular vibrations at resonance, potentially altering chemical reactivity.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"19 1","pages":""},"PeriodicalIF":6.475,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144269418","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}
Wenhui Deng, Yuhao Luo, Kewei Wu, Yanqiu Wang, Hongtao Liu, Xiaoqing Qiu, Kang Liu, Junwei Fu, Wenzhang Li, Min Liu
{"title":"Self-Catalyzed Carbon Nanotubes with Dual-Active-Site Co/CoN4 Motifs for High-Efficiency Bifunctional Oxygen Electrocatalysis","authors":"Wenhui Deng, Yuhao Luo, Kewei Wu, Yanqiu Wang, Hongtao Liu, Xiaoqing Qiu, Kang Liu, Junwei Fu, Wenzhang Li, Min Liu","doi":"10.1021/acs.jpclett.5c01105","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c01105","url":null,"abstract":"Carbon nanotubes (CNTs) have garnered significant attention due to their large specific surface area and efficient mass transfer properties. However, the construction of well-ordered CNT catalysts with high-efficiency bifunctional oxygen electrocatalytic activity remains a significant challenge. Herein, the uniform size of CNTs with high-density dual-active-site Co/CoN<sub>4</sub> motifs (A-Co/Co-NC) is rationally designed and fabricated through an in situ metal–ligand anchoring method (N → Co<sup>2+</sup>) followed by a pyrolysis process. The selected 2,6-diaminopurine (DAP) can anchor and disperse Co ions in N sites, which will form uniform CNTs with Co NPs and CoN<sub>4</sub> active sites during the pyrolysis process. Theoretical calculation and in situ characteristics clearly proved that Co NP works as an OER active unit and that CoN<sub>4</sub> acts as an ORR active site. Benefiting from the high-density dual-active-site Co/CoN<sub>4</sub> motifs, the A-Co/Co-NC catalyst displays superior bifunctional performance (<i>ΔE</i> = 0.76 V). Therefore, the A-Co/Co-NC-based zinc–air battery (ZAB) exhibits distinguished reversibility. Remarkably, the A-Co/Co-NC-based Al–air battery (AAB) has a high power density (129.12 mW cm<sup>–2</sup>). This work provides a feasible design concept to obtain well-organized CNTs with highly dispersed active sites.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"22 1","pages":""},"PeriodicalIF":6.475,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144269450","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":"Brief Guide to Transformation of Constant Phase Element Impedance to Equivalent Capacitor or Inductor","authors":"Juan Bisquert*, and , Enrique H. Balaguera, ","doi":"10.1021/acs.jpclett.5c0113110.1021/acs.jpclett.5c01131","DOIUrl":"https://doi.org/10.1021/acs.jpclett.5c01131https://doi.org/10.1021/acs.jpclett.5c01131","url":null,"abstract":"<p >Formulas to convert the impedance parameters of a Constant Phase Element into an equivalent capacitor or inductor are provided, using the time constant associated with an additional resistance in the equivalent circuit. We justify the formulas and show the interpretation for both frequency domain impedance spectroscopy measurements and time domain transient charging current.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"16 23","pages":"5779–5783 5779–5783"},"PeriodicalIF":4.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144261022","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}
Rentong Duan, Yang Li, Shengnan Feng, Fengrui Hu, Yan Lv, Chunfeng Zhang, Min Xiao, Xiaoyong Wang
{"title":"Neutral-Exciton Emission from Single Perovskite Nanocrystals Memorizing the Pre-Existence of a Local Electric Field.","authors":"Rentong Duan, Yang Li, Shengnan Feng, Fengrui Hu, Yan Lv, Chunfeng Zhang, Min Xiao, Xiaoyong Wang","doi":"10.1021/acs.jpclett.5c01084","DOIUrl":"10.1021/acs.jpclett.5c01084","url":null,"abstract":"<p><p>Semiconductor lead-halide perovskite nanocrystals (NCs) are associated with a soft ionic lattice interacting strongly with the photogenerated charge carriers, which can bring about very novel photophysical properties in these quantum-confined materials with a large surface-to-volume ratio. Here we have performed high-resolution optical measurements on single perovskite CsPbI<sub>3</sub> NCs at the cryogenic temperature of ∼4 K, with a specific focus on how an extra charge trapped on the surface influences the recombination energies of their neutral and charged excitons. As expected, the surface-trapped charge can impart a local electric field on the charged exciton inside a single CsPbI<sub>3</sub> NC, leading to the shift of its recombination energy mainly by the quantum-confined Stark effect. Interestingly, the neutral-exciton recombination energy is also shifted even after the surface-trapped charge has disappeared for a time period longer than ∼2 μs, signifying that the lattice distortion induced by the previous local electric field is not fully relaxed at this time scale. The above findings have established very unique charge-property relationships in lead-halide perovskite NCs, the understanding and manipulation of which are critical to their practical performance in various classical and quantum optical applications.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":" ","pages":"5827-5834"},"PeriodicalIF":4.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214387","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}
