{"title":"SPICA Force Field for Nucleic Acids and Its Application to Lipid Nanoparticles.","authors":"Akhil Pratap Singh, Hiroki Tanaka, Yusuke Miyazaki, Wataru Shinoda","doi":"10.1021/acs.jpcb.5c01729","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01729","url":null,"abstract":"<p><p>Nucleic acid therapies have emerged as promising treatments for various diseases associated with aberrant gene expression. Cationic lipid-nucleic acid complexes (lipoplexes) remain at the forefront of such therapeutic approaches as drug delivery carriers. To facilitate the study of these carriers through coarse-grained molecular dynamics (CG-MD) simulations, we extend our surface property fitting coarse-grained (SPICA) force field to develop a reliable DNA model with enhanced compatibility with lipids. In our DNA-CG model, the backbone is represented using three CG segments: the phosphate group is mapped to a single CG site, the deoxyribose to two CG sites, and nucleic bases are depicted as three- or four-atom rings. The bonded parameters were optimized to reproduce the mean and distribution of bond lengths, angles, and dihedrals obtained from all-atom (AA) MD simulations. Additionally, nonbonded parameters were fine-tuned to match experimental and AA-MD reference data, including the solvation free energy of nucleic bases, the free energy profile of base stacking interactions, and the transfer free energy of bases across different lipid bilayers. We also optimize the parameter of our CG model to reproduce the radius of gyration of single-stranded DNA obtained by AA-MD simulations. Further, by incorporating an elastic network to maintain the secondary structure of double-stranded DNA (dsDNA), we achieved a reasonable persistence length for dsDNA. Finally, we applied our DNA model to simulate lipoplexes, demonstrating its compatibility with lipids. The structural characteristics of these lipoplexes showed excellent agreement with experimental data, reinforcing the reliability of our model. Our model provides a solid foundation for large-scale simulations of complex DNA-lipid systems, such as lipid nanoparticles, in future studies.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493126","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}
Zachary C Drake, Alexa G Fowler, Ashley A Blum, Steffen Lindert
{"title":"Enhanced Protein Complex Prediction via Rosetta, AlphaFold, and Nondifferential Covalent Labeling Mass Spectrometry.","authors":"Zachary C Drake, Alexa G Fowler, Ashley A Blum, Steffen Lindert","doi":"10.1021/acs.jpcb.5c02872","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02872","url":null,"abstract":"<p><p>Covalent labeling (CL) mass spectrometry is a versatile structural technique for elucidating structural information about proteins, including protein-protein complexes. When integrated with computational protein structure prediction, CL can generate accurate protein complex models. Structural insights from CL are more readily interpreted when differential data (e.g., monomer versus complex) are available, as changes in labeling can directly pinpoint interface residues. However, isolating and labeling monomeric subunits can be experimentally challenging, leading to the common scenario in which labeling data are available only in the complex form. However, importantly, nondifferential CL still encodes useful structural information that has yet to be utilized for automated protein complex prediction. In this work, we present a framework for using nondifferential CL in protein complex prediction. We introduced a new hydroxyl radical protein footprinting (HRPF)-derived scoring term that penalizes docked models based on their agreement with experimentally measured CL data. In a benchmark set, the best-scoring models showed an average root-mean-square deviation (RMSD) improvement of 4.6 Å when HRPF data was used. With the inclusion of CL data, four of the top-scoring complexes exhibited RMSDs below 5Å, whereas none did without it. This study demonstrates that CL can enhance protein complex prediction, even when only bound-state CL measurements are available.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144482518","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}
Shuangxiu Max Ma, Patrícia Pereira, Christian W Pester, Phillip E Savage, Bhavik R Bakshi, Li-Chiang Lin
