The Journal of Physical Chemistry B最新文献

{"title":"Influence of CTAB Reverse Micellar Confinement on the Tetrahedral Structure of Liquid Water.","authors":"Anupama Sharma, Mywish Anand, Sudip Chakraborty","doi":"10.1021/acs.jpcb.4c04773","DOIUrl":"10.1021/acs.jpcb.4c04773","url":null,"abstract":"<p><p>The effect of confinement on the tetrahedral ordering of liquid water plays a vital role in controlling their microscopic structure and dynamics as well as their spectroscopic properties. In this article, we have performed the classical molecular dynamics simulations of four different CTAB/water/chloroform reverse micelles with varied water content to study how the tetrahedral ordering of nanoscale water inside reverse micellar confinement influences the microscopic dynamics and the structural relaxation of water···water hydrogen bonds and its impact on the low-frequency intermolecular vibrational bands. We have noticed from the results obtained from simulated trajectories the lowering trends of tetrahedral ordering of water pools in reverse micellar confinements as we move from bulk to confined and strictly confined environments. We have observed that the order of confinements significantly altered the relaxation pattern of water···water hydrogen bonds present in the nanoscale water pool of reverse micelles. The recrossing related to hydrogen bond dynamics can effectively explain the relaxation pattern of <math><msubsup><mi>C</mi><mi>HB</mi><mi>WW</mi></msubsup><mrow><mo>(</mo><mi>t</mi><mo>)</mo></mrow></math> under confinement. The Br^-1···water hydrogen bond depicts a much slower relaxation compared to the water···water hydrogen bonds inside reverse micelles. We have also explored the correlation between the tetrahedral ordering of nanoscale water pools and the relaxation of water···water hydrogen bonds with the 50 cm^-1 band for water inside reverse micelles. The computations reported that compared to bulk water, the band appearing at 50 cm^-1 for O···O···O triplet bending is nonuniformly blue-shifted by 18-45 cm^-1 for the nanoscale water pool inside reverse micelles, and the intensity of the band drops from bulk to confined and strictly confined environments, which indicates the reduced tendency of such triplet formation. It is observed that a significant intensity variation at the 200 cm^-1 band correlates with the effect of confinement on the tetrahedral ordering of the water pool inside reverse micelles. So, our observations support the influence of strictly confined environments on the tetrahedral water structure to adopt the quasi-two-dimensional water network and experience restricted longitudinal translations. It is further noticed that the 500 cm^-1 librational band is also found to be blue-shifted by 71-112 cm^-1 for the water pool in reverse micelles, and the extent of the shift being more noticeable for strictly confined environments correlates excellently with the sluggish relaxation of water···water hydrogen bonds in such environments.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1289-1300"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996338","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":"Ion-Ion Association in Bulk Mixed Electrolytes Using Global and Local Electroneutrality Constraints.","authors":"Elizabeth A Ploetz, Nathan D Smyers, Paul E Smith","doi":"10.1021/acs.jpcb.4c07583","DOIUrl":"10.1021/acs.jpcb.4c07583","url":null,"abstract":"<p><p>Ion atmospheres play a critical role in modulating the interactions between charged components in solutions. However, a detailed description of the nature of ion atmospheres remains elusive. Here, we use Kirkwood-Buff theory, an exact theory of solution mixtures, together with a series of local and bulk electroneutrality constraints to provide relationships between all the net ion-ion distributions in bulk electrolyte mixtures. The validity of the underlying relationships is then confirmed using classical explicit solvent molecular simulations of a range of electrolyte mixtures. Further analysis indicates the ion distributions can be separated into two contributions, one resulting in charge neutralization, for which each ion contributes in proportion to its ionic strength, and the other accounting for all the solution thermodynamics. The relationships hold for atomic and molecular ions of any size and valency regardless of ionic strength, temperature, or pressure, in any solvent system.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1387-1398"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996339","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":"Pretrained Deep Neural Network Kin-SiM for Single-Molecule FRET Trace Idealization.","authors":"Leyou Zhang, Jieming Li, Nils G Walter","doi":"10.1021/acs.jpcb.4c05276","DOIUrl":"10.1021/acs.jpcb.4c05276","url":null,"abstract":"<p><p>Single-molecule fluorescence resonance energy transfer (smFRET) has emerged as a pivotal technique for probing biomolecular dynamics over time at nanometer scales. Quantitative analyses of smFRET time traces remain challenging due to confounding factors such as low signal-to-noise ratios, photophysical effects such as bleaching and blinking, and the complexity of modeling the underlying biomolecular states and kinetics. The dynamic distance information shaping the smFRET trace powerfully