Ida Moszczyńska, Marek Szafrański, Andrzej Katrusiak
{"title":"New Osmocene and Ruthenocene Phases Reveal the Common Conformational Behavior Regulated by Anagostic Bonds in Prototypical Metallocenes.","authors":"Ida Moszczyńska, Marek Szafrański, Andrzej Katrusiak","doi":"10.1021/acs.jpclett.5c00686","DOIUrl":"10.1021/acs.jpclett.5c00686","url":null,"abstract":"<p><p>Ruthenocene and osmocene, under normal conditions isostructural to low-temperature ferrocene phase III, have been regarded as prototypical metallocenes exclusively present in the energetically favored eclipsed conformation. This strong preference contrasts with ferrocene, which exhibits the staggered, rotated, eclipsed, disordered, and modulated conformations in its five polymorphic forms. Here we show that ruthenocene at 394.0 K and osmocene at 421.5 K transform to new higher-symmetry isostructural phases, where the cyclopentadienyl rings become disordered in two modes: seesaw tilts hinged on the metal cation and rotations about the molecular pseudo-<i>C</i><sub>5</sub> axis. The transitions entropy change and the Fourier transformations of the diffraction data indicate the hindered rotations, with molecules dynamically disordered between the staggered and eclipsed conformations, whereas in the final structural models the electron density distribution around the rings, calculated from the atomic displacement parameters of refined atomic sites, is continuous. For the prototypical metallocenes, a common pattern of transformations leading to disordered conformations has been connected with intramolecular anagostic bonds CH···<i>M</i> (<i>M</i> = Fe, Ni, Ru, Os). Their strength correlates with the critical temperatures of phase transitions when the anagostic bonds are broken.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":" ","pages":"5755-5762"},"PeriodicalIF":4.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12169653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207133","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}
Nastasia Mauger, Thomas Plé, Louis Lagardère, Simon Huppert, Jean-Philip Piquemal
{"title":"The Q-AMOEBA (CF) Polarizable Potential.","authors":"Nastasia Mauger, Thomas Plé, Louis Lagardère, Simon Huppert, Jean-Philip Piquemal","doi":"10.1021/acs.jpclett.5c00797","DOIUrl":"10.1021/acs.jpclett.5c00797","url":null,"abstract":"<p><p>We present Q-AMOEBA (CF), an enhanced version of the Q-AMOEBA polarizable model that integrates a geometry-dependent charge flux (CF) term while designed for an explicit treatment of nuclear quantum effects (NQE). The inclusion of CF effects allows matching experimental data for the molecular structure of water in both gas and liquid phases, addressing limitations faced by most force fields. We show that Q-AMOEBA (CF) provides highly accurate results for a wide range of thermodynamical properties of liquid water. Using the computational efficiency of the adaptive Quantum Thermal Bath method, which accounts for NQE at a cost comparable to classical molecular dynamics, we evaluate the robustness and transferability of Q-AMOEBA (CF) by calculating hydration free energies of various ions and organic molecules. Finally, we apply this methodology to the alanine dipeptide and compute the corresponding dihedral angle potential of mean force and hydration free energy. Unexpectedly, the latter quantity displays significant NQE. These results pave the way to a finer understanding of their role in biochemical systems.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":" ","pages":"5723-5731"},"PeriodicalIF":4.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207136","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}
Pietro Nicolò Brangi, Francesca Martini, Pierluigi Cudazzo, Matteo Calandra
{"title":"Interplay of Superconductivity, Ferromagnetism, and Half-Metallicity in Gated Single-Layer g-C<sub>3</sub>N<sub>4</sub>.","authors":"Pietro Nicolò Brangi, Francesca Martini, Pierluigi Cudazzo, Matteo Calandra","doi":"10.1021/acs.jpclett.5c01013","DOIUrl":"10.1021/acs.jpclett.5c01013","url":null,"abstract":"<p><p>Graphitic carbon nitride (g-C<sub>3</sub>N<sub>4</sub>) hosts lone pairs arising from broken carbon-nitrogen bonds in its heptazine structure. These strongly localized and weakly hybridized states form ultraflat bands, potentially leading to correlated states when doped. Using first-principles calculations, we show that field-effect hole doping in single-layer g-C<sub>3</sub>N<sub>4</sub> depletes these lone pairs, unveiling a rich phase diagram with a complex interplay of superconducting, half-metallic, and insulating ferromagnetic phases, even at very low charging and in the absence of transition metal ions. Our work highlights gated two-dimensional systems hosting lone pairs as a novel platform for strongly correlated states.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":" ","pages":"5739-5744"},"PeriodicalIF":4.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12169656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207132","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}