The Journal of Physical Chemistry B最新文献

Here, we investigate composition fluctuations in theTRUEX organicphase, a chemical system developed for liquid–liquid extraction(LLE) of transuranic elements from acidic aqueous media. This organicphase consists of two amphiphilic extractants, TBP (tributyl phosphate)and CMPO (octyl(phenyl)-N,N-diisobutylcarbamoylmethylphosphine oxide)dissolved in dodecane. Previous studies of similar LLE systems involvingonly a single extractant have found critical fluctuations associatedwith phase separation within the organic phase that are consistentwith the 3D Ising universality class. Here we use small-angle X-rayscattering (SAXS) to observe the growth of equilibrium fluctuationsas a function of temperature approaching the instability (spinodal).We also use X-ray photon correlation spectroscopy (XPCS) to characterizethe dynamics of the fluctuations. Both the statics and dynamics obeyscaling laws from the theory of critical fluctuations but with parametersthat differ from those expected for binary fluids. Viewing the mesoscalestructures in these LLE systems in terms of critical fluctuationsprovides a general framework for understanding their function.

Essential fatty acids, particularly the ω-3 speciessuchas α-linolenic acid, are critical nutritional components, withtheir biosynthetic dysregulation implicated in neurodegenerative disorders.At the molecular scale, unsaturated fatty acids are recognized fortheir ability to modulate membrane physicochemical properties, primarilyfluidity, but these interactions remain mechanistically complex andpoorly defined. This study combines atomistic molecular dynamics simulationswith depth-dependent fluorescence spectroscopy to systematically evaluatethe impact of increasing acyl chain unsaturation on model lipid bilayers.By examining both protonated and deprotonated states, we demonstratethat ionization significantly dictates fatty acid localization withinthe bilayer, but the differences in membrane properties are relativelyless pronounced. Our findings reveal that fatty acid effects are highlyanisotropic, resulting in non-uniform perturbations to membrane structuraland mechanical profiles. Crucially, the relationship between degreeof unsaturation and membrane fluidity is nonlinear. Paradoxically, α-linolenic acid, despite possessing three doublebonds, does not always induce the largest degree of membrane disorder.Instead, fatty acids with lower unsaturation, such as oleic and linoleicacids, could exhibit more pronounced increase in fluidity in a position-dependentmanner. This non-monotonic behavior challenges the prevailing assumptionin membrane biophysics that unsaturation correlates linearly withdisorder, suggesting that existing predictive models require refinementto account for these specific molecular differences.

Electrostatic interactions often play a role in determiningthethermodynamic and kinetic properties of protein–protein interactions.However, the role of long-range electrostatic interactions in intrinsicallydisordered protein (IDP) binding is less clear, as they often bindin multiple steps, including initial formation of a disordered encountercomplex, followed by rearrangement into the bound state. We variedthe salt concentration to probe the role of long-range electrostaticinteractions in the binding of the highly charged AbpSH3 domain andthe oppositely charged IDP ArkA. Using isothermal titration calorimetry,we observed that salt enthalpically destabilizes the bound complex.Molecular dynamics and NMR experiments revealed that salt has littleeffect on the bound state structure. However, simulations show thatsalt destabilizes the encounter complex intermediate, which primarilyaffects the association rate as measured by NMR. Consistent with theseresults, salt has the largest stabilizing effect on the apo SH3 domain,as cations substitute for the transient and long-range electrostaticinteractions that can form with ArkA in the complex. We revealed adetailed picture of how a highly charged domain uses long-range, fuzzy,electrostatic interactions to help reach the bound state, a mechanismthat is likely common among other highly charged domains that bindIDPs.

Temperature-dependent Fourier-transform infrared (FTIR)and two-dimensionalinfrared (2D IR) spectroscopic measurements are performed on CH₃COOH dissolved in CH₃CN over the temperature rangeof 4–62 °C. CH₃COOH exists as two conformers,the syn- and anti-isomers, whoserelative populations vary with temperature. At each temperature, theirrelative populations are determined by FTIR and 2D IR spectroscopy,supported by numerical simulations of the corresponding spectra. Accuratedetermination of the temperature-dependent populations enables theenthalpy difference (ΔH) and entropy difference(ΔS) between the two isomers to be obtainedfrom a van ’t Hoff analysis. The resulting thermodynamic parametersfor the syn ⇄ anti isomerizationare ΔH = 6.34 ± 0.27 kJ·mol^–1 and ΔS = −0.64 ± 0.88 J·mol^–1·K^–1, indicating that the conformationalequilibrium is dominated by the enthalpic contribution.