{"title":"Understanding PET Hydrolysis via Reactive Molecular Dynamics Simulation and Experimental Investigation.","authors":"Shuangxiu Max Ma, Patrícia Pereira, Christian W Pester, Phillip E Savage, Bhavik R Bakshi, Li-Chiang Lin","doi":"10.1021/acs.jpcb.5c03080","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c03080","url":null,"abstract":"<p><p>Polyethylene terephthalate (PET), a widely used polymer in packaging applications, has posed significant environmental challenges due to its resistance to environmental degradation. Chemical recycling via hydrolysis offers a circular solution by breaking PET down into its monomers, terephthalic acid and ethylene glycol, which can then be repolymerized into new PET. Despite its promise, the detailed pathways of PET hydrolysis─particularly the interplay between hydrolysis and thermal degradation─remain a topic of scientific debate. We combine reactive molecular dynamics (MD) simulations with experimental studies to elucidate key reaction pathways, intermediate species, and the temperature-dependent evolution of degradation products. Molecular dynamics simulations offer detailed insights into molecular motions and interactions that are often elusive in experimental setups, thus enhancing our understanding of the complex dynamics at play during PET decomposition. By systematically examining bond dissociation, intermediate species, and product formation at various temperatures, this study elucidates how hydrolysis and thermal degradation pathways evolve and interact. Furthermore, a severity index approach is employed to directly compare TPA yields from simulations with corresponding experimental data.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473358","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}
Agustín Iborra, Cristian Villa-Pérez, Juan M Padró, Juan M Giussi, Isabel N Vega, Juan J Romero
{"title":"Shedding Light on the Role of Short-Chain Alcohols in Amphiphilic Polymer Assembly: Implications for Oil and Gas Recovery Operations.","authors":"Agustín Iborra, Cristian Villa-Pérez, Juan M Padró, Juan M Giussi, Isabel N Vega, Juan J Romero","doi":"10.1021/acs.jpcb.5c01365","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01365","url":null,"abstract":"<p><p>In this work, we investigated the supramolecular organization of self-assembled poly(LMA-<i>co-</i>PEGMA) structures in aqueous solution in the presence of short-chain alcohols, focusing on their compartmentalization between molecular aggregates and the bulk aqueous phase, as well as their implications for polymer-based methods in enhanced oil recovery. Polymers were synthesized using reversible addition-fragmentation chain transfer polymerization and characterized by nuclear magnetic resonance and size exclusion chromatography coupled with multi-angle light scattering and differential refractive index detectors. Dynamic light scattering revealed differences in the supramolecular organization of self-assembled aggregates in the presence of short-chain alcohols, reflected by changes in the aggregation number and critical aggregation concentrations. Additionally, fluorescence-based experiments were carried out to characterize compartment properties within the aggregates─such as polarity and microviscosity─and the influence of spatial organization and conformation. Moreover, we used nuclear Overhauser effect spectroscopy and inversion recovery experiments to gain deeper insight into monomer-alcohol and copolymer-alcohol interaction and dynamics. Finally, oil transfer experiments reflected the effect of short-chain alcohols on the solubilization process. The obtained results allowed us to propose a cooperative mechanism that explained the aggregation behavior observed for different alcohols and its effects on oil solubility, a key factor considering applications related to enhanced oil recovery.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473357","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}
Eric Lindgren, Jan Swenson, Christian Müller, Paul Erhart
{"title":"Probing Glass Formation in Perylene Derivatives via Atomic-Scale Simulations and Bayesian Regression.","authors":"Eric Lindgren, Jan Swenson, Christian Müller, Paul Erhart","doi":"10.1021/acs.jpcb.5c00837","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00837","url":null,"abstract":"<p><p>While the structural dynamics of chromophores are of interest for a range of applications, it is experimentally very challenging to resolve the underlying microscopic mechanisms. At the same time, glassy dynamics are also challenging for atomistic simulations due to the underlying dramatic slowdown over many orders of magnitude. Here, we address this issue by combining atomic scale simulations with autocorrelation function analysis and Bayesian regression, and apply this approach to a set of perylene derivatives as prototypical chromophores. The predicted glass transition temperatures and kinetic fragilities are in semiquantitative agreement with experimental data. We suggest that the remaining error could be caused by an overestimation of the intermolecular cohesion by the force field used in this work. By analyzing the underlying dynamics via the normal vector autocorrelation function, we are able to connect the β and α-relaxation processes in these materials to caged (or librational) dynamics and cooperative rotations of the molecules, respectively. The workflow presented in this work serves as a stepping stone toward understanding glassy dynamics in many-component mixtures of perylene derivatives and is readily extendable to other systems of chromophores.