Microsecond Time Scale Research Articles

Autoionization from the plasmon resonance in isolated 1-cyanonaphthalene.

Polycyclic aromatic hydrocarbons have widely been conjectured to be ubiquitous in space, as supported by the recent discovery of two isomers of cyanonaphthalene, indene, and 2-cyanoindene in the Taurus molecular cloud-1 using radioastronomy. Here, the photoionization dynamics of 1-cyanonaphthalene (1-CNN) are investigated using synchrotron radiation over the hν = 9.0-19.5eV range, revealing that prompt autoionization from the plasmon resonance dominates the photophysics for hν = 11.5-16.0eV. Minimal photo-induced dissociation, whether originating from an excited state impulsive bond rupture or through internal conversion followed by a statistical bond cleavage process, occurs over the microsecond timescale (as limited by the experimental setup). The direct photoionization cross section and photoelectron angular distributions are simulated using an ezDyson model combining Dyson orbitals with Coulomb wave photoejection. When considering these data in conjunction with recent radiative cooling measurements on 1-CNN+, which showed that cations formed with up to 5eV of internal energy efficiently stabilize through recurrent fluorescence, we conclude that the organic backbone of 1-CNN is resilient to photodestruction by VUV and soft XUV radiation. These dynamics may prove to be a common feature for the survival of small polycyclic aromatic hydrocarbons in space, provided that the cations have a suitable electronic structure to support recurrent fluorescence.

Mesoscale computer modeling of asphaltene aggregation in liquid paraffin.

Asphaltenes represent a novel class of carbon nanofillers that are of potential interest for many applications, including polymer nanocomposites, solar cells, and domestic heat storage devices. In this work, we developed a realistic coarse-grained Martini model that was refined against the thermodynamic data extracted from atomistic simulations. This allowed us to explore the aggregation behavior of thousands of asphaltene molecules in liquid paraffin on a microsecond time scale. Our computational findings show that native asphaltenes with aliphatic side groups form small clusters that are uniformly distributed in paraffin. The chemical modification of asphaltenes via cutting off their aliphatic periphery changes their aggregation behavior: modified asphaltenes form extended stacks whose size increases with asphaltene concentration. At a certain large concentration (44 mol. %), the stacks of modified asphaltenes partly overlap, leading to the formation of large, disordered super-aggregates. Importantly, the size of such super-aggregates increases with the simulation box due to phase separation in the paraffin-asphaltene system. The mobility of native asphaltenes is systematically lower than that of their modified counterparts since the aliphatic side groups mix with paraffin chains, slowing down the diffusion of native asphaltenes. We also show that diffusion coefficients of asphaltenes are not very sensitive to the system size: enlarging the simulation box results in some increase in diffusion coefficients, with the effect being less pronounced at high asphaltene concentrations. Overall, our findings provide valuable insight into the aggregation behavior of asphaltenes on spatial and time scales that are normally beyond the scales accessible for atomistic simulations.

Melting domain size and recrystallization dynamics of ice revealed by time-resolved x-ray scattering

The phase transition between water and ice is ubiquitous and one of the most important phenomena in nature. Here, we performed time-resolved x-ray scattering experiments capturing the melting and recrystallization dynamics of ice. The ultrafast heating of ice I is induced by an IR laser pulse and probed with an intense x-ray pulse which provided us with direct structural information on different length scales. From the wide-angle x-ray scattering (WAXS) patterns, the molten fraction, as well as the corresponding temperature at each delay, were determined. The small-angle x-ray scattering (SAXS) patterns, together with the information extracted from the WAXS analysis, provided the time-dependent change of the size and the number of liquid domains. The results show partial melting (~13%) and superheating of ice occurring at around 20 ns. After 100 ns, the average size of the liquid domains grows from about 2.5 nm to 4.5 nm by the coalescence of approximately six adjacent domains. Subsequently, we capture the recrystallization of the liquid domains, which occurs on microsecond timescales due to the cooling by heat dissipation and results to a decrease of the average liquid domain size.

Parametric study of 1D plasma photonic crystals with smooth and discontinuous density profiles

Plasma photonic crystals (PPCs) have the potential to significantly expand the capabilities of current millimeter wave technologies by providing high speed (microsecond time scale) control of energy transmission characteristics in the GHz through low THz range. Furthermore, plasma-based devices can be used in higher power applications than their solid-state counterparts without experiencing significant changes in function or incurring damage. Plasmas with periodic variations in density can be created externally, or result naturally from instabilities or self-organization. Due to plasma's diffuse nature, PPCs cannot support rapid changes in density. Despite this fact, most theoretical work in PPCs is based on solid-state photonic crystal methods and assumes constant material properties with abrupt changes at material interfaces. In this work, a linear model is derived for a one-dimensional cold-plasma photonic crystal with an arbitrary density profile. The model is validated against a discontinuous Galerkin method numerical solution of the same device configuration. Bandgap maps are then created from derived group velocity data to elucidate the operating regime of a theoretical PPC device. The bandgap maps are compared for one-dimensional PPCs with both smooth and discontinuous density profiles. This study finds that bandgap behavior is strongly correlated with the density profile Fourier content and that density profile shapes can be engineered to produce specific transmission characteristics.