uncovers even transient conformational changes in single biomolecules both at or far from equilibrium, relying on trace idealization to identify specific interconverting states. Conventional trace idealization methods based on hidden Markov models (HMMs) require substantial a priori knowledge of the system under study, manual intervention, and assumptions about the number of states and transition probabilities. Here, we present a deep learning framework using long short-term memory (LSTM) to automate the trace idealization, termed Kin-SiM. Our approach employs neural networks pretrained on simulated data to learn high-order correlations in the multidimensional FRET trajectories. Without user input of Markovian assumptions, the trained LSTM networks directly idealize the FRET traces to extract the number of underlying biomolecular states, their interstate dynamics, and associated kinetic parameters. On benchmark smFRET data sets, Kin-SiM achieves a performance similar to conventional HMM-based methods but with less hands-on time and lower risk of bias. We further systematically evaluate the key training factors that affect network performance to define the correct hyperparameter tuning for applying deep neural networks to smFRET data analyses.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1167-1175"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982004","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 Understanding of Activity Changes of Alcohol Dehydrogenase in Deep Eutectic Solvents.","authors":"Jan Philipp Bittner, Ningning Zhang, Pablo Domínguez de María, Irina Smirnova, Selin Kara, Sven Jakobtorweihen","doi":"10.1021/acs.jpcb.4c06523","DOIUrl":"10.1021/acs.jpcb.4c06523","url":null,"abstract":"<p><p>Deep eutectic solvents (DESs) have emerged as promising solvents for biocatalysis. While their impact on enzyme solvation and stabilization has been studied for several enzyme classes, their role in substrate binding is yet to be investigated. Herein, molecular dynamics (MD) simulations of horse-liver alcohol dehydrogenase (HLADH) are performed in choline chloride-ethylene glycol (ChCl-EG) and choline chloride-glycerol (ChCl-Gly) at varying water concentrations. In the DES solutions, the active site was significantly constricted, and its flexibility reduced when compared to the aqueous medium. Importantly, the cavity size follows a similar trend as the catalytic activity of HLADH and as such explains previously observed activity changes. To understand the impact on the binding of the substrate (cyclohexanone), an umbrella sampling (US) setup was established to calculate the free energy changes along the substrate binding tunnel of HLADH. The US combined with replica exchange and NADH in its cofactor pocket provided the best sampling of the entire active site, explaining why the cyclohexanone binding on HLADH is reduced with increasing DES content. As different components in these multicomponent mixtures influence the substrate binding, we additionally applied the US setup to study the ability of the DES components to be present inside the substrate tunnel. The presented approach may become useful to understand enzyme behaviors in DESs and to enable the design of more enzyme-compatible and tunable solvents.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1197-1213"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996342","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":"Evaluation of Mesoporous Silica Nanoparticles as Carriers of Triarylmethyl Radical Spin Probes for EPR Oximetry.","authors":"Misa A Shaw, Martin Poncelet, Derrick A Banerjee, Konstantinos A Sierros, Benoit Driesschaert","doi":"10.1021/acs.jpcb.4c06480","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06480","url":null,"abstract":"<p><p><i>In vivo</i> measurement and mapping of oxygen levels within the tissues are crucial in understanding the physiopathological processes of numerous diseases, such as cancer, diabetes, or peripheral vascular diseases. Electron paramagnetic resonance (EPR) associated with biocompatible exogenous spin probes, such as Ox071 triarylmethyl (TAM) radical, is becoming the new gold standard for oxygen mapping in preclinical settings. However, these probes do not show tissue selectivity when injected systemically, and they are not cell permeable, reporting oxygen from the extracellular compartment only. Recently, Ox071-loaded mesoporous silica nanoparticles (MSNs) were proposed for intracellular tumor oxygen mapping in both <i>in vitro</i> and <i>in vivo</i> models. However, the EPR spectrum of the Ox071 spin probe is poorly sensitive to mobility due to the small anisotropy of its g-factor and the absence of hyperfine splitting, making it more difficult to study the mobility of the radical inside the MSNs or its location. Using ¹³C₁ isotopologues of Ox071 and the deuterated Finland trityl (dFT) spin probes, which are highly sensitive to molecular tumbling, we showed that the loading of the probes inside homemade and commercial cationic MSNs drastically decreases their mobility while the high local concentration of the probe inside the MSNs leads to dipolar line width broadening (self-relaxation). This decrease in molecular tumbling and line broadening hampers the oxygen-sensing properties of Ox071 or dFT probes used for EPR oximetry when loaded into MSNs.