The Journal of Physical Chemistry B最新文献

{"title":"Comparative Study of Polymer Globules and Liquid Droplets in Poor Solvents: Effects of Cosolvents and Solvent Quality.","authors":"Tushar Mahendrakar, Kaustubh Rane","doi":"10.1021/acs.jpcb.4c07137","DOIUrl":"10.1021/acs.jpcb.4c07137","url":null,"abstract":"<p><p>We compare the structures of polymer globules, composed of flexible polymer chains, with liquid droplets made of nonbonded monomers of the same polymer in poor solvents. This comparison is performed in three different poor solvents, with and without the addition of cosolvents. Molecular dynamics simulations are used to analyze the properties of the polymer globules, while semigrand canonical Monte Carlo simulations are used to form metastable liquid droplets of nonbonded monomers through homogeneous nucleation in the same solvents. Our findings show that both globules and droplets are nearly spherical, although droplets display slightly more anisotropy. In the absence of cosolvents, the surrounding solvent structures are similar for both globules and droplets. However, in the presence of cosolvents, significant differences arise in the liquid structure, with the disparities increasing as the solvent quality worsens. Cosolvents tend to accumulate near the surface of globules due to the restricted movement of bonded monomers, which partially immobilizes the cosolvents. This effect becomes more pronounced as the solvent quality declines. Interfacial free energy calculations reveal that cosolvents act like surfactants, promoting larger interfacial areas for both globules and droplets. This effect is more significant for globules due to the greater accumulation of cosolvents at their surface. Therefore, modeling polymer globules as liquid droplets may underestimate the impact of cosolvents on the stability of the globule state. Additionally, the transition states involved in polymer collapse in the presence of cosolvents differ from those involved in the nucleation of liquid droplets in the same solution.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"979-989"},"PeriodicalIF":2.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941581","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":"Study on Microscopic Properties of Molten NaF-AlF₃-CaF₂/LiF/KF Using First-Principles Molecular Dynamics.","authors":"Wendi Zhang, Xianwei Hu, Mouhamadou Aziz Diop, Hongguang Kang, Jiangyu Yu, Aimin Liu, Zhongning Shi, Zhaowen Wang","doi":"10.1021/acs.jpcb.4c07434","DOIUrl":"10.1021/acs.jpcb.4c07434","url":null,"abstract":"<p><p>This study employs first-principles molecular dynamics (FPMD) simulations combined with the Voronoi tessellation method to explore the microstructure, transport properties, electronic properties, and Raman spectra of the NaF-AlF₃-CaF₂/LiF/KF systems with varying cryolite ratios, additive types, and concentrations. The results indicate that Na⁺, Ca²⁺, Li⁺, and K⁺ exist in a free state in the molten salts, while Al³⁺ forms complex ion groups in the form of [AlF_<i>x</i>]^3-<i>x</i> with F^-, and free F^- also exists in the molten salts. In the NaF-AlF₃-CaF₂ system, the average Al-F distance is slightly shorter than that in the other two systems, while the Al-F coordination number is higher in NaF-AlF₃-LiF. Cryolite ratios and additive concentrations have little effect on the average Al-F distance. The diffusion abilities of different ions follow the order: Li⁺ > Na⁺ > F^- > Al³⁺, with the diffusion ability of K⁺ being close to that of Li⁺. In Al-F chemical bonds, both ionic and covalent bonds coexist and double bonds can be observed in certain transient structures. The Al-F complex ion groups mainly consist of [AlF₄]^-, [AlF₅]^2-, and [AlF₆]^3-, with the concentration of [AlF₆]^3- being higher in the NaF-AlF₃-LiF system compared to the other two systems. This study establishes the relationship between the microscopic properties and the composition of aluminum electrolytes, demonstrating the suitability of FPMD combined with Voronoi tessellation for probing the microstructural properties of aluminum electrolytes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1007-1015"},"PeriodicalIF":2.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941793","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 Impact of Minor Water Content on Polymer Electrolytes with Molecular Dynamics.","authors":"Aysha Siddika Asha, Mubeen Jamal, Simon Gravelle, Maricris L Mayes, Caiwei Shen","doi":"10.1021/acs.jpcb.4c04984","DOIUrl":"10.1021/acs.jpcb.4c04984","url":null,"abstract":"<p><p>Solid-state polymer electrolytes (SPEs) are increasingly favored over liquid electrolytes for emerging energy storage devices due to their safety features, enhanced stability, and multifunctionality. Minor solvents (such as water) are often introduced unintentionally or intentionally into SPEs. Although it can significantly affect SPEs' electrochemical and mechanical properties, the fundamental role of such solvent content has rarely been studied. Here, we investigate the effects of minor water content on two representative SPEs through molecular dynamics simulations. Focusing on SPEs composed of different base polymers, namely, poly(ethylene oxide) (PEO) and poly(lactic acid) (PLA), and the same salt, lithium perchlorate (LiClO₄), our simulations reveal that slight hydration facilitates an increase in ionic conductivity while preserving the mechanical integrity of the SPEs. Notably, these water contents appear to affect ionic conductivity more effectively in certain systems than others, which is attributed to the unique interactions among ions, water, and the polymer matrix. Moreover, small amounts of water can maintain the stiffness of SPEs rather than reducing it. Such results suggest a facile approach to developing SPEs with balanced ionic conductivity and mechanical properties, suitable for a range of energy storage applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1061-1069"},"PeriodicalIF":2.