Advanced electrochemical potential monitoring for improved understanding of electrical neurostimulation protocols

Objective. Current-controlled neurostimulation is increasingly used in the clinical treatment of neurological disorders and widely applied in neural prostheses such as cochlear implants. Despite its importance, time-dependent potential traces of electrodes during microsecond-scale current pulses, especially with respect to a reference electrode (RE), are not precisely understood. However, this knowledge is critical to predict contributions of chemical reactions at the electrodes, and ultimately electrode stability, biocompatibility, and stimulation safety and efficacy. Approach. We assessed the electrochemistry of neurostimulation protocols in vitro with Pt microelectrodes from millisecond (classical electroanalysis) to microsecond (neurostimulation) timescales. We developed a dual-channel instrumentation amplifier to include a RE in neurostimulation setups. Uniquely, we combined potential measurements with potentiostatic prepolarization to control and investigate the surface status, which is not possible in typical stimulation setups. Main results. We thoroughly validated the instrumentation and highlighted the importance of monitoring individual electrochemical electrode potentials in different configurations of neurostimulation. We investigated electrode processes such as oxide formation and oxygen reduction by chronopotentiometry, bridging the gap between milli- and microsecond timescales. Our results demonstrate how much impact on potential traces the electrode’s initial surface state and electrochemical surface processes have, even on a microsecond scale. Significance. Our unique use of preconditioning in combination with stimulation reveals that interpreting potential traces with respect to electrode processes is misleading without rigorous control of the electrode’s surface state. Especially in vivo, where the microenvironment is unknown, simply measuring the voltage between two electrodes cannot accurately reflect the electrode’s state and processes. Potential boundaries determine charge transfer, corrosion, and alterations of the electrode/tissue interface such as pH and oxygenation, particularly in long-term in vivo use. Our findings are relevant for all use-cases of constant-current stimulation, strongly advocating for electrochemical in situ investigations in many applications like the development of new electrode materials and stimulation methods.

Long-lived molecular anions of brominated diphenyl ethers.

Resonance electron attachment in a series of brominated diphenyl ethers, namely 4-bromodiphenyl ether (BDPE), 4-bromophenyl ether (BPE), and decabromodiphenyl ether (DBDE), was investigated in the gas phase by means of dissociative electron attachment spectroscopy. In addition to channels of dissociation into stable fragments, long-lived molecular negative ions with an average lifetime relative to autodetachment of the order of 60 µs were found for the last two molecules. In the case of BDPE and BPE, the most intense dissociation channel is the bromine anion, and for DBDE-the [C6Br5O]- anion. The [C6Br5O]- anion sequentially decomposes with the elimination of the bromide anion on a microsecond time scale, which is confirmed by the registration of metastable ions with an apparent mass of 12.8 a.m.u. The electron affinity of the studied molecules and the appearance energy of fragment ions were estimated with CAM-B3LYP/6-311+G(d,p).

Parameterization of the miniPEG-Modified γPNA Backbone: Toward Induced γPNA Duplex Dissociation.

γ-Modified peptide nucleic acids (γPNAs) serve as potential therapeutic agents against genetic diseases. Miniature poly(ethylene glycol) (miniPEG) has been reported to increase solubility and binding affinity toward genetic targets, yet details of γPNA structure and dynamics are not understood. Within our work, we parameterized missing torsional and electrostatic terms for the miniPEG substituent on the γ-carbon atom of the γPNA backbone in the CHARMM force field. Microsecond timescale molecular dynamics simulations were carried out on six miniPEG-modified γPNA duplexes from NMR structures (PDB ID: 2KVJ). Three NMR models for the γPNA duplex (PDB ID: 2KVJ) were simulated as a reference for structural and dynamic changes captured for the miniPEG-modified γPNA duplex. Principal component analysis performed on the γPNA backbone atoms identified a single isotropic conformational substate (CS) for the NMR simulations, whereas four anisotropic CSs were identified for the ensemble of miniPEG-modified γPNA simulations. The NMR structures were found to have a 23° helical bend toward the major groove, consistent with our simulated CS structure of 19.0°. However, a significant difference between simulated methyl- and miniPEG-modified γPNAs involved the opportunistic invasion of miniPEG through the minor and major groves. Specifically, hydrogen bond fractional analysis showed that the invasion was particularly prone to affect the second G-C base pair, reducing the Watson-Crick base pair hydrogen bond by 60% over the six simulations, whereas the A-T base pairs decreased by only 20%. Ultimately, the invasion led to base stack reshuffling, where the well-ordered base stacking was reduced to segmented nucleobase stacking interactions. Our 6 μs timescale simulations indicate that duplex dissociation suggests the onset toward γPNA single strands, consistent with the experimental observation of decreased aggregation. To complement the insight of miniPEG-modified γPNA structure and dynamics, the new miniPEG force field parameters allow for further exploration of such modified γPNA single strands as potential therapeutic agents against genetic diseases.