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062524","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":"Deciphering the Photophysical Properties of Nonplanar Heterocyclic Compounds in Different Polarity Environments.","authors":"Rajeswari Kainda, Santosh Kumar Behera, Asish K Dehury, Yatendra S Chaudhary","doi":"10.1021/acs.jpcb.4c06300","DOIUrl":"10.1021/acs.jpcb.4c06300","url":null,"abstract":"<p><p>Nonplanar (butterfly-shaped) phenothiazine (<b>PTZ</b>) and its derivative's (<b>M-PTZ</b>) photophysical and spectral properties have been tuned by varying the solvents and their polarity and investigated employing spectroscopic techniques such as UV-Vis, steady-state and time-resolved fluorescence, and TDDFT calculations. The UV-Vis absorption studies and TDDFT calculations reveal two distinct bands for both compounds: a strong π-π* transition at shorter wavelengths and a weaker <i>n</i>-π* transition, which displays a little bathochromic shift in polar solvents. The detailed emission studies reveal that such dual emission is a result of the photoinduced excited-state conjugation enhancement (ESCE) process. The band at a shorter wavelength corresponds to the locally excited (LE) state, while the longer wavelength band arises from the planarized excited state resulting from ESCE. With the increase in solvent polarity, the LE band is less affected, whereas strong positive solvatochromism is observed for the ESCE band. As the solvent polarity increases, the ESCE band demonstrates significant positive solvatochromism, while emission intensity decreases with higher solvent polarity, suggesting stabilization of the excited state. The biexponential decay of fluorescence lifetimes further corroborates the dual emission behavior of <b>PTZ</b> and <b>M-PTZ</b>. <b>PTZ</b> exhibits a higher photoluminescence quantum yield (PLQY) than that observed for <b>M-PTZ</b>, and the solvent viscosity influences the PLQY, indicating that nonradiative decay is activated during the planarization of the excited state, also known as excited-state conjugation enhancement. Furthermore, the (time-dependent) density functional theory (TD) DFT calculations performed to understand the geometrical parameters and the electronic transitions of these model molecules further corroborate experimental findings. These findings underscore the significant influence of solvent polarity and molecular structure on the dual emission and excited-state dynamics of <b>PTZ</b> and <b>M-PTZ</b>, which eventually hold substantial implications for advanced photophysical applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1323-1330"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981999","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":"Capturing the Effect of Anion Type on the Intermolecular Interactions between Water and Imidazolium-Based Ionic Liquids: A Comparative DFT Study.","authors":"Forough Rezaie, Mohammad H Kowsari","doi":"10.1021/acs.jpcb.4c06749","DOIUrl":"10.1021/acs.jpcb.4c06749","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The studies on ionic liquids (ILs) and their interaction with different solvents have always been an interesting topic for experimental and computational chemists. Recently, however, deep insights on the molecular structures of the IL-water binary mixtures have been mainly performed through classical simulations. Here, a comprehensive quantum mechanical study is presented on seven 1-butyl-3-methylimidazolium-based ILs in the absence and presence of water. As the most important intermolecular interaction between ionic moieties of ILs and water molecules, hydrogen bonding is studied through different bonding analyses. The effect of different anions, [NO&lt;sub&gt;3&lt;/sub&gt;]&lt;sup&gt;-&lt;/sup&gt;, [HSO&lt;sub&gt;4&lt;/sub&gt;]&lt;sup&gt;-&lt;/sup&gt;, [SCN]&lt;sup&gt;-&lt;/sup&gt;, [DCA]&lt;sup&gt;-&lt;/sup&gt;, [BF&lt;sub&gt;4&lt;/sub&gt;]&lt;sup&gt;-&lt;/sup&gt;, [PF&lt;sub&gt;6&lt;/sub&gt;]&lt;sup&gt;-&lt;/sup&gt;, and [NTf&lt;sub&gt;2&lt;/sub&gt;]&lt;sup&gt;-&lt;/sup&gt;, on the behavior of ILs interacting with a sample of water molecules is investigated. Comparing the implicit and explicit approaches to consider water solvent indicated that the structure of ILs in the solvent depends on the selected solvent model. By considering explicit water molecules, we analyzed the intermolecular interactions between ILs and the water sample. The energy decomposition analysis indicated that the stability of the IL···water systems is mainly due to the electrostatic component of the total interaction energy. The interaction region indicator (IRI) analysis discovered that chemical bond and van der Waals (vdW) interactions are important in the IL···water systems. Indeed, investigation of each ion/ion pair surrounded by ten nearest neighbor water molecules discovered that the vdW interactions are responsible for the cation···anion and the cation···water interactions, while chemical bonding is important in the anion···water and the water···water interactions. Therefore, the anion···water interaction requires further analysis. The quantum theory of atoms in molecules verified the ionic nature of the H-bond in the anion···water interaction. The IRI analysis showed that the interaction between water molecules and cyano-based