The Journal of Physical Chemistry B最新文献

Polymer-grafted nanoparticles are versatile building blocks that self-assemble into a diverse range of mesostructures. Coarse-grained molecular simulations have commonly accompanied experiments by resolving structure formation pathways and predicting phase behavior. Past simulations represented nanoparticles as spheres and the ligands as flexible chains of beads, isotropically tethered to the nanoparticles. Here, we investigate a different minimal coarse-grained model. The model consists of an attractive rod tethered to a repulsive sphere. The motivation of this rod–sphere model is to describe nanospheres with a partially crystallized, stretched polymeric bundle as well as other complex building blocks such as rigid surfactants and end-tethered nanorods. Varying the ratio of sphere size to rod radius stabilizes self-limited clusters and other mesostructures with reduced dimensionality. The complex phase behavior we observe is a consequence of geometric frustration.

The interaction of low energy electrons (LEEs; 1–30 eV) with genomic material can induce multiple types of damage that may cause the loss of genetic information, mutations, genome instability, and cell death. For all damages measurable by electrophoresis, we provide the first complete set of G-values (yield of a specific product per energy deposited) induced in plasmid DNA by the direct and indirect effects of LEEs (G_LEE) and 1.5 keV X-rays (G_X) under identical conditions. Low energy photoelectrons are produced via X-rays incident on a tantalum (Ta) substrate covered with DNA and placed in a chamber filled with nitrogen at atmospheric pressure, under four different humidity levels, ranging from dry conditions to full hydration (Γ = 2.5 to Γ = 33, where Γ is the number of water molecules/nucleotide). Damage yields are measured as a function of X-ray fluence and humidity. G_LEE values are between 2 and 27 times larger than those for X-rays. At Γ = 2.5 and 33, G_LEE values for double strand breaks are 27 and 16 times larger than G_X, respectively. The indirect effect contributes ∼50% to the total damage. These G-values allow quantification of potentially lethal lesions composed of strand breaks and/or base damages in the presence of varying amounts of water, i.e., closer to cellular conditions.

The Microtubule-binding repeat region (MTBR) of Tau has been studied extensively due to its pathological implications in neurodegenerative diseases like Alzheimer’s disease. The pathological property of MTBR is mainly due to the R3 repeat’s high propensity for self-aggregation, highlighting the critical molecular grammar of the repeat. Utilizing the R1R3 construct (WT) and its G326E mutant (EE), we determine the distinct characteristics of various peptide segments that modulate the aggregation propensity of the R3 repeat using NMR spectroscopy. Through time-dependent experiments, we have identified ³¹⁷KVTSKCGS³²⁴ in R3 repeat as the aggregation initiating motif (AIM) due to its role at the initial stages of aggregation. The G326E mutation induces changes in conformation and dynamics at the AIM, thereby effectively abrogating the aggregation propensity of the R1R3 construct. We further corroborate our findings through MD simulations and propose that AIM is a robust site of interest for tauopathy drug design.

The photoionization dynamics of indole, the ultraviolet-B chromophore of tryptophan, were explored in water and ethanol using ultrafast transient absorption spectroscopy with 292, 268, and 200 nm excitation. By studying the femtosecond-to-nanosecond dynamics of indole in two different solvents, a new photophysical model has been generated that explains many previously unsolved facets of indole’s complex solution phase photochemistry. Photoionization is only an active pathway for indole in aqueous solution, leading to a reduction in the fluorescence quantum yield in water-rich environments, which is frequently used in biophysical experiments as a key signature of the protein-folded state. Photoionization of indole in aqueous solution was observed for all three pump wavelengths but via two different mechanisms. For 200 nm excitation, electrons are ballistically ejected directly into the bulk solvent. Conversely, 292 and 268 nm excitation populates an admixture of two ¹ππ* states, which form a dynamic equilibrium with a tightly bound indole cation and electron–ion pair. The ion pair dissociates on a nanosecond time scale, generating separated solvated electrons and indole cations. The charged species serve as important precursors to triplet indole production and greatly enhance the overall intersystem crossing rate. Our proposed photophysical model for indole in aqueous solution is the most appropriate for describing photoinduced dynamics of tryptophan in polypeptide sequences; tryptophan in aqueous pH 7 solution is zwitterionic, unlike in peptides, and resultantly has a competitive excited state proton transfer pathway that quenches the tryptophan fluorescence.

Polarized Fourier transform infrared (p-FTIR) spectroscopy is a widely used technique for determining orientational information in thin organic materials. Conventionally, a single polarizer is placed in the path of the incident light (termed the polarizer). Occasionally, a second polarizer is also placed after the sample (referred to as the analyzer). However, this polarizer–analyzer configuration has the potential to induce polarization-dependent variances in the final spectra beyond those that are expected, i.e., the squared-cosine relationship of absorptance with respect to polarization angle is no longer accurate. These variances are due to changes in the polarization state of the transmitted light induced by the sample and have yet to be explored in the context of p-FTIR. Consequently, this study employs both theoretical and experimental approaches to identify the effects of including a second polarizer in p-FTIR analyses of anisotropic organic samples. For thin samples, the most significant spectral variance arising from only birefringence is observed on the shoulders of the dichroic peaks. By adopting a crossed polarizer configuration, it is shown that there is potential to identify anisotropy of samples that are generally considered too thick for p-FTIR analysis by exploiting this feature. Furthermore, the squared-cosine relationship of absorptance with respect to the polarization angle is also shown to be inapplicable when a second parallel-oriented polarizer is included. Accordingly, a function that accounts for the second polarizer is proposed for multiple polarization techniques.

