The Journal of Physical Chemistry B最新文献

Protein MJ0366 is a hypothetical protein from Methanocaldococcus jannaschii that has a rare and complex knot in its structure. The knot is a right-handed trefoil knot that involves about half of the protein’s residues. In this work, we investigate the thermal stability of protein MJ0366 using numerical simulations based on molecular dynamics and Monte Carlo methods. We compare the results with those of a similar unknotted protein and analyze the effects of the knot on the folding and unfolding processes. We show that the knot in protein MJ0366 increases its thermal stability by creating a topological barrier that prevents the protein from unfolding at high temperatures.

This work focuses on the reaction mechanism of poly(sulfur nitride) ((SN)_x, (S¹⁵N)_x), with the ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate [EMIm][OAc]. We compare this with the reaction of the IL with S₄N₄ or its ¹⁵N-labeled form S₄¹⁵N₄, a precursor for the synthesis of (SN)_x and (S¹⁵N)_x. After purification of the S₄N₄–IL- and S₄¹⁵N₄–IL systems via column chromatography, we characterized the reaction products with ¹H, ¹³C, and ¹⁵N nuclear magnetic resonance spectroscopy and with electron spray ionization time-of-flight mass spectrometry. Furthermore, time-resolved electron paramagnetic resonance spectroscopy and time-resolved ultraviolet–visible spectroscopy were carried out. Thus, radical intermediates were detected, which were consumed with reaction time. Finally, we postulate a reaction mechanism for the S₄N₄–IL- and S₄¹⁵N₄–IL systems and compare this with the respective data for the (SN)_x −IL- and (S¹⁵N)_x–IL-systems.

As demonstrated in in vitro studies, polystyrene nanoplastics (PSNPs) are effectively internalized by various cells. All known mechanisms of PSNP internalization involve the initial step of their interaction with the cell membrane, highlighting the importance of understanding such interactions at the molecular level. Here we consider the effects of PSNPs obtained from disposable food packaging on zwitterionic lipid membranes, used as a model system for protein-free cell membranes. We combined microscopic imaging and unbiased atomistic molecular dynamics (MD) to investigate the behavior of PSNPs on the surface and inside the lipid membrane. Our results show that PSNPs are hydrated and have a high negative surface charge when dispersed in an aqueous media. The penetration of PS nanoparticles into the lipid bilayer requires the removal of water molecules at the nanoparticle–membrane interface, which is an effective barrier to the entry of PSNPs into its hydrophobic region. Overcoming this energy barrier by slightly inserting the PS nanoparticle into the polar region of the membrane leads to its rapid penetration into the center of the bilayer and coating its surface with lipid molecules. PS nanoplastics do not disaggregate after penetrating the lipid membrane, which affects the molecular structure of the bilayer. In addition, our MD simulations demonstrated that small-molecule additives (e.g., unreacted monomers) present in nanoplastics can be released into lipid membranes if they are located close to the nanoparticle surface. The outcomes of this study are important for understanding the passive uptake of nanoplastics by cells.

The shear viscosity (η) and kinetic friction coefficient (μ) of highly confined, quasi-two-dimensional ionic liquids (2D ILs) subject to stationary linear flow at constant temperature are studied in this work through coarse-grained numerical simulations. Using stationary state linear flow under increasing shear rate (γ̇), η and μ are predicted as functions of γ̇ for growing coupling constant values (Γ*). The structural changes of the fluid due to the increasing coupling of the charged particles are found to yield increasing shear viscosity and friction coefficient. Shear-thinning is found in all systems, regardless of the value of Γ*. Additionally, it is shown that η and μ obey universal scaling laws, η ∼ γ̇^ζ and μ ∼ γ̇^κ, respectively, with the exponents fulfilling the relationship κ - ζ = 1, in agreement with previous reports by other groups. The implications of our predictions are discussed, in the context of current applications.

In this study, we investigated the intermolecular dynamics, including intermolecular vibration and orientational dynamics, of five deep eutectic solvents (DESs) consisting of lithium bis(trifluoromethylsulfonyl)amide and organic amides, such as acetamide, propanamide, N-methylacetamide, butyramide, and urea, at a mole ratio of 1:3 using femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES) and subpicosecond optical Kerr effect spectroscopy (ps-OKES). The fs-RIKES results showed that the line shape of the low-frequency band of the N-methylacetamide was trapezoidal, while that of the other organic amide-based DESs was bimodal. The peak and first moment of the intermolecular vibrational band appearing in the frequency range less than 250 cm^–1 for the acetamide- and urea-based DESs were in a higher-frequency region compared to the other three DESs, indicating stronger intermolecular interactions. Furthermore, analysis of the intramolecular vibrational bands of the bis(trifluoromethylsulfonyl)amide anion showed that the population of the transoid conformer of the anion was slightly higher in the urea-based DES than in the other organic amide-based DESs, suggesting that urea solvate lithium cations more than the other organic amides. The slow relaxation dynamics of all five DESs were captured for up to 1 ns using ps-OKES. The slow relaxation dynamics also depended on the organic amide species. However, the slow relaxation time constant did not show a clear correlation with the viscosity; therefore, the relaxation dynamics of the DESs did not follow the Stokes–Einstein–Debye hydrodynamic model. The densities, viscosities, surface tensions, and electrical conductivities of the DESs were also measured for comparison with spectroscopic results.

