The Journal of Physical Chemistry B最新文献

Perceiving a suitably tuned aqueous solution to unravel water's liquid-liquid critical point (LLCP) has become challenging. In this work, we investigated the structures of light and heavy water in the presence of MgCl₂ using excess infrared spectroscopy and density functional theory calculations. The excess spectroscopy enabled us to differentiate the low-density liquid (LDL) water from the other liquid domains of pure water and reveal the new interaction modes between water and the ions. The addition of salt decreases and then increases the population of LDL in aqueous solutions. At the concentrations of 0.4 M in H₂O and 0.6 M in D₂O, the LDL structures undergo the most significant disruption under ambient conditions in the bulk phase. Furthermore, threshold concentrations of 1 and 1.3 M for light and heavy water, respectively, were found to induce higher LDL populations. The current investigation sheds light on the intriguing liquid-liquid phase transition (LLPT) and the LLCP of water.

Cyclic peptides (CPs) possess the ability to self-assemble into cyclic peptide nanotubes (CPNTs), which find extensive applications in nanotechnology. The formation and stability of these nanotubes are influenced by multiple factors. The present study explores the stability of CPNTs in various solvents with varying polarity, focusing on three specific peptide sequences: DK₄, WL₄, and DLKL₂. Using molecular dynamics simulations, the effect of solvent polarity and peptide composition on the stability of CPNTs is assessed through the determination of electrostatic, van der Waals, and hydrogen-bonding interactions. The binding free energy between adjacent cyclic peptide rings is analyzed via MM/GBSA and MM/PBSA methods, revealing that DLKL₂, an amphiphilic peptide, exhibits greater stability than DK₄ and WL₄ in nonpolar solvents. The introduction of leucine residues in DLKL₂ reduces intramolecular hydrogen bonding and electrostatic interactions, promoting stronger interpeptide backbone hydrogen bonds and maintaining the nanotube's structural integrity. Hydrogen bond lifetimes, computed using the corresponding time correlation function, indicate the longest-lasting hydrogen bonds occur in all the solvent environments except water, further contributing to the stability of DLKL₂ nanotubes. Additionally, deformation from circularity in the peptide rings, analyzed using ellipticity values, highlights the degree of structural distortion across solvents, with DK₄ showing the highest deviation due to stronger intramolecular interactions. These findings offer valuable insights into the roles of solvent and peptide composition in the self-assembly and stability of CPNTs, which have significant implications for their potential applications in nanotechnology and biomedicine.

This article presents experimental characterization information and synchrotron X-ray scattering measurements on a set of novel O- and S-substituted phosphonium-based ionic liquids (ILs) all coupled with the bis(fluorosulfonyl)imide (FSI^-) anion. The ILs include the ethoxyethyltriethylphosphonium (P_222(2O2)⁺) and triethyl[2-(ethylthio)ethyl]phosphonium (P_222(2S2)⁺) cations, and we contrast results on these with those for unsubstituted triethylpentylphosphonium (P₂₂₂₅⁺). The article also introduces a physics-based protocol that combines classical force field studies on larger simulation boxes with classical and first-principles studies on smaller boxes. The method produces significantly improved S(q) functions in the regime which in prior publications we have associated with inter- and intraionic adjacency correlations. By understanding which shorter-range structural changes improve S(q) in the q-regime of interest, we are also able to pinpoint specific deficiencies in the classical force field model. The approach we take should be quite general and could help study other complex liquids on different length scales.

