The Journal of Physical Chemistry B最新文献

{"title":"Initial Conditions for Excited-State Dynamics in Solvated Systems: A Case Study.","authors":"Ethan R Curtis, Chey M Jones, Todd J Martínez","doi":"10.1021/acs.jpcb.4c06536","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06536","url":null,"abstract":"<p><p>Simulating excited-state dynamics or computing spectra for molecules in condensed phases requires sampling the ground state to generate initial conditions. Initial conditions (or snapshots for spectra) are typically produced by QM/MM Boltzmann sampling following MM equilibration or optimization. Given the switch from a MM to a QM/MM potential energy surface, one should discard a set period of time (which we call the \"healing time\") from the beginning of the QM/MM trajectory. Ideally, the healing time is as short as possible (to avoid unnecessary computational effort), but long enough to equilibrate to the QM/MM ground state distribution. Healing times in previous studies range from tens of femtoseconds to tens of picoseconds, suggesting the need for guidelines to choose a healing time. We examine the effect of healing time on the nonadiabatic dynamics and spectrum of a first-generation Donor-Acceptor Stenhouse Adduct in chloroform. Insufficient healing times skew the branching ratio of ground state products and alter the relaxation time for one pathway. The influence of the healing time on the absorption spectrum is less pronounced, warning that the spectrum is not a sensitive indicator for the quality of a set of initial conditions for dynamics. We demonstrate that a reasonable estimate for the healing time can be obtained by monitoring the solute temperature during the healing trajectory. We suggest that this procedure should become standard practice for determining healing times to generate initial conditions for nonadiabatic QM/MM simulations in large molecules and condensed phases.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389521","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":"Intermolecular Forces in Bioactive Resveratrol Complexes with Alcohols: A Study of Stability and Electronic Structure.","authors":"Natarajan Elangovan, Natarajan Arumugam, Madhappan Santhamoorthy, Renjith Thomas","doi":"10.1021/acs.jpcb.4c08634","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08634","url":null,"abstract":"<p><p>Noncovalent interactions, particularly hydrogen bonding, play a pivotal role in determining the structural stability and functional properties of molecules, including bioactive compounds like resveratrol. This study focuses on the hydrogen-bonding behavior and other noncovalent interactions in gas-phase resveratrol-ethanol (EtOH) and resveratrol-methanol (MtOH) complexes, referred to as System 1 and System 2, respectively. These systems were optimized using the ωB97XD functional and cc-pVDZ basis set, providing a detailed picture of their stability and intermolecular interactions. By employing advanced methods such as Domain-Based Local Pair Natural Orbital Coupled Cluster (DLPNO-CCSD)(T) for energy decomposition, natural bond orbital (NBO) for charge analysis, atoms in molecule (AIM) for electron density topology, and noncovalent interaction (NCI) techniques, we decompose interaction energies into meaningful components like electrostatic, dispersion, and exchange-repulsion. The findings indicate that, while hydrogen bonding contributes to the stability of these complexes, London dispersion and other attractive interactions are substantial factors as well. The resveratrol-EtOH and resveratrol-MtOH systems demonstrate a robust electronic environment with significant contributions from various intermolecular forces, underscoring the importance of noncovalent interactions in stabilizing bioactive compounds. This study adds to our understanding of molecular interactions in resveratrol complexes, with potential implications for medicinal chemistry and material science, particularly where solvation effects are critical.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389522","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":"Tuning Low-Density Liquid Water with MgCl₂.","authors":"Hamad Ashraf, Payam Kalhor, Jin-Cheng Liu, Zhi-Wu Yu","doi":"10.1021/acs.jpcb.4c08266","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08266","url":null,"abstract":"<p><p>Perceiving a suitably tuned aqueous solution to unravel water's liquid-liquid critical point (LLCP) has become challenging. In this work, we investigated the structures of light and heavy water in the presence of MgCl₂ using excess infrared spectroscopy and density functional theory calculations. The excess spectroscopy enabled us to differentiate the low-density liquid (LDL) water from the other liquid domains of pure water and reveal the new interaction modes between water and the ions. The addition of salt decreases and then increases the population of LDL in aqueous solutions. At the concentrations of 0.4 M in H₂O and 0.6 M in D₂O, the LDL structures undergo the most significant disruption under ambient conditions in the bulk phase. Furthermore, threshold concentrations of 1 and 1.3 M for light and heavy water, respectively, were found to induce higher LDL populations. The current investigation sheds light on the intriguing liquid-liquid phase transition (LLPT) and the LLCP of water.