Rafael G. Viegas, Anushree Sinha, Avijit Mainan, Karissa Y. Sanbonmatsu, José N. Onuchic, Susmita Roy* and Vitor B.P. Leite*,
{"title":"Critical Role of Mg2+ Ions in RNA Folding Transitions: Anchoring the A-Minor Twist in the SAM-II Riboswitch","authors":"Rafael G. Viegas, Anushree Sinha, Avijit Mainan, Karissa Y. Sanbonmatsu, José N. Onuchic, Susmita Roy* and Vitor B.P. Leite*, ","doi":"10.1021/acs.jpcb.5c02586","DOIUrl":"10.1021/acs.jpcb.5c02586","url":null,"abstract":"<p >Magnesium ions (Mg<sup>2+</sup>) play a crucial role in stabilizing various RNA tertiary motifs, such as pseudoknots, G-quadruplexes, kissing loops, and A-minor motifs, to name a few. Despite their importance, the precise location and role of Mg<sup>2+</sup> ions in RNA folding are challenging to characterize both experimentally and computationally. In this study, we employ an all-atom structure-based model integrated with the dynamic counterion condensation (DCC) model to investigate the folding and unfolding transitions of apo SAM-II riboswitch RNA at physiological concentrations of Mg<sup>2+</sup>. Using the Energy Landscape Visualization Method (ELViM), we trace the transitions between conformational phases, focusing on magnesium interactions. ELViM reveals key structural ensembles during the transition from the unfolded to the folded state, facilitated by a partially folded intermediate, which is conformationally similar to that found in early <sup>13</sup>C-CEST NMR. Interestingly, this study finds the rate-limiting transition from the unfolded state to this intermediate initiated by the formation of an A-minor twist interaction, a stable scaffold in the aptamer domain, stabilized by specific Mg<sup>2+</sup> coordination. The contact probability map shows that this specific Mg<sup>2+</sup> bridges a helical region and an internal loop, mitigating electrostatic repulsion at the phosphate level. As a result, a set of hydrogen-bond-mediated interactions between the loop and the minor groove of the helix is stabilized, supporting the formation of the A-minor twist. This study underscores the critical role of Mg<sup>2+</sup> in driving the rate-limiting event of RNA folding and highlights its strategic location in stabilizing the A-minor twist motif, essential for the global packing and regulatory function of the SAM-II riboswitch aptamer.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 36","pages":"9058–9067"},"PeriodicalIF":2.9,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c02586","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936405","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":"Efficient Sampling of Free Energy Landscapes for the Calculation of Protein–Protein Binding Affinities in Membranes","authors":"Ayan Majumder, and , John E. Straub*, ","doi":"10.1021/acs.jpcb.5c04286","DOIUrl":"10.1021/acs.jpcb.5c04286","url":null,"abstract":"<p >The accurate simulation of realistic biomembranes is a long-term goal in the field of membrane biophysics. Efforts to simulate increasingly complex lipid bilayers, consisting of multiple lipid types and proteins, have been hindered by the shortcomings of current force fields, both coarse-grained and all-atom, in the modeling of protein–protein and protein–lipid interactions. Due to the fundamental importance of protein dimerization to cellular signaling and protein trafficking, the study of protein–protein association and the related dimerization free energies has received significant attention in both simulations and experiments. Detailed comparisons of simulation results with NMR, crystallography, and FRET studies served as a test of the accuracy of the simulation methods and provided insights into the underlying structural distributions and thermodynamic driving forces defining the interactions. These comparisons have led to the conclusion that existing state-of-the-art simulation methods have failed to effectively sample the equilibrium between associated and dissociated states, leading to inaccurate estimates of binding constants and misrepresentation of the associated structural ensembles. Here, we discuss the drawbacks of previously used protocols and review our systematic development of effective computational methods for enhanced sampling simulations that exhaustively sample the native and non-native dimer conformations and provide precise estimates of the associated equilibrium binding constants. We conclude by identifying the most important current challenges to the field that must be met in closing the gap between simulation and experiment in the study of protein–protein association in the membrane.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 36","pages":"9031–9042"},"PeriodicalIF":2.9,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936445","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}
