The Journal of Physical Chemistry B最新文献

{"title":"The Role of Electron Donating Ability of Pendant Groups in the Photophysics of Donor-Acceptor-Donor Diaminoterephthalate Derivatives.","authors":"Arkaprava Chowdhury, Sucheta Kundu, Souradip Dasgupta, Ayushi Chand, Anindya Datta","doi":"10.1021/acs.jpcb.5c02113","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02113","url":null,"abstract":"<p><p>The electron-donating ability of the pendant group has been found to have a very strong influence on the excited state processes of donor-acceptor-donor diaminoterephthalate derivatives. The derivative with the strongest electron donating moiety is found to have the maximum degree of stabilization of the dipolar excited state in polar solvents, while the emission of the one with the weakest electron donor originates from a relatively less stabilized charge transfer state. Blue shifted emission band along with significantly increased lifetime at low temperature (77 K) bolsters the contention behind intramolecular charge transfer (ICT) as the main excited state process involved in this library of molecules.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525435","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":"Microscopic Solvation Dynamics and Transport in LiFSA-Sulfone Electrolytes via Optimized Force Fields: A Classical MD Perspective.","authors":"Yati, Anirban Mondal","doi":"10.1021/acs.jpcb.5c02097","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02097","url":null,"abstract":"<p><p>Lithium bis(fluorosulfonyl)amide (LiFSA) is a commonly used lithium salt in electrolyte formulations due to its electrochemical stability, favorable ionic dissociation, and potential for enhancing lithium-ion transport in energy storage applications. Understanding the solvation dynamics and transport properties of LiFSA, particularly in mixtures with sulfone-based solvents, is crucial for optimizing electrolyte performance. Accurate force field parametrization is essential for simulating complex electrolyte systems with reliable predictive power. This study presents a robust workflow combining a genetic algorithm (GA) and Gaussian process regression (GPR) to develop optimized Lennard-Jones parameters for pure LiFSA, which are subsequently transferred to LiFSA-sulfone mixtures. The optimized parameters accurately capture nonbonded interactions and reproduce experimental transport properties, including viscosity and ionic conductivity, with deviations within 7.5%. Using the Green-Kubo formalism, viscosity and conductivity trends were computed and linked to solvation dynamics, revealing that mixtures containing symmetric sulfones (sulfolane and dimethyl sulfone) exhibit lower viscosities and higher conductivities compared to those with asymmetric sulfones (ethyl methyl sulfone and 3-methyl sulfolane). Analysis of relative coordination numbers further demonstrates the pivotal role of solvent oxygen (O_S) in modulating ion transport, with enhanced O_S coordination reducing viscosity and improving conductivity by facilitating ion mobility. This study provides a microscopic understanding of how ion-solvent interactions and solvation structures govern macroscopic transport behavior. The GA-GPR parametrization framework not only delivers transferable force fields capable of accurately predicting electrolyte properties but also offers practical insights for tailoring electrolytes with optimized performance in energy storage and conversion applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525432","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":"Binding Free Energy Calculations Based on the Path Collective Variable along a String Pathway.","authors":"Alessia Ghidini, Andrea Cavalli, Benoît Roux","doi":"10.1021/acs.jpcb.5c02258","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02258","url":null,"abstract":"<p><p>Calculating the binding free energy of small drug-like molecules to a macromolecular receptor is one of the most important applications of molecular dynamics simulations. One computational approach (the \"geometrical route\") seeks to determine the binding free energy of a ligand by calculating the potential of mean force along a physical path corresponding to the dissociation of the ligand from its receptor. We show here that it is possible to rigorously map the entire ligand-receptor separation process onto a curvilinear separation pathway constructed from the string method and then sample the longitudinal and orthogonal order parameters defined from the Path Collective Variable (PCV) along this pathway to calculate the binding free energy. The theory is illustrated by computing the absolute binding free energy of a glycogen synthase kinase-3 beta (GSK-3β) inhibitor, and the results are compared with the result from a calculation based on the standard alchemical double decoupling approach.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525519","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 the Guanine Functionalization of Single-Wall Carbon Nanotubes.","authors":"Nima Soltani, R Bruce Weisman","doi":"10.1021/acs.jpcb.5c02824","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02824","url":null,"abstract":"<p><p>In the guanine functionalization reaction, single-wall carbon nanotubes (SWCNTs) coated with physisorbed single-stranded DNA become covalently bonded to guanine bases in the DNA. The resulting perturbations to SWCNT electronic and optical properties depend on the spacings between the sites of covalent bonding. To model those spacings, we have used advanced molecular dynamics simulations (replica exchange with solute tempering) to study adsorbed conformations of (GT)₁₀ ssDNA strands and the corresponding distributions of guanine locations prior to reaction. The simulations explored the effects of interstrand interactions, nanotube end effects, solution ionic strength, DNA/SWCNT mass ratio, and SWCNT diameter on conformations and guanine spacings. We analyzed the impacts of such simulation conditions on the spatial distribution of guanine nucleobases along the nanotube axis. Irregularities in those spacings are suggested to cause inhomogeneities in exciton energy landscapes and be a source of spectral broadening in SWCNTs modified by guanine functionalization.