ACS Physical Chemistry Au最新文献

Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various “in silico” techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.

Nanosecond resolved fluorescence correlation spectroscopy (ns-FCS) based on two-color fluorescence detection is a powerful strategy for investigating the fast dynamics of biological macromolecules labeled with donor and acceptor fluorophores. The standard methods of ns-FCS use two single-photon avalanche diodes (SPADs) for the detection of single-color signals (four SPADs for two-color signals) to eliminate the afterpulse artifacts of SPAD at the expense of the efficiency of utilizing photon data in the calculation of correlograms. Herein, we demonstrated that hybrid photodetectors (HPDs) enable the recording of fluorescence photons in ns-FCS based on the minimal system using two HPDs for the detection of two-color signals. However, HPD exhibited afterpulses at a yield with respect to the rate of photodetection (<10^–4) much lower than that of SPADs (∼10^–2), which could still hamper correlation measurements. We demonstrated that the simple subtraction procedure could eliminate afterpulse artifacts. While the quantum efficiency of photodetection for HPDs is lower than that for high-performance SPADs, the developed system can be practically used for two-color ns-FCS in a time domain longer than a few nanoseconds. The fast chain dynamics of the B domain of protein A in the unfolded state was observed using the new method.

Aβ1–40 peptide and Aβ1–42 peptide are the building units of beta-amyloid plaques present in Alzheimer’s disease (AD)-affected brain. The binding affinity of various divalent metal ions such as Cu and Zn present in AD-affected brain with different amino acids available in Aβ-peptide became the focus to explore their role in soluble neurotoxic oligomer formation. Cu²⁺ metal ions are known to enhance the neurotoxicity of the Aβ1–42 peptide by catalyzing the formation of soluble neurotoxic oligomers. The competitive preference of both Cu²⁺ and Zn²⁺ simultaneously to interact with the Aβ-peptide is unknown. The divalent Cu and Zn ions were inserted in explicit aqueous Aβ1–42 peptide configurations to get insights into the binding competence of these metal ions with peptides using classical molecular dynamics (MD) simulations. The metal-ion interactions reveal that competitive binding preferences of various peptide sites become metal-ion-specific and differ significantly. For Cu²⁺, interactions are found to be more significant with respect to those of Asp-7, His-6, Glu-11, and His-14. Asp-1, Glu-3, Asp-7, His-6, Glu-11, and His-13 amino acid residues show higher affinity toward Zn²⁺ ions. MD simulations show notable variation in the solvent-accessible surface area in the hydrophobic region of the peptide. Infinitesimal mobility was obtained for Zn²⁺ compared to Cu²⁺ in an aqueous solution and Cu²⁺ diffusivity deviated significantly at different time scales, proving its labile features in aqueous Aβ1–42 peptides.

The development of high-activity and low-price cathodic catalysts to facilitate the electrochemically sluggish O₂ reduction reaction (ORR) is very important to achieve the commercial application of fuel cells. Here, we have investigated the electrocatalytic activity of the two-dimensional single-layer Nb-doped zirconium diselenide (2D Nb-ZrSe₂) toward ORR by employing the dispersion corrected density functional theory (DFT-D) method. Through our study, we computed structural properties, electronic properties, and energetics of the 2D Nb-ZrSe₂ and ORR intermediates to analyze the electrocatalytic performance of 2D Nb-ZrSe₂. The electronic property calculations depict that the 2D monolayer ZrSe₂ has a large band gap of 1.48 eV, which is not favorable for the ORR mechanism. After the doping of Nb, the electronic band gap vanishes, and 2D Nb-ZrSe₂ acts as a conductor. We studied both the dissociative and the associative pathways through which the ORR can proceed to reduce the oxygen molecule (O₂). Our results show that the more favorable path for O₂ reduction on the surface of the 2D Nb-ZrSe₂ is the 4e^– associative path. The detailed ORR mechanisms (both associated and dissociative) have been explored by computing the changes in Gibbs free energy (ΔG). All of the ORR reaction intermediate steps are thermodynamically stable and energetically favorable. The free energy profile for the associative path shows the downhill behavior of the free energy vs the reaction steps, suggesting that all ORR intermediate structures are catalytically active for the 4e^– associative path and a high 4e^– reduction pathway selectivity. Therefore, 2D Nb-ZrSe₂ is a promising catalyst for the ORR, which can be used as an alternative ORR catalyst compared to expensive platinum (Pt).