We present a structural characterization of a low-transition-temperature mixture (LTTM), consisting of thymol and carvacrol, at an equimolar ratio. Carvacrol and thymol are natural regioisomers of terpenes. When combined at an equimolar ratio, they form a liquid mixture at room temperature, with supercooling capability and glass transition at ca. 210 K. Using small- and wide-angle X-ray scattering and molecular dynamics, we describe the structural complexity within this system. X-ray scattering reveals a low-Q peak at around 0.6 Å^-1, indicating the existence of mesoscale structural heterogeneities, likely related to the segregation of polar moieties engaged in hydrogen bond (HB) interactions within an aromatic, apolar matrix. These polar interactions are predominantly a result of HBs involving thymol as the HB donor species. The liquid structure is also driven by O-H···π interactions, prevalently due to the ability of the carvacrol π-site to engage in this type of weak interaction as a HB acceptor. Besides, dispersive interactions affect the local arrangement of molecules, with a propensity of carvacrol rings to orient their first neighbors with a perpendicular orientation, while thymol tends to induce a closer approach of other thymol molecules with a preferential parallel alignment. Overall, we observed a complex structural arrangement driven by the interplay of both conventional and weak hydrogen bond interactions, with the aromatic nature of the compounds playing a pivotal role in shaping the system's architecture. Carvacrol and thymol, despite being very similar compounds, are characterized by distinctly different behavior in terms of the interactions they engage in with their neighbors, likely due to the different steric hindrance experienced by their hydroxyl groups, which are close to either a small methyl or a bulky isopropyl group, respectively. Such observations can provide useful hints to develop new solvents with tailored properties.

It is well-known that ionic liquids (ILs) can alter the structural stability of proteins. The change in protein conformation is closely related to the interaction between the protein residue and ILs. To probe the impact of hydrophobic interactions on protein stability in ILs, we conducted molecular dynamic simulations and compared the unfolding process of two proteins, the wild-type villin headpiece protein HP35 and its doubly mutant form HP35NN which contains two hydrophobic norleucine (NLE) substitutions at Lys24/29, in hydrated 1-butyl-3-methylimidazolium chloride ([BMIM]Cl). By sampling at a long time scale, the denaturation ability of ILs was well captured. Specifically, HP35NN exhibits greater structural instability than HP35, characterized by the unfolding of helix-3 where the mutated hydrophobic residues are located. These findings highlight the thermodynamic instability of the protein caused by the mutation of two hydrophobic residues in the ILs. By evaluating the hydration kinetics of helix-3 with ILs, we found that the intramolecular hydrogen bonds of HP35NN were broken. At the same time, HP35NN binds to more ILs through hydrophobic interactions. Therefore, we propose that the hydrophobic interaction between ILs and the mutated hydrophobic residue plays a crucial role in the denaturation of HP35NN. The stability comparison and verification of the alkyl chain model of hydrophobic residues in ILs also further prove the instability of hydrophobic residue mutation in ILs. These findings may provide valuable basic information for understanding the effect of ILs on the conformational stability of proteins.

Quantum chemical methods and time-resolved laser spectroscopy are employed to elucidate ultrafast charge-separation processes in triphenylamine (TPA) derivatives upon photoexcitation. When changing the ambient solvent from non-electron-accepting to electron-acceptor solvents, such as chloroform, a vastly extended and multifaceted photochemistry of TPA derivatives is observed. Following initial excitation, two concurrent charge-transfer processes are identified. When the TPA derivative and solvent molecules are arranged in a configuration that favors efficient electron transfer, charge separation occurs immediately, leading to the formation of a radical cation of the TPA derivative. This highly reactive species can subsequently combine with other TPA derivative molecules to yield a dimeric species. Alternatively, if the molecular positioning upon photoexcitation is not optimal, relaxation back to the S₁ state occurs. From this state, an electron transfer process leads to the formation of a charge-transfer complex, where the negatively charged solvent molecule remains closely associated with the positively charged TPA derivative. Within 30 ps, charge recombination occurs in this complex, resulting in the formation of triplet states. This transition to the triplet state is driven by a lower reaction barrier for charge separation compared to that for the formation of the singlet state.

Vapor-liquid equilibrium (VLE) data of fragrance components are crucial for product development and separation processes. However, experimentally obtaining these data can often be a high-cost and challenging task. In order to address this issue, simulations of VLE data using molecular dynamics (MD) methods have gained attention, though there are still relatively few studies about the vapor-liquid equilibrium calculations of fragrance components using MD. In this study, we focused on a mixture of d-limonene and 1-pentanol as representative components and conducted MD simulations. The VLE data obtained by varying the molar fraction of d-limonene, including x-y phase diagrams and activity coefficients, showed a high degree of agreement with the experimental data. Additionally, an analysis of the density profiles on a molecular level revealed a slight increase in the concentration of 1-pentanol at the vapor-liquid interface.