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389523","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":"All-Atom Molecular Dynamics Simulations of Grafted Poly(<i>N</i>,<i>N</i>-dimethylaminoethyl methacrylate) Brushes.","authors":"Simon Tippner, David Hernández-Castillo, Felix H Schacher, Leticia González","doi":"10.1021/acs.jpcb.4c07928","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07928","url":null,"abstract":"<p><p>Modeling polymer brushes is essential for understanding their complex behavior at surfaces and interfaces, enabling the design of materials with tunable properties. We present a computational protocol to model polymer brushes composed of grafted, brush-like chains of the charged polymer poly(<i>N</i>,<i>N</i>-dimethylaminoethyl methacrylate) (p(DMAEMA)) using an all-atom representation that captures detailed molecular interactions and structural properties. The approach is flexible and non-grid-based and allows for randomized strand configurations and the incorporation of periodic boundary conditions, enabling the construction of asymmetric polymer brush setups. An atactic p(DMAEMA) configuration is demonstrated as an example, though the protocol can be readily adapted to construct other brush-like polymer systems with varying tacticities or compositions, depending on the pH environment. Furthermore, this can be extended to stimuli-responsive materials, which generate conformation or charge upon changes in pH value or other external triggers. Molecular dynamics simulations are then employed to gain insights into the conformational behavior of the grafted p(DMAEMA) brushes and their surrounding aqueous environment, as well as their response to temperature, protonation, and variations in grafting densities, in terms of the solvent-accessible surface area, radius of gyration, and radial distribution functions. This versatile protocol provides a robust tool for simulating and analyzing the properties of diverse polyelectrolyte polymer brush systems and also as composite materials.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389519","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 Interaction of RBD with Human β Defensin Type 2 Point Mutants: Insights from Molecular Dynamics Simulations.","authors":"Ishrat Jahan, Liqun Zhang","doi":"10.1021/acs.jpcb.4c07004","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07004","url":null,"abstract":"<p><p>The global health crisis triggered by the SARS-CoV-2 virus has highlighted the urgent need for effective treatments. As existing drugs are not specifically targeted at this virus, there is a growing interest in exploring natural antimicrobial peptides such as defensin as potential therapeutic options. Human β defensin type 2 (hBD-2), which is a cationic cysteine-rich peptide, serves as the initial barrier against bacterial and fungal invaders in mammals. It can bind with Spike-RBD and occupy the same site as the ACE2 receptor, thereby hindering viral entry into cells expressing ACE2. To explore the effect of different point mutations on the binding of hBD-2 with RBD, the binding dynamics and interactions between hBD-2 point mutants with RBD were studied and compared with that of RBD&hBD-2 wild-type complex. In total, 247 hBD-2 point mutants were built with the mutation sites at the binding region of hBD-2 (RES18-30) with the RBD of CoV-2. All-atom molecular dynamics simulations were carried out on RBD binding with hBD-2 point mutants. Analysis based on root-mean-square deviation (RMSD), hydrogen bonds analysis, and binding free energy using the MM/PBSA method revealed that many point mutants of hBD-2 exhibit weaker binding with RBD compared to the wild type; however, a subset of mutants, including C20I, C20K, R22W, R23H, R23L, Y24L, K25F, K25H, G28Y, T29R, and C30K, displayed enhanced binding with RBD. The findings can offer insights designing hBD-2-based novel drugs to combat SARS-CoV-2 in the long term.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389520","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":"Asynchronous and Interferometric Nonlinear Spectroscopy (AI-NS): Expanding Temporal and Spectral Horizons.","authors":"Gi Rim Han, Hyunmin Jang, Tai Hyun Yoon, Minhaeng Cho","doi":"10.1021/acs.jpcb.4c08228","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08228","url":null,"abstract":"<p><p>Since the advent of time-resolved spectroscopy based on precision frequency technology of laser sources, it has been considered an alternative way to study dynamic processes in photochemical systems. This Perspective introduces asynchronous and interferometric nonlinear spectroscopy (AI-NS), a spectroscopic technique that combines asynchronously generated laser pulses and interferometric detection, offering an unprecedented temporal dynamic range with high spectral resolution and rapid data acquisition capabilities. By eliminating the need for mechanical delay stages, AI-NS facilitates the rapid collection of time-resolved data on dynamics ranging from femtoseconds to nanoseconds while simultaneously distinguishing frequency-dependent responses. Here, we detail the technical methodology of AI-NS and explore its applications to the studies of various systems, including semiconductors and biological systems. Additionally, we highlight prospective advancements, such as integration with multidimensional spectroscopy techniques. AI-NS not only expands the scope of spectroscopic analysis but also opens new avenues for the exploration of diverse materials and molecular systems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143363270","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":"Nuclear