The shear viscosity (η) and kinetic friction coefficient (μ) of highly confined, quasi-two-dimensional ionic liquids (2D ILs) subject to stationary linear flow at constant temperature are studied in this work through coarse-grained numerical simulations. Using stationary state linear flow under increasing shear rate (γ̇), η and μ are predicted as functions of γ̇ for growing coupling constant values (Γ*). The structural changes of the fluid due to the increasing coupling of the charged particles are found to yield increasing shear viscosity and friction coefficient. Shear-thinning is found in all systems, regardless of the value of Γ*. Additionally, it is shown that η and μ obey universal scaling laws, η ∼ γ̇^ζ and μ ∼ γ̇^κ, respectively, with the exponents fulfilling the relationship κ – ζ = 1, in agreement with previous reports by other groups. The implications of our predictions are discussed, in the context of current applications.

The size, shape, and charge of structures, such as proteins and amphiphile assemblies, respond in an interconnected manner to solution ionic conditions. We analyze assemblies of an amphiphile (C₁₆K₂), with two ionizable amino acids [lysine (K)] coupled to a 16-carbon alkyl tail, via small-angle X-ray scattering (SAXS), nonlinear Poisson-Boltzmann theory (nl-PB), and hybrid Monte Carlo-molecular dynamics (MC-MD) simulations. SAXS revealed structural transitions from spherical micelles to cylindrical micelles to bilayers with increasing pH. By combining SAXS-determined structural information and nl-PB, we derived the molecular degree of ionization as a function of pH. The back-calculated titration curves matched the experimental data over an extended pH range, without adjustable parameters. Similarly, the SAXS data on the evolution of spherical micelle structure with ionic strength were combined with nl-PB and MC-MD to derive the bare and effective charges. MC-MD, which considered finite ion sizes, showed that bare and effective charges saturate quickly with increasing salt concentration. Furthermore, the calculated effective charges closely matched results from Zeta-potential measurements. The presented approach has advantages over customary methods for charge regulation, such as the Henderson-Hasselbalch (HH) or Hill models, where molecular ionization/deionization in assemblies is described by effective pKs that are distinct from the pK for isolated molecules. However, these models lack a physical explanation for these pK shifts. By contrast, our approach of combining structural details with an electrostatic model and simulations provides a more intuitive understanding of structure-charge coupling and a framework for understanding charge regulation in many synthetic and biological systems.

A Morita–Baylis–Hillman adduct (MBHA) derivative bearing a triphenylamine (TPA) moiety was previously found to react with Nα-acetyl-l-lysine methyl ester with the formation of the corresponding diadduct derivative as the major reaction product and a monoadduct as the minor one. The characterization of photochemical features of the diadduct bearing two triphenylaminocinnamic (TPAC) fluorophores suggested that this compound shows the tendency to undergo the [2 + 2] photocycloaddition reaction. This hypothesis was evaluated in the present study in both the diadduct derivatives obtained with Nα-acetyl-l-lysine methyl ester and Nα-acetyl-l-lysine. The hypothesis was confirmed in the case of the diadduct derivative obtained from Nα-acetyl-l-lysine methyl ester, whereas the UV-A irradiation of the diadduct derivative obtained from Nα-acetyl-l-lysine led to the formation of a strongly emissive (QY = 69%, λ_em = 460 nm) symmetric dimer.

The size, shape, and charge of structures, such as proteins and amphiphile assemblies, respond in an interconnected manner to solution ionic conditions. We analyze assemblies of an amphiphile (C₁₆K₂), with two ionizable amino acids [lysine (K)] coupled to a 16-carbon alkyl tail, via small-angle X-ray scattering (SAXS), nonlinear Poisson–Boltzmann theory (nl-PB), and hybrid Monte Carlo-molecular dynamics (MC-MD) simulations. SAXS revealed structural transitions from spherical micelles to cylindrical micelles to bilayers with increasing pH. By combining SAXS-determined structural information and nl-PB, we derived the molecular degree of ionization as a function of pH. The back-calculated titration curves matched the experimental data over an extended pH range, without adjustable parameters. Similarly, the SAXS data on the evolution of spherical micelle structure with ionic strength were combined with nl-PB and MC-MD to derive the bare and effective charges. MC-MD, which considered finite ion sizes, showed that bare and effective charges saturate quickly with increasing salt concentration. Furthermore, the calculated effective charges closely matched results from Zeta-potential measurements. The presented approach has advantages over customary methods for charge regulation, such as the Henderson–Hasselbalch (HH) or Hill models, where molecular ionization/deionization in assemblies is described by effective pKs that are distinct from the pK for isolated molecules. However, these models lack a physical explanation for these pK shifts. By contrast, our approach of combining structural details with an electrostatic model and simulations provides a more intuitive understanding of structure-charge coupling and a framework for understanding charge regulation in many synthetic and biological systems.

Flavocytochrome c sulfide dehydrogenase (FCC) is an important enzyme of sulfur metabolism in sulfur-oxidizing bacteria, and its catalytic properties have been extensively studied. However, the ultrafast dynamics of FCC is not well understood. We present ultrafast transient absorption and fluorescence spectroscopy measurements to unravel the early events upon excitation of the heme and flavin chromophores embedded in the flavocytochrome c (FccAB) from the bacterium Thiocapsa roseopersicina. The fluorescence kinetics of FccAB suggests that the majority of the photoexcited species decay nonradiatively within the first few picoseconds. Transient absorption spectroscopy supports these findings by suggesting two major dynamic processes in FccAB, internal conversion occurring in about 400 fs and the vibrational cooling occurring in about 4 ps, mostly affecting the heme moiety.