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525433","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":"CO₂ Capture Characteristics of Hyperbranched Poly(alkylene imine): A Molecular Dynamics Simulation Approach.","authors":"Junhe Chen, Guilherme R Weber Nakamura, Christopher W Jones, Sung Hyun Kwon, Seung Soon Jang","doi":"10.1021/acs.jpcb.5c03162","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c03162","url":null,"abstract":"<p><p>This study explores the CO₂ capture characteristics of hyperbranched poly(ethylenimine) (HB-PEI) and poly(propyleneimine) (HB-PPI) through molecular dynamics simulations using density functional theory-calibrated force fields. Key features such as density, free volume, glass transition temperature, CO₂/H₂O distribution, and molecular diffusion are systematically investigated to elucidate structure-function relationships under dry and hydrated conditions. HB-PEI demonstrates a slightly higher density and lower free volume compared to HB-PPI yet shows superior CO₂ capture due to the high amine concentration. Glass transition analysis indicates a higher thermal mobility in HB-PEI, enhancing the CO₂ diffusivity. Pair correlation and coordination analyses confirm a stronger affinity of CO₂ with primary and secondary amines, particularly in hydrated environments where water competes with CO₂ for binding sites. Despite its more compact structure, HB-PEI outperformed HB-PPI in CO₂ and H₂O transport, as confirmed by higher diffusion coefficients across all hydration levels. These findings highlight a critical balance among polymer architecture, amine accessibility, and hydration in designing next-generation solid amine sorbents for efficient direct air capture applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525521","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":"Isotope-Substitution Effects on the Thermodynamic, Dynamic, and Structural Properties of Water: H₂O, HDO, D₂O, and T₂O.","authors":"Ali Eltareb, Gustavo E Lopez, Nicolas Giovambattista","doi":"10.1021/acs.jpcb.5c01657","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01657","url":null,"abstract":"<p><p>We study the isotope-substitution effects on the thermodynamic, dynamical, and structural properties of liquid water at (i) constant molar volume (<i>v</i> = 18.0 cm³/mol, corresponding to a density for H₂O of ρ = 1.0 g/cm³) and (ii) constant pressure (<i>P</i> = 0.1 MPa) over a wide temperature range, 200 ≤ <i>T</i> ≤ 400 K. Our results are based on path-integral and classical computer simulations of H₂O, HDO, D₂O, and T₂O using the q-TIP4P/F water model. We find that some properties, such as the pressure <i>P</i>(<i>T</i>) (at constant <i>v</i>) and molar volume <i>v</i>(<i>T</i>) (at constant <i>P</i>) are weakly sensitive to isotope substitution effects, while others, including the isochoric/isobaric heat capacity, self-diffusion coefficient, vibrational density of states, and infrared (IR) spectra, are considerably affected by nuclear quantum effects (NQE). The IR spectra and diffusion coefficients obtained from ring-polymer molecular dynamics (RPMD) simulations are in very good agreement with available experimental data. Our path integral computer simulations, particularly at low temperatures, show that the (H → D → T)-substitution in water leads to a slightly <i>more structured</i> liquid with shorter (smaller OO distance) and more linear (smaller HOO angle) hydrogen bonds (HB). This is rationalized in terms of the very small <i>decrease</i> in the atom delocalization (NQE) along the sequence (H → D → T). In all three cases, the H/D/T atoms are preferentially delocalized along the direction perpendicular to the O-(H/D/T) covalent bond. The different delocalization of H/D/T leads to a <i>slightly</i> more energetic HB (<4%) and hence, to a <i>slightly</i> stronger HB-network, along the sequence H₂O → HDO → D₂O → T₂O (as NQE becomes less pronounced). Interestingly, some properties of HDO, such as the IR spectra, radial distribution functions, and HB geometry, suggest that the OD and OH covalent bonds of HDO behave, respectively, as the OD covalent bond of D₂O and the OH covalent bond of H₂O.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525431","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":"Insulin and Human Serum Albumin Interactions with Core-Shell Fe₃O₄@SiO₂ Nanoparticles Functionalized with Carboranes.","authors":"Katarzyna Ludzik, Monika Marcinkowska, Barbara Klajnert-Maculewicz, Liangliang Huang, Monika Jazdzewska, Ilya V Korolkov, Artem L Kozlovskiy, Maxim V Zdorovets, Natalia Jasiak","doi":"10.1021/acs.jpcb.5c00731","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00731","url":null,"abstract":"<p><p>In a biological medium, nanoparticles (NPs) can spontaneously interact with proteins, adsorb onto their surface, and cause conformational and orientation changes of the proteins. As a result, the protein function is influenced in a complex manner. Therefore, a detailed understanding of the nature and specificity of protein-nanoparticle interactions is crucial for the application of functional NPs in medicine. In the presented work, we studied the interactions of GMA-treated SiO₂ NPs with the Fe₃O₄ core and attached carborane compounds (Fe₃O₄/TEOS/TMSPM/GMA/Carborane), designed for boron neutron capture therapy, with human serum albumin (HSA) and insulin. We combined different techniques: spectrofluorometry, circular dichroism spectroscopy, and isothermal titration calorimetry to address this issue. The results show that the adsorption of protein onto the NP surface is