anions, [SCN]&lt;sup&gt;-&lt;/sup&gt; and [DCA]&lt;sup&gt;-&lt;/sup&gt;, is only due to chemical bonding, while in the oxygenated anions, [NO&lt;sub&gt;3&lt;/sub&gt;]&lt;sup&gt;-&lt;/sup&gt; and [HSO&lt;sub&gt;4&lt;/sub&gt;]&lt;sup&gt;-&lt;/sup&gt;, the vdW forces are also important. For the other anions, [BF&lt;sub&gt;4&lt;/sub&gt;]&lt;sup&gt;-&lt;/sup&gt;, [PF&lt;sub&gt;6&lt;/sub&gt;]&lt;sup&gt;-&lt;/sup&gt;, and [NTf&lt;sub&gt;2&lt;/sub&gt;]&lt;sup&gt;-&lt;/sup&gt;, the vdW forces have the main contribution in the anion···water interaction. Natural bond orbital analysis indicated that these intermolecular interactions originate from n&lt;sub&gt;anion&lt;/sub&gt; → σ&lt;sub&gt;O-H&lt;/sub&gt;&lt;sup&gt;*&lt;/sup&gt; electron transfer. Finally, the law of matching water affinity (LMWA) using energy-based parameters was used to predict the hydrophilicity of ILs as follows: [BMIM][NO&lt;sub&gt;3&lt;/sub&gt;] &gt; [BMIM][SCN] &gt; [BMIM][DCA] &gt; [BMIM][HSO&lt;sub&gt;4&lt;/sub&gt;] &gt; [BMIM][BF&lt;sub&gt;4&lt;/sub&gt;] &gt; [BMIM][NTf&lt;sub&gt;2&lt;/sub&gt;] &gt; [BMIM][PF&lt;sub&gt;6&lt;/sub&gt;]. Results obtained in the cu","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1343-1359"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996306","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":"Investigating the Restricted Dynamical Environment in and Around Aβ Peptide Oligomers in Aqueous Ionic Liquid Solutions.","authors":"Subhadip Sahoo, Sanjoy Bandyopadhyay","doi":"10.1021/acs.jpcb.4c07336","DOIUrl":"10.1021/acs.jpcb.4c07336","url":null,"abstract":"<p><p>It is widely believed that the aggregation of amyloid β (Aβ) peptides into soluble oligomers is the root cause behind Alzheimer's disease. In this study, we have performed room-temperature molecular dynamics (MD) simulations of aggregated Aβ oligomers of different sizes (pentamer (O(5)), decamer (O(10)), and hexadecamer (O(16))) in binary aqueous solutions containing 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF₄]) ionic liquid (IL). Investigations have been carried out to obtain a microscopic understanding of the effects of the IL on the dynamic environment around the exterior surfaces and within the confined nanocores of the oligomers. The calculations revealed that in contrast to nearly uniform dynamics near the exterior surface, heterogeneous structural distortions of oligomers of varying sizes and nonuniform distributions of water and IL components within their core volumes modify the core dynamics in a differential manner. It is demonstrated that increasingly restricted mobility of water and IL components is the origin behind the longer time scale of dynamic heterogeneity in and around the oligomers. Importantly, due to the equivalent nondirectional nature of the B-F bonds, BF₄^- anions are found to reorient on a time scale faster than that of water molecules. Further, the structural relaxation of protein-anion (PA) hydrogen bonds around the oligomers has been found to be correlated with sluggish translational motions of the anions but anticorrelated with their reorientational time scale. In addition, it is quantified that compared to the pure aqueous medium, strengthening of protein-water (PW) hydrogen bonds in the presence of the IL leads to their longer lifetimes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1214-1228"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982001","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":"https://doi.org/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":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-29","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}

{"title":"An Implicit Solvation Model for Binding Free Energy Estimation in Nonaqueous Solution.","authors":"David Elsing, Wolfgang Wenzel, Mariana Kozlowska","doi":"10.1021/acs.jpcb.4c08592","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08592","url":null,"abstract":"<p><p>Implicit solvation models permit the approximate description of solute-solvent interactions, where water is the most often considered solvent due to its relevance in biological systems. The use of other solvents is less common but is relevant for applications such as in nuclear magnetic resonance (NMR) or chromatography. As an example, chloroform is commonly used in anisotropic NMR to measure residual dipolar couplings (RDCs) of chiral analytes weakly aligned by an alignment medium. They can be calculated from molecular dynamics (MD) simulations with explicit solvent, but it is computationally expensive, because tens of microseconds-long MD trajectories should be collected. Here, we develop a computational protocol and numerical implementation for binding free energies of rigid organic molecules to poly-γ-benzyl-l-glutamate using an implicit solvation model of chloroform. The model parameters are fit to alchemical binding free energies obtained from MD simulations in explicit chloroform and compared to the MD results and another implicit solvation model. Possible applications of the method are docking or Monte Carlo simulations based on a physically meaningful scoring function for the fast prediction of interaction poses of ligands for selective binding or the alignment of analytes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057503","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}