Magnetic Resonance and Computational Studies of Sodium Ions in an Ionic Liquid/Water Mixture.","authors":"Katarzyna Dziubinska-Kühn, Renaud B Jolivet, Christopher A Rumble","doi":"10.1021/acs.jpcb.4c08267","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08267","url":null,"abstract":"<p><p>We report a computational protocol for simulating electric field gradient dynamics around Na⁺ cations in mixtures of 1-ethyl-3-methylimidazolium tetrafluoroborate ([Im₂₁][BF₄]) and water validated by comparison to measurements of nuclear magnetic resonance (NMR) <i>T</i>₁ relaxation times. Our protocol combines classical molecular dynamics simulations of a scaled charge model of [Im₂₁][BF₄] and TIP4Pew water to generate the electric field gradient (EFG) correlation function, <i>C</i>_EFG(<i>t</i>), with quantum chemical calculations for determining the EFG variance <math><mo>⟨</mo><msubsup><mi>V</mi><mrow><mi>z</mi><mi>z</mi></mrow><mn>2</mn></msubsup><mo>⟩</mo></math>. Although we demonstrate that the Sternheimer approximation is as valid in these mixtures as it is in neat water, we do not recommend using the Sternheimer approximation as it underestimates <math><mo>⟨</mo><msubsup><mi>V</mi><mrow><mi>z</mi><mi>z</mi></mrow><mn>2</mn></msubsup><mo>⟩</mo></math> by ∼10% compared to a set of computationally efficient density functional theory calculations. Our protocol is capable of reproducing both the composition- and temperature-dependence of <i>T</i>₁ over the full range of experimentally accessible [Im₂₁][BF₄]/water compositions and a temperature range of 285-350 K. We also show that scaling the [Im₂₁][BF₄] charges does not simply speed up the dynamics of the solvent, but has effects on the shape of <i>C</i>_EFG(<i>t</i>). Following validation of our protocol, we analyze the shape and relaxation times of <i>C</i>_EFG(<i>t</i>) to show that the mechanism by with <i>T</i>₁ changes is different when the composition of the mixture varies compared to changes in temperature. As composition changes, the balance between inertial and diffusive relaxation alters, whereas temperature only affects the time scale of the diffusion portion of the relaxation. We also show that solvation shell of Na⁺ in these mixtures is significantly more labile than in neat [Im₂₁][BF₄] and that water and BF₄^- anions compete to be in the Na⁺ solvation shell. This validated computational protocol opens the door to more detailed interpretation of NMR <i>T</i>₁ relaxation experiments of monatomic ions in complex liquid environments.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143363276","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":"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":"1462-1474"},"PeriodicalIF":2.8,"publicationDate":"2025-02-06","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":"Flexible Tail of Antimicrobial Peptide PGLa Facilitates Water Pore Formation in Membranes.","authors":"Chunsuo Tian, Xuyang Liu, Yuelei Hao, Haohao Fu, Xueguang Shao, Wensheng Cai","doi":"10.1021/acs.jpcb.4c06190","DOIUrl":"10.1021/acs.jpcb.4c06190","url":null,"abstract":"<p><p>PGLa, an antimicrobial peptide (AMP), primarily exerts its antibacterial effects by disrupting bacterial cell membrane integrity. Previous theoretical studies mainly focused on the binding mechanism of PGLa with membranes, while the mechanism of water pore formation induced by PGLa peptides, especially the role of structural flexibility in the process, remains unclear. In this study, using all-atom simulations, we investigated the entire process of membrane deformation caused by the interaction of PGLa with an anionic cell membrane composed of dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylglycerol (DMPG). Using a deep learning-based key intermediate identification algorithm, we found that the C-terminal tail plays a crucial role for PGLa insertion into the membrane, and that with its assistance, a variety of water pores formed inside the membrane. Mutation of the tail residues revealed that, in addition to electrostatic and hydrophobic interactions, the flexibility of the tail residues is crucial for peptide insertion and pore formation. The full extension of these flexible residues enhances peptide-peptide and peptide-membrane interactions, guiding the transmembrane movement of PGLa and the aggregation of PGLa monomers within the membrane, ultimately leading to the formation of water-filled pores in the membrane. Overall, this study provides a deep understanding of the transmembrane mechanism of PGLa and similar AMPs, particularly elucidating for the first time the importance of C-terminal flexibility in both insertion and oligomerization processes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1453-1461"},"PeriodicalIF":2.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027479","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, Vikum K Dewasurendra, Mst Nigar Sultana, Sultan Mahmud, Chandrima Banerjee, Mohammad Rahman, Peng Li, David E Clemmer, Matthew B Johnson, Stephen J Valentine","doi":"10.1021/acs.jpcb.4c04842","DOIUrl":"10.1021/acs.jpcb.4c04842","url":null,"abstract":"<p><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 (<+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 (>+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":" ","pages":"1626-1639"},"PeriodicalIF":2.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057502","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}