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968685","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":"Sequence-Dependent Slowdown of DNA Translocation Using Transmembrane RNA-DNA Interactions in MoS₂ Nanopore.","authors":"Dong Zhang, Mingjiao Zhang, Ruhong Zhou","doi":"10.1021/acs.jpcb.4c07041","DOIUrl":"10.1021/acs.jpcb.4c07041","url":null,"abstract":"<p><p>The emergence of nanopores in two-dimensional (2D) nanomaterials offers an attractive solid-state platform for high-throughput and low-cost DNA sequencing. However, several challenges remain to be addressed before their wide application, including the too-fast DNA translocation speed (compared to state-of-the-art single nucleoside detection techniques) and too large noise/signal ratios due to DNA fluctuations inside the nanopores. Here, we use molecular dynamics (MD) simulations to demonstrate the feasibility of utilizing RNA-DNA interactions in modulating DNA translocations in 2D MoS₂ nanopores. By constructing a transmembrane-RNA-oligonucleotide-decorated nanopore (TOD nanopore), we find that the translocation speed of DNA can be significantly slowed in a sequence-dependent manner, with up to 160-fold deceleration compared with the naked control. The strong interactions between the translocating DNA and the first and second guanines of transmembrane RNAs are thought to play a key role in regulating the translocation process. Moreover, the observed suppression of base conformational fluctuations within the TOD nanopore can further improve the single nucleotide detecting resolution. Therefore, our investigations demonstrate that the proposed TOD nanopore can be a potential candidate for enhanced DNA sequencing with solid-state nanopores.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"876-885"},"PeriodicalIF":2.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968715","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":"Ligand and Residue Free Energy Perturbations Solve the Dual Binding Mode Proposal for an A_2BAR Partial Agonist.","authors":"Tana Tandarić, Hugo Gutiérrez-de-Terán","doi":"10.1021/acs.jpcb.4c07391","DOIUrl":"10.1021/acs.jpcb.4c07391","url":null,"abstract":"<p><p>Adenosine receptors, particularly A_2BAR, are gaining attention for their role in pathological conditions such as cancer immunotherapy, prompting the exploration for promising therapeutic applications. Despite numerous selective A_2BAR antagonists, the lack of selective full agonists makes the partial agonist BAY60-6583 one of the most interesting activators of this receptor. Recent cryo-EM structures have univocally revealed the binding mode of nonselective ribosidic agonists such as adenosine and its derivative NECA to A_2BAR; however, two independent structures with BAY60-6583 show alternative binding orientations, raising the question of which is the physiologically relevant binding mode. In situations such as this, computational simulations that accurately predict shifts in binding free energy can complement experimental structures. Our study combines QligFEP and QresFEP protocols to directly compare the binding affinity of BAY60-6583 between alternative binding modes as well as providing a direct comparison of in silico mutagenesis studies on each pose with experimental mutational effects. Both methods converge on the experimentally determined binding mode that better explains both the existing SAR and mutagenesis data for this ligand. Our results allow the elucidation of the experimental binding orientation that should be considered as a basis for designing partial agonist derivatives with improved affinity and selectivity and underscore the value of free energy perturbation methods in aiding structure-based drug design.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"886-899"},"PeriodicalIF":2.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11770768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941652","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":"Photocurrent Generation by Plant Light-Harvesting Complexes is Enhanced by Lipid-Linked Chromophores in a Self-Assembled Lipid Membrane.","authors":"Masaharu Kondo, Ashley M Hancock, Hayato Kuwabara, Peter G Adams, Takehisa Dewa","doi":"10.1021/acs.jpcb.4c07402","DOIUrl":"10.1021/acs.jpcb.4c07402","url":null,"abstract":"<p><p>The light-harvesting pigment-protein complex II (LHCII) from plants can be used as a component for biohybrid photovoltaic devices, acting as a photosensitizer to increase the photocurrent generated when devices are illuminated with sunlight. LHCII is effective at photon absorption in the red and blue regions of the visible spectrum, however, it has low absorption in the green region (550-650 nm). Previous studies have shown that synthetic chromophores can be used to fill this spectral gap and transfer additional energy to LHCII, but it was uncertain whether this would translate into an improved performance for photovoltaics. In this study, we demonstrate amplified photocurrent generation from LHCII under green light illumination by coupling this protein to Texas Red (TR) chromophores that are coassembled into a lipid bilayer deposited onto electrodes. Absorption spectroscopy shows that LHCII and lipid-linked TR are successfully incorporated into lipid membranes and maintained on electrode surfaces. Photocurrent action spectra show that the increased absorption due to TR directly translates into a significant increase of photocurrent output from LHCII. However, the absolute magnitude of the photocurrent appears to be limited by the lipid bilayer acting as an insulator and the TR enhancement effect reaches a maximum due to protein, lipid or substrate-related quenching effects. Future work should be performed to optimize the use of extrinsic chromophores within novel biophotovoltaic devices.