Surface functionality and pH play a decisive role ingoverningthe structural dynamics, hydration, and drug-binding behavior of dendrimers.Here, all-atom molecular dynamics (MD) simulations were performedon five generations of PAMAM (G1-G5) and PETIM (G2-G6) dendrimerswith O-core and N-core architectures, functionalized with amine, carboxylicacid, or sugar terminal groups under different protonation states.Protonation of the tertiary branch-point amines expands the dendrimerstructure, increases internal porosity and hydration, and enhancesstructural fluctuations across both families. In contrast, nonprotonatedamine –NH₂ (NP)- and carboxylic acid −COOH(NP)-terminated dendrimers, together with deprotonated carboxylate−COO^– (DeP) systems, retain comparativelycompact conformations. Sugar-functionalized dendrimers (β-galactose-terminatedPETIM and d-glucose-terminated PAMAM) are most hydrated andstructurally rigid, whereas amine-terminated dendrimers exhibit thegreatest conformational dynamics. PAMAM dendrimers with –NH₂, –NH₃⁺, and −COO^– terminal groups are generally more hydrated than theirPETIM counterparts. However, β-galactose-terminated PETIM dendrimersare more hydrophilic than d-glucose-terminated PAMAM dendrimers.N-core PETIM dendrimers also adopt more compact and spherical conformationsthan equivalent O-core PETIM dendrimers. Drug-binding MD simulationsshow that curcumin binding is dominated by van der Waals (vdW) interactions,whereas doxorubicin complexation is primarily driven by electrostaticinteractions. Among the investigated surface functionalities, –NH₂ (NP), –NH₃⁺ (P), −COOH(NP), and −COO^– (DeP) terminations exhibitthe most favorable drug-binding characteristics. Except for deprotonatedcarboxylate systems, curcumin binds more strongly than doxorubicin.Further, drug clustering and spatial organization are governed bydendrimer surface functionality, protonation state, drug loading,and drug-specific interactions. Protonation and higher loading promotedrug–drug association, with curcumin and doxorubicin preferentiallylocalizing toward the inner and outer dendrimer regions, respectively.Overall, these findings establish molecular-level relationships betweensurface functionality, protonation state, dendrimer architecture,and drug-binding behavior, providing design principles for pH-responsivedendrimer nanocarriers with enhanced drug-loading and controlled-releaseperformance.

The performance of doped organic semiconductors (OSCs)is governedby a strong coupling between the doping equilibrium and the film morphology,yet capturing both simultaneously in a single atomistic model hasremained difficult. Here we use the reactive Monte Carlo moleculardynamics (RMCMD) method to study poly(3-hexylthiophene) (P3HT) dopedwith 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ),a prototypical OSC-dopant pair, and show that dopant aggregation anddoping efficiency are mutually determined. We find that ionizationconverts a preaggregated dopant cluster into a mixed P3HT/F4TCNQ “coaggregate”whose extent is set by the reaction free energy; as dopants ionize,Coulomb repulsion drives them apart and pulls in ionized P3HT so thathigher doping efficiency and greater OSC-dopant mixing are self-reinforcing.Introducing explicit solvent, we observe ionization-driven P3HT/F4TCNQcoaggregation and displacement of solvent from the dopant coordinationshell, consistent with experimentally reported poor solubility ofionized P3HT/F4TCNQ complexes. We also observe a higher doping efficiencyin the more polar solvent acetonitrile than in chlorobenzene.

Keratin-derived antimicrobial peptides (KAMPs) from humancornealepithelial cells have received considerable attention due to theirbiocidal activity against both Gram-positive and Gram-negative bacteriawithout possessing the conventional characteristics of known antimicrobialpeptides (AMPs), such as ordered secondary structure elements anda net positive charge. Here, we perform unbiased, all-atom moleculardynamics (MD) simulations for seven members of the glycine-rich KAMPfamily and for Pw-Antibac12₃, which is a distinct keratin-derivedpeptide obtained through chicken feather hydrolyzates. This studyfirst aims to investigate the structural dynamics of these peptidesin dilute and semidilute aqueous solutions. Our results verify thenoncanonical structure of KAMPs and validate the molecular model ofPw-Antibac12₃ that has been proposed in the literature.Increasing the peptide concentration in the aqueous solution leadsto self-assembly and peptide aggregation, due to the development ofinterpeptide hydrogen bonds and the strong effect of electrostaticinteractions. The effect of intermolecular amino acid interactionson the secondary structure of KAMPs is also discussed, allowing usto identify strong synergies between specific amino acid pairs, suchas serine and glycine, valine and leucine, and arginine and isoleucine.Subsequently, we focus on how KAMP-18C, an 18-residue-long KAMP, interactswith model Gram-positive lipid bilayers. Since spontaneous aggregationis not observed, we construct artificial pores and embed peptideswithin the membrane to assess the stability of these systems. We discusshow our findings correlate with proposed mechanisms of action forAMPs.