Hoang Anh Nguyen, Trung Hai Nguyen, Van V Vu, Philippe Derreumaux, Son Tung Ngo
{"title":"Varoglutamstat Inhibits the Dimerization of the Aβ<sub>25-35</sub> Fragment in Aqueous Solution.","authors":"Hoang Anh Nguyen, Trung Hai Nguyen, Van V Vu, Philippe Derreumaux, Son Tung Ngo","doi":"10.1021/acs.jpcb.5c03306","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c03306","url":null,"abstract":"<p><p>The self-aggregation of amyloid-beta (Aβ) peptides is strongly associated with Alzheimer's disease. In this study, the influence of the small varoglutamstat compound on the conformations of the FAβ<sub>25-35</sub> dimer was extensively characterized by using MD simulations. The influence of the ligand on the conformation of the FAβ<sub>25-35</sub> dimer was studied during the first 10.0 μs. However, its real influence was clarified when the trajectory was extended to 20.0 μs. This indicates that the investigation of a ligand inhibiting Aβ requires a longer MD simulation than previously thought. The ligand changes ensemble properties by reducing the formation of nonbonded intermolecular contacts and β-content. Although varoglutamstat has weak binding to the FAβ<sub>25-35</sub> dimer, the free energy landscape is impacted in shape, free energy barrier, and number of minima. Notably, it is found that the population of the amyloid-competent dimer structure is substantially reduced upon ligand addition. Furthermore, the change from β-hairpin conformation to antiparallel structure may occur through a transition state forming a random coil conformation.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936059","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}
Steffane Q. Nascimento, Rodrigo M. Iost, Thiago C. Oliveira, Erika R. Manuli, Geovana M. Pereira, Ester C. Sabino and Frank N. Crespilho*,
{"title":"Differential Capacitance Spectroscopy for Real-Time Monitoring of RNA Amplification","authors":"Steffane Q. Nascimento, Rodrigo M. Iost, Thiago C. Oliveira, Erika R. Manuli, Geovana M. Pereira, Ester C. Sabino and Frank N. Crespilho*, ","doi":"10.1021/acs.jpcb.5c01815","DOIUrl":"10.1021/acs.jpcb.5c01815","url":null,"abstract":"<p >RNA amplification is central to viral diagnostics, yet current optical and fluorometric methods, such as PCR and RT-qPCR, remain costly, complex, and resource-intensive. Here, we introduce differential capacitance spectroscopy (DCS) as a real-time electrochemical method for RNA detection using loop-mediated isothermal amplification. By applying sinusoidal currents to flexible carbon fiber electrodes (0.05 cm<sup>2</sup>, 1 mm apart), DCS monitors changes in electrode–electrolyte interface capacitance, generating a unique arm-shoulder diagram (ASD) for RNA amplification. The ASD reveals exponential and polynomial capacitance variations, distinguishing amplified RNA under isothermal conditions. Our method eliminates the need for sophisticated instrumentation and reduces diagnostic costs while enabling rapid, high-sensitivity detection. Validated with COVID-19 patient samples, DCS provides a promising platform for affordable, scalable, and real-time RNA-based diagnostics, positioning itself as a transformative tool for disease surveillance and clinical applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 36","pages":"9051–9057"},"PeriodicalIF":2.9,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5c01815","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936423","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":"Influence of Orientation on the Dynamic Compression Properties of Poly(methyl methacrylate)","authors":"Hongyu Lu, Zitong Lu, Xueting Xu, Hanqin Rui, Mengyao Zheng, Zezong Yu, Mengyu Qi, Mao Wang, Xiaowen Zhang* and Yue Yan, ","doi":"10.1021/acs.jpcb.5c02703","DOIUrl":"10.1021/acs.jpcb.5c02703","url":null,"abstract":"<p >Poly(methyl methacrylate) with biaxial stretching