enthalpy-entropy-driven, with ensuing structural changes of the protein. As for albumin, the percentage of the α-helix structure in the protein is significantly reduced from 87.59 (free protein) to 40.9% for an NP concentration of 1.8 mg/mL, while the content of the β-sheet and random coil increases from 0.48 to 8.78% and from 11.93 to 50.32%, respectively. The interaction between NPs and small protein-insulin is weaker than that for HSA, confirming less negative Δ<i>H</i> and a 15% decrease in the α-structure content for the highest concentration of NPs. For both proteins, the exposure on Fe₃O₄/TEOS/TMSPM/GMA/Carborane affects the polarity of the microenvironment around Trp, which is consequently exposed to a more hydrophobic environment. Calculated values of the radius of gyration and the minimum distance between the proteins and the NPs indicate a stronger interaction and closer binding proximity to the NPs, corroborating experimental observations of the higher binding affinity of HSA to NPs.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525430","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":"Photoactivated Nano-Compatibilized Two-Phase Polymer Blends: An Approach for Determining Mechanical Behavior.","authors":"Surbhi Khewle, Pratyush Dayal","doi":"10.1021/acs.jpcb.5c02717","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02717","url":null,"abstract":"<p><p>Light-activated polymers (LAPs) are shape-shifting materials capable of transforming their shapes in response to photoinduced chemical reactions, such as <i>cis-trans</i> isomerization and dimerization. Owing to the underlying photochemical reaction, these materials often exhibit behavior analogous to multicomponent/phase polymer blends. In this work, we present a free-energy-based theoretical framework to predict the mechanical behavior of nanoparticle-compatibilized elastic LAP blends that exhibit phase separation. In particular, we incorporate the impact of domain sizes and interfacial areas and establish a criterion for the materials' susceptibility to mechanical failure under various loading conditions, namely uniaxial and biaxial stretching. Our framework can also be adapted to high-entropy polymers and thermoresponsive or light-activated systems, with potential applications in soft robotics, biomedical devices, micromechanics, 4D printing, and material origami. Additionally, by integrating our model with physics-informed neural networks, we facilitate efficient analysis of complex domain geometries and enable comprehensive parametric studies.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525434","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":"Energies Exploration for Glycine Molecule Supported on Zinc Oxide Clusters: Computational and Experimental Study.","authors":"Laura Catalina Duque Ossa, José Gerardo Altamirano Ramírez, Brenda García Farrera, José Angel Reyes-Retana","doi":"10.1021/acs.jpcb.5c01286","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01286","url":null,"abstract":"<p><p>Density functional theory calculations of 0D (zero-dimensional) metal oxide nanomaterials and protein amino acids have been used to evaluate the disease progression for biosensing applications. In this study, the interaction of glycine with ZnO clusters was evaluated, incorporating a van der Waals correction. Glycine was rotated to interact with the nanoparticles at different active sites. Binding and cohesion energies, the density of states, and charge transfer were calculated for each system. The results indicate that glycine interacting with the ZnO(3) cluster in the <i>XZ</i>-plane exhibits greater stability due to higher binding and cohesion energies. A higher charge transfer was also observed for this interaction. Furthermore, the density of state analysis shows a significant decrease in all band gaps, indicating a reduction in the cluster's semiconductive behavior. To experimentally validate this interaction, atomic force microscopy (AFM) was performed as a proof of concept. A silicon contact tip in pinpoint mode was used with ZnO nanoparticles and a functionalized silicon wafer containing glycine. The AFM results confirm the binding affinity between glycine and ZnO nanoparticles.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504227","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":"Approximation of Anisotropic Pair Potentials Using Multivariate Interpolation.","authors":"Mohammadreza Fakhraei, Chris A Kieslich, Michael P Howard","doi":"10.1021/acs.jpcb.5c01451","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01451","url":null,"abstract":"<p><p>The interaction between two particles with shape or interaction anisotropy can be modeled by using a pairwise potential energy function that depends on their relative position and orientation; however, this function is often challenging to mathematically formulate. Data-driven approaches for approximating anisotropic pair potentials have gained significant interest due to their flexibility and generality but often require large sets of training data, potentially limiting their feasibility when training data are computationally demanding to collect. Here, we investigate the use of multivariate polynomial interpolation to approximate anisotropic pair potentials from a limited set of prescribed particle configurations. We consider both standard Chebyshev polynomial interpolation and mixed-basis polynomial interpolation that uses trigonometric polynomials for coordinates along which the pair potential is known to be periodic. We exploit mathematical reasoning and physical knowledge to refine the interpolation domain and to design our interpolants. We test our approach on two-dimensional and three-dimensional model anisotropic nanoparticles, finding that satisfactory approximations can be constructed in all cases.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504225","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}