Low-energy (<20 eV) electrons (LEEs) can resonantly interact with DNA to form transient anions (TAs) of fundamental units, inducing single-strand breaks (SSBs), and cluster damage, such as double-strand breaks (DSBs). Shape resonances, which arise from electron capture in a previously unfilled orbital, can induce only a SSB, whereas a single core-excited resonance (i.e., two electrons in excited orbitals of the field of a hole) has been shown experimentally to cause cluster lesions. Herein, we show from time-dependent density functional theory (TDDFT) that a core-excited resonance can produce a DSB, i.e., a single 5 eV electron can induce two close lesions in DNA. We considered the nucleotide with the G–C base pair (ds[5′-G-3′]) as a model for electron localization in the DNA double helix and calculated the potential energy surfaces (PESs) of excited states of the ground-state TA of ds[5′-G-3′], which correspond to shape and core-excited resonances. The calculations show that shape TAs start at ca. 1 eV, while core-excited TAs occur only above 4 eV. The energy profile of each excited state and the corresponding PES are obtained by simultaneously stretching both C5′–O5′ bonds of ds[5′-G-3′]. From the nature of the PES, we find two dissociative (σ*) states localized on the PO₄ groups at the C5′ sites of ds[5′-G-3′]. The first σ* state at 1 eV is due to a shape resonance, while the second σ* state is induced by a core-excited resonance at 5.4 eV. As the bond of the latter state stretches and arrives close to the dissociation limit, the added electron on C transfers to C5′ phosphate, thus demonstrating the possibility of producing a DSB with only one electron of ca. 5 eV.

Using Langevin dynamics simulations and a coarse-grained primitive model of electrolytes, we show that the behavior of knotted circular strong polyelectrolytes (PEs) in diluted aqueous solution is largely affected by the diameter of the counterions (CIs), σ_CI. Indeed, we observe that both gyration radius and knot length vary nonmonotonically with σ_CI, with both small and bulky CIs favoring knot localization, while medium-sized ones promote delocalized knots. We also show that the conformational change from delocalized to tight knots occurs via the progressive coalescence of the knot’s essential crossings. The emerging conformers correspond to the minima of the free energy landscape profiled as a function of the knot length or PE size. We demonstrate that different conformational states can coexist, the transition between them appearing first-order-like and controlled by the enthalpic and entropic trade-off of the amount of CIs condensed on the PE. Such balance can be further altered by varying CI concentrations, thus providing an additional and more convenient tuning parameter for the system properties. Our results lay the foundation for achieving broader and more precise external adjustability of knotted PE size and shape by choosing the nature of its CIs. Thus, they offer new intriguing possibilities for designing novel PE-based materials that are capable of responding to changes in ionic solution properties.

Ultrasmall gold nanoparticles were functionalized with peptides of two to seven amino acids that contained one cysteine molecule as anchor via a thiol–gold bond and a number of alanine residues as nonbinding amino acid. The cysteine was located either in the center of the molecule or at the end (C-terminus). For comparison, gold nanoparticles were also functionalized with cysteine alone. The particles were characterized by UV spectroscopy, differential centrifugal sedimentation (DCS), high-resolution transmission electron microscopy (HRTEM), and small-angle X-ray scattering (SAXS). This confirmed the uniform metal core (2 nm diameter). The hydrodynamic diameter was probed by ¹H-DOSY NMR spectroscopy and showed an increase in thickness of the hydrated peptide layer with increasing peptide size (up to 1.4 nm for heptapeptides; 0.20 nm per amino acid in the peptide). ¹H NMR spectroscopy of water-dispersed nanoparticles showed the integrity of the peptides and the effect of the metal core on the peptide. Notably, the NMR signals were very broad near the metal surface and became increasingly narrow in a distance. In particular, the methyl groups of alanine can be used as probe for the resolution of the NMR spectra. The number of peptide ligands on each nanoparticle was determined using quantitative ¹H NMR spectroscopy. It decreased with increasing peptide length from about 100 for a dipeptide to about 12 for a heptapeptide, resulting in an increase of the molecular footprint from about 0.1 to 1.1 nm².

The adsorption properties toward methyl orange (MO) were evaluated for poly[2-methyl-1H-indole] and its derivatives. The influence of pH, ionic strength of solution, composition, and amount of sorbent on the adsorption of MO dye was investigated; the kinetics of dye adsorption was studied. The adsorption isotherms were analyzed using different models of sorption equilibrium. The presence of chemical interaction between polyindoles and dye was proved by IR and UV spectroscopy methods. The sorption of MO with polymers is realized mainly due to the formation of electrostatic interactions between the sulfogroup of the dye and the imino group of the sorbent. Microphotographs demonstrate the change in the morphology of polyindoles after adsorption, which further confirms the structural changes in the polymers. It was found that the main factors affecting the sorption capacity of the studied materials are the position and nature of substituents in the polymers and the sorption conditions. For example, polyindoles containing a methoxy group in their structure (o-OMePIn and m-OMePIn) have the best sorption activity. These polymers are effective in adsorbing dyes, which means that they can be used in wastewater treatment.