orientation (BO-PMMA) has superior mechanical properties compared to casting (unoriented, UO-PMMA), and is therefore widely used in the field of transparent structures. To investigate the effect of orientation on the dynamic compression properties of PMMA and establish a constitutive model applicable to BO-PMMA at different strain rates and service temperatures, this study conducted compression experiments on BO-PMMA at relatively low strain rates (1, 10, 100 s<sup>–1</sup>) and high strain rates (2000, 3000, 4000 s<sup>–1</sup>), as well as at room temperature (RT), 80 °C, and −40 °C. Through the quantitative comparison of the stress–strain curves of BO-PMMA and UO-PMMA, the influence mechanism of orientation on compressive mechanical behavior was elucidated. Based on the experimental results, the parameters of the DSGZ (Duan-Saigal-Greif-Zimmerman) phenomenological constitutive equation were fitted. Using this model, the PMMA with different orientations was numerically simulated and analyzed. The results indicated that increasing the strain rate or decreasing the temperature will increase the yield stress of PMMA. In particular, it was found that BO-PMMA performs more significant strain rate and low-temperature sensitivity than UO-PMMA. Meanwhile, the established constitutive model can effectively describe the dynamic compressive mechanical behavior of BO-PMMA and UO-PMMA at different strain rates and temperatures. Accordingly, it has a certain engineering application guidance value.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 36","pages":"9256–9267"},"PeriodicalIF":2.9,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936387","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}
Zahra Ostadsharif Memar, Majid Moosavi* and Zahra Keyvanfard,
{"title":"Binary Mixtures of Ionic Liquids to Enhance Dicationic Ionic Liquid Performance: Insights from Molecular Dynamics Simulations and Quantum Mechanics","authors":"Zahra Ostadsharif Memar, Majid Moosavi* and Zahra Keyvanfard, ","doi":"10.1021/acs.jpcb.5c02254","DOIUrl":"10.1021/acs.jpcb.5c02254","url":null,"abstract":"<p >In this work, the effect of adding a monocationic ionic liquid (MIL) on the properties of a dicationic ionic liquid (DIL) was investigated using molecular dynamics (MD) simulations and quantum mechanical (QM) calculations. The binary mixture of [C<sub>6</sub>(mim)<sub>2</sub>][NTf<sub>2</sub>]<sub>2</sub> (DIL) and [P<sub>1</sub>EOE][NTf<sub>2</sub>] (MIL) was analyzed in terms of thermophysical, structural, and dynamical properties, along with density functional theory (DFT) and atoms-in-molecules (AIM) analyses. These properties were compared to those of the pure DIL system. Structural properties were examined using radial distribution functions (RDFs) and hydrogen-bonding networks, providing insights into ion arrangement, spatial heterogeneity, and interaction strength. RDF analysis revealed that increasing the MIL mole fraction enhances the local density of anions near the ring hydrogen atoms more significantly than the bulk density. Furthermore, the orientation of imidazolium rings suggests that MIL promotes π–π stacking interactions among [C<sub>6</sub>(mim)<sub>2</sub>]<sup>2+</sup> cations. Notably, the system with <i>x</i><sub>MIL</sub> = 0.50 exhibited the lowest structural heterogeneity among the investigated mixtures. Dynamical properties, including mean square displacement (MSD), ionic conductivity, and van Hove correlation functions, were also analyzed. The results indicate that adding MIL enhances microheterogeneity and reduces ion cage strength, thereby facilitating ion mobility and increasing ionic conductivity. QM calculations further demonstrate that adding MIL lowers ion interaction energies due to the formation of stronger hydrogen bonds in the mixture. Additionally, AIM analysis reveals that the presence of MIL increases electron density between the dication and anions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 36","pages":"9190–9205"},"PeriodicalIF":2.9,"publicationDate":"2025-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936458","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}
George I. Makhatadze*, Caitlyn Moustouka, Carleton Coffin and Franco O. Tzul,