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"900-910"},"PeriodicalIF":2.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11770764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941735","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":"A Complete Description of the Ultrafast Proton Transfer Dynamics in the Excited State of D-Luciferin.","authors":"Prabhat Sahu, Sk Imadul Islam, Rajib Kumar Mitra, Dipak K Palit","doi":"10.1021/acs.jpcb.4c08407","DOIUrl":"10.1021/acs.jpcb.4c08407","url":null,"abstract":"<p><p>Excited-state proton transfer (ESPT) in organic photoacids is a widely studied phenomenon in which D-luciferin is of special mention, considering the fact that apart from its phenolic OH group, the nitrogen atoms at either of the two thiazole moieties could also participate in hydrogen bonding interactions with a proton-donating solvent during ESPT. As a result, several transient species could appear during the ESPT process. We hereby deploy subpicosecond time-resolved fluorescence upconversion (FLUP) and transient absorption (TA) spectroscopic techniques to understand the detailed photophysics of D-luciferin in water as well as in dimethyl sulfoxide (DMSO) and ethanol. These transient-state spectroscopic studies reveal the population of two kinds of hydrogen-bonded (HB) complexes (HBCs) in the excited singlet (S₁) state─HBC-I, which is formed at the OH site of the hydroxy benzothiazole moiety with a proton-accepting solvent, and the other one is HBC-II, which is formed at the N atom site of the thiazoline moiety with a proton-donating solvent. This study provides a complete description of the mechanism of the deprotonation process in HBC-I through distinct identification and characterization of the spectroscopic properties and temporal dynamics of those transient species associated with the four stages of the ESPT process as proposed by the Eigen-Weller model. This study also identifies and characterizes HBC-II, which, however, does not participate in the deprotonation process but provides an efficient nonradiative relaxation mechanism via geminate proton recombination.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1046-1060"},"PeriodicalIF":2.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941580","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":"Synergistic Chloroform-Methanol Binary Solvent Mixture Is Inherently Spatially and Dynamically Heterogeneous.","authors":"Ndege Simisi Clovis, Soumya Chaudhury, Pratik Sen","doi":"10.1021/acs.jpcb.4c07326","DOIUrl":"10.1021/acs.jpcb.4c07326","url":null,"abstract":"<p><p>Nonideality in a binary solvent mixture is manifested through anomalies in various physical properties like viscosity, dielectric constant, polarity, freezing point, boiling point, and so forth. Sometimes, such anomalies become much more prominent, leading to a synergistic behavior, where the physical property of the mixture is way different from its bulk counterparts. Various alcohols/chlorinated methane binary solvent mixtures show such a synergistic behavior. The reason is attributed to the unique but diverse interactions present in the system. We speculated that these diverse interactions must manifest heterogeneity in such a binary solvent mixture. Using the improved methodology developed by our group, we investigate the presence of dynamic and spatial heterogeneity in the chloroform/methanol synergistic binary solvent mixture. To our delight, we found that our projection is accurate, and indeed, the chloroform/methanol binary solvent mixtures are heterogeneous. Two maxima for the synergistic behavior have been observed for the chloroform/methanol binary solvent mixture (at ∼0.45 and 0.75 mole fractions of methanol in chloroform) in the literature, where the extent of heterogeneity was also found to be the highest. The present study portrays the intriguing complexity of simple binary solvent mixtures, and the findings may provide valuable insights into solvent engineering for diverse applications like extraction/purification media, reaction media, polymer processing, nanomaterial synthesis, pollutant extraction, active ingredient delivery, biofuel production, and battery technology.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"998-1006"},"PeriodicalIF":2.