The hydrophobic effect is often considered a major drivingforcefor molecular recognition in water, whether through classical desolvationof nonpolar surfaces or through the release of confined high-energywater from host cavities. However, the interplay between protonation,ion–dipole interactions, and hydration remains poorly understood.Here we show that amino-acid recognition by cucurbit[7]uril (CB7)is best described as a population-weighted ensemble of proton-linkedhydration states, rather than as a single water-release process. Bycombining pH-dependent isothermal titration calorimetry, X-ray crystallography,molecular dynamics simulations, and interaction-energy analysis, weconnect the pH-dependent apparent binding affinities with cavity andportal hydration coupled to ammonium–portal ion–dipolestabilization. Aromatic amino acids differ not by adopting fundamentallydifferent binding modes, but by redistributing population among fourhydration states defined by the position of water relative to thecavity and ammonium anchor. Phe and Trp represent opposite limits,with Phe favoring cooperative cavity-water contact and Trp dominatedby dry-cavity filling, whereas Tyr and DOPA shift the ensemble towardportal-solvated states. These results show that confined water canstrengthen, rather than oppose, hydrophobic recognition when integratedinto the ion–dipole binding motif and proton linkage. CB7–amino-acidrecognition therefore emerges as a coupled process in which hydrophobicinclusion, ammonium anchoring, hydration, and proton linkage act together.

Lipid nanoparticles(LNPs) are the leading platform forRNA delivery,enabling applications ranging from mRNA vaccines to CRISPR therapeutics.Ionizable lipids, such as DLin-MC3-DMA (MC3), play a central rolein nucleic acid encapsulation and intracellular delivery, yet themolecular mechanisms governing LNP structure and function remain incompletelyunderstood. The internal organization of LNP cores is highly sensitiveto pH and has been described by inverse hexagonal, cubic, and lamellarphases that influence delivery performance. Here, we investigate thepH-dependent structure and dynamics of MC3-containing LNPs using two-dimensionalinfrared (2D IR) spectroscopy and molecular dynamics (MD) simulations.Both experiments and simulations reveal pronounced pH-dependent changesin the local environment surrounding the lipid ester linkage. At pH4, strong electrostatic interactions between RNA and protonated MC3produce broader spectral features consistent with increased interfacialheterogeneity and hydration. In addition, the frequency fluctuationdynamics exhibit a 46% slowdown in RNA-loaded LNPs relative to emptyLNPs. In contrast, increasing the pH from 4 to 8 narrows the estercarbonyl band by ∼10 cm^–1 and yields nearlyidentical dynamics for loaded and empty LNPs, indicating a more homogeneousand less hydrated lipid interface. MD simulations further demonstratethat MC3 protonation modulates RNA binding, interfacial hydration,and lipid packing. Together, these results highlight RNA-lipid electrostaticinteractions as an important factor influencing the local environmentwithin LNPs and potentially their pH-dependent behavior, providingmolecular-level insights into the rational design of next-generationRNA delivery systems.

The acid-catalyzed hydrolysis mechanism of the N-glycosidic bond in pyrimidine 2′,3′-didehydro-2′,3′-dideoxynucleosides(d4Ns), including d4U, d4T, d4C, and d4FC, was investigated usingmolecular dynamics (MD) simulations to refine microsolvated models,followed by density functional theory (DFT) calculations at the M06-2X(CPCM)/6-31+G(d)level of theory, with single-point energies refined at the M06-2X(CPCM)/6-311++G(d,p)level. Three plausible pathways─α-path (inversion atC1′), β-path (retention at C1′), and γ-path(aromatization to form a furfuryl alcohol)─were evaluated.The first stage, cleavage of the N-glycosidic bondto form an oxacarbenium ion intermediate, is the rate-determiningstep (RDS) for all pathways. Acidic conditions dramatically catalyzethe hydrolysis, lowering the activation free energy by approximately10 kcal mol^–1 compared to neutral conditions. Theγ-path exhibits a distinct kinetic and thermodynamic advantagefor d4U and d4T, driven by aromatization of the furfuryl alcohol sugar,which aligns with experimental observations of γ-product formation.The 5-methyl group in d4T increases the activation barrier relativeto d4U, while the 5-fluoro group in d4FC lowers the barrier by ∼2kcal mol^–1 compared to d4C, indicating an electron-withdrawingpromoting effect. Heterolytic dissociation of the N-glycosidic bond is favored over homolytic dissociation in both gasand aqueous phases, consistent with the charge-separated intermediatesidentified. Nucleus-independent chemical shift (NICS) analyses quantifythe increasing aromaticity along the γ-path, rationalizing itsthermodynamic favorability. These computational insights elucidatehow nucleobase protonation and substituent effects govern the stabilityof the glycosidic bond and the unusual formation of γ-cleavageproducts in acidic d4N hydrolysis.