{"title":"Effects of Pressure and Temperature on the Thermodynamics of α-Helices: Implications for Piezophilic Adaptation","authors":"George I. Makhatadze*, Caitlyn Moustouka, Carleton Coffin and Franco O. Tzul, ","doi":"10.1021/acs.jpcb.5c04293","DOIUrl":"10.1021/acs.jpcb.5c04293","url":null,"abstract":"<p >In light of the recent realization that a significant fraction of microbial biomass lives under high hydrostatic pressure, there is a renewed interest in understanding the molecular details by which proteins in these organisms modulate their functional native state. The effects of pressure on protein stability are defined by the volume changes between the native and denatured states. The conformational ensemble of the denatured state can depend on several extrinsic variables, such as pH and ionic strength of the solvent, temperature, and pressure. The effect of the latter on the elements of the secondary structures, including α-helical structures, has been inconclusive. This has been mainly due to the inherent difficulties associated with high-pressure experiments. Here, we adapted the method of choice, circular dichroism spectroscopy, on a well-established series of model peptides to study helical structure formation while focusing on the pressure and temperature dependencies of the helix–coil transition. We find that at low temperatures, pressure stabilizes the helical structure, suggesting that the volume of the helix–coil transition is positive. However, at higher temperatures (>40 °C), the volume changes become negative, and pressure destabilizes the helical structure. The stabilizing effect of pressure on the helical structure at low temperature correlates with the increase in the fraction of high-helix-forming amino acid residues at the expense of low-helix forming residues in psychrophilic bacterial strains adapted to live at the bottom of the ocean.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 36","pages":"9113–9123"},"PeriodicalIF":2.9,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936461","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}
Alessio Olivieri, Alessandro Nicola Nardi, Marco D'Abramo
{"title":"Theoretical Modeling of the Redox Thermodynamics of Nucleic Acid Building Blocks in the Condensed Phase.","authors":"Alessio Olivieri, Alessandro Nicola Nardi, Marco D'Abramo","doi":"10.1021/acs.jpcb.5c03817","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c03817","url":null,"abstract":"<p><p>Low-energy solvated electrons can be captured by nitrogenous bases and localized on the nucleic acid to form a stable anion. The interaction between electrons and the bases is related to alterations in the stability and function of nucleic acids. Here, we report the theoretical-computational estimates of the adiabatic electron affinities (AEAs) and the reduction potentials of the nucleobases in solution. Our data show that pyrimidine bases exhibit the highest tendency to form stable anions in both the gas phase and condensed phases (water and <i>N</i>,<i>N</i>-dimethylformamide solutions). The addition of a ribose moiety increases the electron affinities of the nucleobases in the corresponding nucleosides across both environments. Finally, the comparison with the available experimental data shows that our QM/MM approach, based on a statistical-mechanical treatment of the system, is capable of furnishing accurate reduction-free energy differences in the condensed phase.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935993","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":"Spectroscopic and Theoretical Insights into the Binding of Phenothiazinium Dye Methylene Blue with Triple- and Double-Helical Forms of RNA: A Comparative Study","authors":"Rapti Goswami, Lopa Paul, Himal Das, Amar Ghosh, Susmita Chowdhury and Suman Das*, ","doi":"10.1021/acs.jpcb.5c02810","DOIUrl":"10.1021/acs.jpcb.5c02810","url":null,"abstract":"<p >Higher-ordered nucleic acid structures like triplex and quadruplex forms have been the center of attention of the current research field of medicinal chemistry. The triplex is formed through the sequence-specific association of a single-stranded, triplex-forming oligonucleotide (TFO) with nucleic acid duplex structures. In our present study, we have focused on an RNA triplex (U.A*U) because of its various biological relevance including telomerase activity and movement of ribosomal template in mRNA coding regions. Methylene blue (MB), a cationic