External stressors modulate the oligomerization state of photosystem I (PSI) in cyanobacteria. The number of red chlorophylls (Chls), pigments lower in energy than the P₇₀₀ reaction center, depends on the oligomerization state of PSI. Here, we use ultrafast transient absorption spectroscopy to interrogate the effective connectivity of the red Chls in excitonic energy pathways in trimeric PSI in native thylakoid membranes of the model cyanobacterium Synechocystis sp. PCC 6803, including emergent dynamics, as red Chls increase in number and proximity. Fluence-dependent dynamics indicate singlet-singlet annihilation within energetically connected red Chl sites in the PSI antenna but not within bulk Chl sites on the picosecond time scale. These data support picosecond energy transfer between energetically connected red Chl sites as the physical basis of singlet-singlet annihilation. The time scale of this energy transfer is faster than predicted by Förster resonance energy transfer calculations, raising questions about the physical mechanism of the process. Our results indicate distinct strategies to steer excitations through the PSI antenna; the red Chls present a shallow reservoir that direct excitations away from P₇₀₀, extending the time to trapping by the reaction center.

Short noncoding RNA molecules play significant roles in catalysis, biological regulation, and disease pathways. Their assessment through sequence-based approaches has been a challenge, compounded by the significant structural flexibility accrued from six free backbone torsions per nucleotide. To efficiently study the structure and dynamics of an extensive repertoire of these molecules in a high throughput mode, we have built a coarse-grained force field using one, two, three, and four pseudoatoms to represent the phosphate, sugar, pyrimidines, and purines, respectively. The Boltzmann inversion method was applied to structures of 5 piRNA, 8 miRNA, and 13 siRNA from the Nucleic Acid Database (NDB) to estimate the initial force field parameters and iteratively optimized through 1 μs molecular dynamics run by comparing against an equivalent all-atom simulation using the CHARMM36 force field. We applied an elastic net to model the hydrogen bond network stabilizing the local structure for double-stranded cases. A spine using pseudoatoms was calculated for the same from the coarse-grain beads, and all beads within a threshold radial distance were constrained using soft distance potentials. Lennard-Jones and Coulomb's potential function modeled the nonbonded interaction. Benchmarks on 26 molecules compared through root-mean-square deviation graphs against all-atom simulation show close concurrence for single- and double-stranded small noncoding RNA molecules. The rCGMM force field is available for download at https://github.com/majumderS/rCGMM.

Microbial rhodopsins are photoreceptor proteins that utilize light to elicit various biological functions. The best-studied microbial rhodopsins are outward proton (H⁺)-pumping rhodopsins, which transport H⁺ from the cytoplasmic to the extracellular side. Recently, the weak organic acid (WOA) effect, specifically the enhancement of pumping activity by WOAs such as acetic acid and indole-3-acetic acid (IAA), was discovered in outward H⁺-pumping rhodopsins from fungi. However, it remains unclear whether the WOA effect exists in nonfungal H⁺-pumping rhodopsins. Here, we revealed that the H⁺-pumping activity of a bacterial outward H⁺ pump rhodopsin, PspR, from the rhizobacterium Pseudomonas putida, is also enhanced by extracellular acetic acid and IAA. Using transient absorption measurements on purified PspR protein, we found that extracellular WOAs accelerate cytoplasmic H⁺ uptake and extracellular H⁺ release from a protonated counterion during its photocycle. Furthermore, acetic acid applied on the cytoplasmic side has an inhibitory effect on the H⁺ pump activity of PspR, which is less significant for IAA and can be mitigated by increasing the H⁺ concentration or introducing a cytoplasmic donor residue. These findings on the WOA effect in a bacterial rhodopsin provide new insights into the physiological function of outward H⁺-pumping rhodopsins in bacteria, particularly in their interaction with plants.