Incorporation of the phosphorus element into a π-conjugated skeleton offers valuable prospects for adjusting the electronic structure of the resulting functional π-electron systems. Trivalent phosphorus has the potential to decrease the LUMO level through σ*−π* interaction, which is further enhanced by its oxygenation to the pentavalent P center. This study shows that utilizing our computational analysis to examine excited-state dynamics based on radiative/nonradiative rate constants and fluorescence quantum yield (Φ_F) is effective for analyzing the photophysical properties of P-containing organic dyes. We theoretically investigate how the trivalent phosphanyl group and pentavalent phosphine oxide moieties affect radiative and nonradiative decay processes. We evaluate four variations of P-bridged stilbene analogs. Our analysis reveals that the primary decay pathway for photoexcited bis-phosphanyl-bridged stilbene is the intersystem crossing (ISC) to the triplet state and nonradiative. The oxidation of the phosphine moiety, however, suppresses the ISC due to the relative destabilization of the triplet states. The calculated rate constants match an increase in experimental Φ_F from 0.07 to 0.98, as simulated from 0.23 to 0.94. The reduced HOMO–LUMO gap supports a red shift in the fluorescence spectra relative to the phosphine analog. The thiophene-fused variant with the nonoxidized trivalent P center exhibits intense emission with a high Φ_F, 0.95. Our prediction indicates that the ISC transfer is obstructed owing to the relatively destabilized triplet state induced by the thiophene substitution. Conversely, the thiophene-fused analog with the phosphine oxide moieties triggers a high-rate internal conversion mediated by conical intersection, leading to a decreased Φ_F.

Femtosecond stimulated Raman spectroscopy (FSRS) is a powerful nonlinear spectroscopic technique that probes changes in molecular and material structure with high temporal and spectral resolution. With proper spectral interpretation, this is equivalent to mapping out reactive pathways on highly anharmonic excited-state potential energy surfaces with femtosecond to picosecond time resolution. FSRS has been used to examine structural dynamics in a wide range of samples, including photoactive proteins, photovoltaic materials, plasmonic nanostructures, polymers, and a range of others, with experiments performed in multiple groups around the world. As the FSRS technique grows in popularity and is increasingly implemented in user facilities, there is a need for a widespread understanding of the methodology and best practices. In this review, we present a practical guide to FSRS, including discussions of instrumentation, as well as data acquisition and analysis. First, we describe common methods of generating the three pulses required for FSRS: the probe, Raman pump, and actinic pump, including a discussion of the parameters to consider when selecting a beam generation method. We then outline approaches for effective and efficient FSRS data acquisition. We discuss common data analysis techniques for FSRS, as well as more advanced analyses aimed at extracting small signals on a large background. We conclude with a discussion of some of the new directions for FSRS research, including spectromicroscopy. Overall, this review provides researchers with a practical handbook for FSRS as a technique with the aim of encouraging many scientists and engineers to use it in their research.

Organic ligand coatings can modify the surface properties of nanoparticles. With the proper choice of the type of nanoparticles and of the ligand, a targeted modification can be achieved that is suitable for specific applications. In the present work, we employ density functional theory calculations with Hubbard corrections (DFT + U) to treat localized states in order to investigate the magnetic and electrostatic properties of ferrite nanoparticles (CoFe₂O₄ and Fe₂O₃) covered with COOH-terminated [oleic acid (OA)] and OH-terminated [diethylene glycol (DEG)] ligands by varying the ligands coverage. OA results in a decrease of the mean magnetic moment for both particles as the coating coverage increases. The magnetic anisotropy (MAE) significantly decreases for CoFe₂O₄, whereas for Fe₂O₃ a significant increase of MAE is found as the OA coverage percentage increases. For DEG, the variation of both types of nanoparticles in the magnetic moment and the magnetic anisotropy is not significant since DEG shows a weaker attachment on the surface. As COOH shows a larger percentage of covalent bonding than OH, a larger amount of charge is transferred to both particles when OA is attached on their surface. In this case, the particles possess a higher charge, and thus they can produce a larger electrostatic potential in the neighborhood independently of the screening by the coating. Thus, the repulsive Coulombic forces are enhanced mainly in the OA coating case, resulting in an enhancement of their colloidal stability.

This Perspective provides a contextual explanation of the current state-of-the-art alchemical free energy methods and their role in drug discovery as well as highlights select emerging technologies. The narrative attempts to answer basic questions about what goes on “under the hood” in free energy simulations and provide general guidelines for how to run simulations and analyze the results. It is the hope that this work will provide a valuable introduction to students and scientists in the field.

We discovered an anomalous basic dissociation in certain multiprotic compounds. An amine group placed in the middle of a given compound is predicted to behave unusually─at certain pH ranges, its averaged degree of protonation actually increases with pH (!) resulting from interactions with other ionizable groups. This chameleonic behavior results in two pK₅₀ values: one corresponding to a weaker base and the other to a stronger base for the same group.

The present work reports, for the first time, synthesis of dye incorporated o-phenylenediamine (OBB) with a view to obtain a conjugated oligomer with enhanced functionality. The structure was confirmed by IR studies, while the electronic transitions were confirmed by UV visible studies. The dye modified oligomer showed one order higher fluorescence intensity than the pristine Bismarck Brown (BB) dye. Confocal imaging showed red emission which could be utilized in near infra-red imaging. Density functional theory (DFT) studies were carried out to predict the theoretical properties of the oligomers. The energies of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital orbital were computed to explore how the HOMO energies of the reactants initiated the electronic interactions between them. The interaction energies were correlated to conjugation/hyper conjugation stabilization energies of the natural bond orbitals (NBO) via the DFT method using the B3LYP functional with the 6-311G(d) basis set on Gaussian 09 software. Drug binding was evaluated through simulation of interaction energy, (ΔE_A–x) with drugs such as captopril, propranolol, thiazide, and fentanyl. The results predicted that the oligomer could be developed into a fentanyl drug sensor.