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473355","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":"Do α, α-(1-1)-Linked Disaccharides Enhance Stability of the Lipid Bilayer more than α, β-Linked Disaccharides under Desiccation?","authors":"Nirupma Rani, Archita Maiti, Snehasis Daschakraborty","doi":"10.1021/acs.jpcb.5c01946","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01946","url":null,"abstract":"<p><p>Disaccharides play a crucial role in protecting biological membranes from desiccation. Previous studies suggest that disaccharides with α,α-(1-1) glycosidic linkages, which adopt a clamshell conformation in the crystalline phase, are more effective under dry conditions than those with α,β-glycosidic linkages, which have an open structure. However, their relative effectiveness under hydrated conditions remains unclear. To address this, we conducted molecular dynamics (MD) simulations of <i>E. coli</i> lipid membranes across hydration levels (<i>h</i> = 42 to 2) in the presence of α,α-galacto-trehalose and α,β-trehalose, comparing them with previously studied sucrose and α,α-trehalose. This selection allows us to evaluate the role of glycosidic linkages under varying hydration. Our results reveal that in the presence of even minimal water, all four disaccharides exhibit similar membrane-stabilizing effects, mitigating desiccation-induced stress by reducing lipid-lipid interactions and preventing excessive lipid packing. The structural advantage of α,α-(1-1)-linked sugars observed in the crystalline phase does not persist under hydrated conditions. These findings provide molecular-level insights into the protective mechanisms of disaccharides, suggesting that organisms may accumulate different sugars not necessarily for their intrinsic superiority but for availability and metabolic adaptability. This study refines our understanding of sugar-mediated membrane stabilization under desiccation stress, offering a broader perspective on the selection of protective solutes in biological systems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473354","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}
Tao Xiong, Madhusudan Tyagi, Wei Zhou, Hongyu Guo, Robert M Briber, Howard Wang
{"title":"Quasi-Elastic Neutron Scattering on Bimodal Dynamics in Molecular Solutions of Cellulose.","authors":"Tao Xiong, Madhusudan Tyagi, Wei Zhou, Hongyu Guo, Robert M Briber, Howard Wang","doi":"10.1021/acs.jpcb.5c02179","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02179","url":null,"abstract":"<p><p>Local dynamics in molecular solutions of cellulose have been studied using quasi-elastic neutron scattering on ternary mixtures of microcrystalline cellulose, ionic liquid 1-ethyl-3-methyl-imidazolium acetate, and cosolvent dimethylformamide. Two distinct dynamic behaviors in solutions have been identified, with slow dynamics likely attributed to long-range translational diffusion and fast dynamics likely involving the motion of IL in nanoaggregates. The presence of cellulose suppresses both dynamic modes as the residence time for both slow and fast dynamics increases, while the radius of confinement remains invariant upon cellulose dissolution. Arrhenius activation behaviors are followed generally; the activation energy decreases for fast dynamics upon cellulose dissolution while showing no measurable change for slow ones. This study offers new information about the dynamics of an important class of renewable biomaterials.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473356","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 Simulations of Oil Detachment from Hydrophobic Surfaces by Using Janus Nanoparticles.","authors":"Tomasz Staszewski, Małgorzata Borówko","doi":"10.1021/acs.jpcb.5c01850","DOIUrl":"10.1021/acs.jpcb.5c01850","url":null,"abstract":"<p><p>Janus particles composed of two parts with different chemical properties can be used for enhanced oil recovery. We investigated the role of Janus dimers in the process of detachment of oil aggregates from hydrophobic solid surfaces using molecular dynamics. Large-scale simulations were performed for different sets of parameters characterizing the system. The effects of interactions between Janus particles and a solid surface and with an oil droplet were considered. We found two main mechanisms of enhanced oil removal: the \"kidnaping\" of oil aggregates by Janus nanoparticles from the substrate and the competitive adsorption of nanoparticles at the solid surface. In the case of weak affinity of Janus particles with the substrate, the first mechanism dominated, whereas when the affinity was strong, the second mechanism played an important role. We showed how the amphiphilicity of Janus particles and their concentration influence the shape and internal structure of oil aggregates adsorbed on a hydrophobic surface. The high amphiphilicity of Janus particles and their increased concentration promote the process of removing oil from the surface. We analyzed the time evolution of the system after the addition of Janus particles in detail. In the \"kidnaping\" process, the flat oil aggregate left the surface as a large, sandwich-like aggregate, while the adsorption of Janus particles on the surface caused it to break up into small pieces that left the surface as nearly spherical droplets.