dye of phenothiazine families, has diverse pharmacological and clinical applications. Considering the wide range of medicinal uses of MB and the biological importance of higher-ordered structures of RNA, our present study has focused on the elucidation of the comparative binding interaction of methylene blue (MB) with RNA triplex (U.A*U) and duplex (A.U) structures employing various spectroscopic and theoretical tools. MB has been found to show a comparably higher binding affinity toward the triplex form (13.5 × 10<sup>5</sup> M<sup>–1</sup>) than the parent duplex form (2.36 × 10<sup>5</sup> M<sup>–1</sup>). The thermal melting profile revealed that MB substantially stabilized the Watson–Crick base-paired strands of both the RNA triplex and duplex structures; however, it destabilized the Hoogsteen base-paired strand of triple helical RNA. Fluorescence quenching, steady-state anisotropy, and circular dichroic studies all together supported the intercalative mode of binding. Thermodynamic data revealed that the interactions of MB with both RNA triplex and duplex forms were characterized by both negative enthalpy and entropy changes. Ionic strength-dependent study showed that the nonpolyelectrolytic forces are the predominating factors in the binding process, although a minor but certain extent of polyelectrolytic contribution is present. Moreover, theoretical calculations using DFT and TD-DFT methods were explored to validate the experimental spectrophotometric behavior (absorbance) of MB, assigning the energy levels involved in the electronic transition along with the vibrational modes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 36","pages":"9068–9082"},"PeriodicalIF":2.9,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936414","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}
Zeno Romero, Kerstin Münnemann, Hans Hasse and Fabian Jirasek*,
{"title":"Improvement of Diffusion Coefficient Prediction by Active Learning","authors":"Zeno Romero, Kerstin Münnemann, Hans Hasse and Fabian Jirasek*, ","doi":"10.1021/acs.jpcb.5c03825","DOIUrl":"10.1021/acs.jpcb.5c03825","url":null,"abstract":"<p >Methods for predicting diffusion coefficients in mixtures are essential in many applications, as experimental data are scarce. Machine learning (ML) methods offer promising alternatives to established semiempirical models for predicting diffusion coefficients, but their performance strongly depends on the available training data. Increasing the size of data sets is a straightforward strategy for improving ML methods, but measuring diffusion coefficients is costly, limiting the number of experiments that can be carried out. We have therefore studied active learning (AL) strategies for planning diffusion coefficient measurements and the targeted improvement of ML methods for their prediction, specifically matrix completion methods (MCMs) for predicting diffusion coefficients at infinite dilution <i>D</i><sub><i>ij</i></sub><sup>∞</sup> in binary mixtures at 298 K. In the first step, different AL strategies were systematically tested on a synthetic data set for <i>D</i><sub><i>ij</i></sub><sup>∞</sup>, and uncertainty sampling was found to be a simple but effective choice. This strategy was therefore used for planning <i>D</i><sub><i>ij</i></sub><sup>∞</sup> measurements using pulsed-field gradient (PFG) nuclear magnetic resonance (NMR) spectroscopy. In total, <i>D</i><sub><i>ij</i></sub><sup>∞</sup> in 19 mixtures were measured for which previously no data were available, and the data were used for retraining two hybrid MCMs. The results show that significant improvement in the prediction of <i>D</i><sub><i>ij</i></sub><sup>∞</sup> can be achieved with only a few suitably planned experiments, but also that the impact strongly depends on the used prediction model: while no clear influence on the performance of an MCM that was trained on the residuals of the semiempirical SEGWE model was found, the accuracy of a hybrid MCM that incorporates SEGWE predictions as soft prior information could be substantially increased, almost halving the relative mean squared error on the test set.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 36","pages":"9219–9228"},"PeriodicalIF":2.9,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144936428","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}