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941795","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":"QM Investigation of Rare Earth Ion Interactions with First Hydration Shell Waters and Protein-Based Coordination Models.","authors":"Elizabeth E Wait, Christopher R Riley, Monica M Manginell, Amanda Peretti, Erik D Spoerke, George D Bachand, Susan B Rempe, Pengyu Ren","doi":"10.1021/acs.jpcb.4c07361","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07361","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Conventional methods for extracting rare earth metals (REMs) from mined mineral ores are inefficient, expensive, and environmentally damaging. Recent discovery of lanmodulin (LanM), a protein that coordinates REMs with high-affinity and selectivity over competing ions, provides inspiration for new REM refinement methods. Here, we used quantum mechanical (QM) methods to investigate trivalent lanthanide cation (Ln&lt;sup&gt;3+&lt;/sup&gt;) interactions with coordination systems representing bulk solvent water and protein binding sites. Energy decomposition analysis (EDA) showed differences in the energetic components of Ln&lt;sup&gt;3+&lt;/sup&gt; interaction with representatives of solvent (water, H&lt;sub&gt;2&lt;/sub&gt;O) and protein binding sites (acetate, CH&lt;sub&gt;3&lt;/sub&gt;COO&lt;sup&gt;-&lt;/sup&gt;), highlighting the importance of accurate description of electrostatics and polarization in computational modeling of REM interactions with biological and bioinspired molecules. Relative binding free energies were obtained for Ln&lt;sup&gt;3+&lt;/sup&gt; with coordination complexes originating from binding sites in PDB structures of a lanthanum binding peptide (PDB entry 7CCO) and LanM, with explicit consideration of the first hydration shell waters, according to quasi-chemical theory (QCT). Beyond the first shell, the bulk solvent environment was represented with an implicit continuum model. Ln&lt;sup&gt;3+&lt;/sup&gt; interactions with (H&lt;sub&gt;2&lt;/sub&gt;O)&lt;sub&gt;9&lt;/sub&gt; and both binding site models became more favorable, moving down the periodic series. This trend was more pronounced with the protein binding site models than with water, resulting in affinity increasing with periodic number, except for the last REM, Lu&lt;sup&gt;3+&lt;/sup&gt;, which bound less favorably than the preceding element, Yb&lt;sup&gt;3+&lt;/sup&gt;. Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln&lt;sup&gt;3+&lt;/sup&gt; relative binding free energies for the whole 7CCO peptide were reproduced. Conversely, the previously reported experimental data for LanM show a preference for the earlier lanthanides; this is likely due to longer-range interactions and cooperative effects, which are not represented by the reduced models. Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln&lt;sup&gt;3+&lt;/sup&gt; relative binding free energies for the whole 7CCO peptide were reproduced. In contrast to the previously reported experimental data for LanM, the peptide preferentially binds the earlier lanthanides. This difference likely arises due to longer-range interactions and cooperative effects not represented by the peptide. Further investigation of Ln&lt;sup&gt;3+&lt;/sup&gt; interactions with whole proteins using polarizable molecular mechanics models with explicit solvent is warranted to understand the influence of longer-ranged interactions, cooperativity, and bulk solvent. Nevertheless, the present work provides new insights into Ln&lt;sup&gt;3+&lt;/sup&gt; interactions with biomolecules and presents an effective computational platform for ","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027496","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":"ModeHunter: A Package for the Reductionist Analysis, Animation, and Application of Elastic Biomolecular Motion.","authors":"Willy Wriggers, Maytha Alshammari, Joseph N Stember, Sebastian Stolzenberg, Essam Metwally, Manfred Auer, Jing He, Harel Weinstein","doi":"10.1021/acs.jpcb.4c05077","DOIUrl":"10.1021/acs.jpcb.4c05077","url":null,"abstract":"<p><p>ModeHunter is a modular Python software package for the simulation of 3D biophysical motion across spatial resolution scales using modal analysis of elastic networks. It has been curated from our in-house Python scripts over the last 15 years, with a focus on detecting similarities of elastic motion between atomic structures, coarse-grained graphs, and volumetric data obtained from biophysical or biomedical imaging origins, such as electron microscopy or tomography. With ModeHunter, normal modes of biophysical motion can be analyzed with various static visualization techniques or brought to life by dynamics animation in terms of single or multimode trajectories or decoy ensembles. Atomic structures can also be refined against volumetric densities with flexible fitting strategies. The software consists of multiple stand-alone programs for the preparation, analysis, visualization, animation, and refinement of normal modes and 3D data sets. At its core, two spatially reductionist elastic motion engines are currently supported: elastic network models (typically for a Cα level of detail and rectangular meshes) and bend-twist stretch (for trigonal or tetrahedral meshes or trees resulting from spatial clustering). The programs have recently been modernized to Python 3, requiring only the common numpy and scipy external libraries for numerical support. The main advantage of our modular design is that the tools can be combined by the end users for specific modeling applications, either standalone or with complementary tools from our C/C++-based Situs modeling package. The modular design and consistent look and feel facilitate the maintenance of individual programs and the development of novel application workflows. Here, we provide the first complete overview of the ModeHunter package as it exists today, with an emphasis on functionality and workflows supported by version 1.4.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"825-834"},"PeriodicalIF":2.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941697","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}