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144367652","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 Insight into the Coalescence Mechanism of Droplets Stabilized by Amphiphilic Polymer-Grafted Nanoparticles.","authors":"Chiho Inada, Yusei Kobayashi, Masashi Yamakawa","doi":"10.1021/acs.jpcb.5c01676","DOIUrl":"10.1021/acs.jpcb.5c01676","url":null,"abstract":"<p><p>Recent progress in developing amphiphilic polymer-grafted nanoparticles (PGNPs) has led to extensive research on efficiently preparing emulsion droplets stabilized by these PGNPs. However, the molecular-level mechanism of droplet coalescence remains unclear. This study examines the relationship between the interfacial structures of PGNPs and the resistance force of emulsion droplets during coalescence, focusing on various grafting architectures and graft densities. A hybrid simulation approach combining dissipative particle dynamics and steered molecular dynamics is used to investigate this process. We observed various coalescence mechanisms at the molecular level based on the graft density. At low graft densities, the monolayered structure of the PGNP core between two oil droplets significantly contributes to the resistance against droplet-droplet coalescence due to the insufficient number of grafted polymers. Thus, diblock PGNPs with inner hydrophilic blocks are promising candidates for stabilizing emulsions, as they are pushed out from the droplet surface by the block immersed in the oil phase. Conversely, at higher graft density, this graft design causes the formation of the \"sticky\" point, promoting coalescence. On the other hand, diblock PGNPs with outer hydrophilic blocks exhibited a larger resistance force, accompanied by (multiple) layered structures between the two droplets during collision. More interestingly, the layer of Janus PGNPs had insufficient structural robustness, even at a high graft density, due to the penetration of the grafted homopolymers. These results improve the understanding of emulsion droplet coalescence and offer a theoretical guideline for designing optimal PGNPs for specific grafting architectures and graft densities.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144339695","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}
Alexey Bogdanov, Veronica Frydman, Xun-Cheng Su, Daniella Goldfarb
{"title":"Decoherence of Hyperfine Coupled <sup>19</sup>F and <sup>1</sup>H Nuclei in Gadolinium(III) Model Complexes.","authors":"Alexey Bogdanov, Veronica Frydman, Xun-Cheng Su, Daniella Goldfarb","doi":"10.1021/acs.jpcb.5c03224","DOIUrl":"10.1021/acs.jpcb.5c03224","url":null,"abstract":"<p><p>Time-domain electron-nuclear double resonance (ENDOR) was employed to determine the nuclear decoherence rate (1/<i>T</i><sub>2n</sub>) of fluorine nuclei in four model Gd(III) chelates of varying structures, over the temperature range 3.7-10 K. These complexes are derivatives of Gd(III) spin labels used in <sup>19</sup>F-ENDOR distance measurements, which emerged as an efficient method for measuring short-range distances in biomolecules. It was found that the <sup>19</sup>F decoherence originates primarily from electron spin flips, following the relationship <i>T</i><sub>2n</sub> ≈ 2<i>T</i><sub>1e</sub>, where <i>T</i><sub>1e</sub> is the Gd(III) spin-lattice relaxation time. The obtained <sup>19</sup>F decoherence rates (1-8 kHz) indicate that the intrinsic <sup>19</sup>F-ENDOR line widths are small relative to other broadening contributions, and therefore do not significantly limit distance resolution of <sup>19</sup>F ENDOR. Proton decoherence measurements were carried out for comparison, revealing two <sup>1</sup>H populations with different relaxation rates; the faster component was sensitive to the matrix protonation and attributed to dipolar flip-flops among weakly coupled protons, a mechanism absent for <sup>19</sup>F. These results elucidate key factors affecting ENDOR resolution and provide new insights into the nuclear spin relaxation mechanism in paramagnetic systems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144339693","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}