Efficient Electronic Excitation Transfer via Phonon-Assisted Dipole-Dipole Coupling inFe2+:Cr2+:ZnSe

${\mathrm{Cr}}^{2+}$ - and ${\mathrm{Fe}}^{2+}$ -doped $\mathrm{Zn}\mathrm{Se}$ crystals are laser materials with phonon-broadened absorption and emission spectra, which provide broadband laser gain in the 2- to 5-$\text{\ensuremath{\mu}}\mathrm{m}$ wavelength range. While ${\mathrm{Cr}}^{2+}\text{:ZnSe}$ can be directly pumped with high-power Er, Ho, or Tm lasers, no such possibility exists for ${\mathrm{Fe}}^{2+}\text{:ZnSe}$. To this end, electronic excitation transfer between ${\mathrm{Cr}}^{2+}$ and ${\mathrm{Fe}}^{2+}$ ions in codoped ZnSe is investigated as an alternative excitation process in photo luminescence (PL) experiments with sub-10-ns temporal resolution. For a wide range of ion concentrations, we observe nonexponential decays of ${\mathrm{Cr}}^{2+}$ PL on a microsecond time scale, a 60-ns rise time of ${\mathrm{Fe}}^{2+}$ PL at high doping densities, and a prolonged decay of ${\mathrm{Fe}}^{2+}$ PL due to the temporal characteristics of excitation transfer over a range of interionic distances. Using a multirate equation model, the transfer process is analyzed on length scales up to 30 nm and compared to the established continuum model approach. The analysis reveals an unexpectedly efficient excitation transfer from ${\mathrm{Cr}}^{2+}$ to ${\mathrm{Fe}}^{2+}$ ions with an enhancement of the excitation transfer rates by up to a factor of 5 in comparison to resonant dipole-dipole coupling. The enhancement is assigned to (multi)phonon-assisted excitation transfer, in analogy to the phonon-mediated efficient radiationless decay of the excited ${\mathrm{Fe}}^{2+}$ state. As nonradiative losses and excitation transfer show different temperature scaling, a cryogenic temperature regime is found that promises overall efficiencies above 50%, making ${\mathrm{Fe}}^{2+}:{\mathrm{Cr}}^{2+}\text{:ZnSe}$ a much more viable alternative to parametric conversion schemes in the midinfrared range.

Coarse-grained simulations of lysozyme-silica-nanoparticle corona.

Protein coronas, formed by proteins and nanomaterials, have various applications in the biomedical field. Here, large-scale simulations of protein coronas have been carried out by an efficient mesoscopic coarse-grained method with the BMW-MARTINI force field. The effects of protein concentration, size of silica nanoparticles (SNPs), and ionic strength on the formation of lysozyme-SNP coronas are investigated at the microsecond time scale. Simulations results indicate that (i) an increase in the amount of lysozyme is favorable for the conformation stability of adsorbed lysozyme on SNPs. Moreover, the formation of ringlike and dumbbell-like aggregations of lysozyme can further reduce the conformational loss of lysozyme; (ii) for a smaller SNP, the increase of protein concentration exhibits a greater effect on the adsorption orientation of lysozyme. The dumbbell-like lysozyme aggregation is unfavorable for the stability of lysozyme's adsorption orientation; however, the ringlike lysozyme aggregation can enhance the orientation stability; (iii) the increase of ionic strength can reduce the conformation change of lysozyme and accelerate the aggregation of lysozyme during their adsorption process on SNPs. This work provides some insights into the formation of protein coronas and some valuable guidelines for the development of novel biomolecule-NP conjugates.

Achieving Accurate Standard Protein-Protein Binding Free Energy Calculations through the Geometrical Route and Ergodic Sampling.

A new strategy for the prediction of binding free energies of protein-protein complexes is reported in the present article. By combining an ergodic-sampling algorithm with the so-called "geometrical route", which introduces a series of geometrical restraints as a preamble to the physical separation of the two partners, we achieve accurate binding free energy calculations for medium-sized protein-protein complexes within the microsecond timescale. The ergodic-sampling algorithm, namely, Gaussian-accelerated molecular dynamics (GaMD), implicitly helps explore the conformational change of the two binding partners as they associate reversibly by raising the energy wells. Therefore, independent simulations capturing the isomerization of proteins are no longer needed, reducing both the computational cost and human effort. Numerical applications indicate errors on the order of 0.1 kcal/mol for the Abl-SH3 domain binding a decapeptide, of 2.6 kcal/mol for the barnase-barstar complex, and of 0.2 kcal/mol for human leukocyte elastase binding the third domain of the turkey ovomucoid inhibitor. Compared with the classical geometrical route, which resorts to collective variables to describe the isomerization of proteins, our new strategy possesses remarkable convergence properties and robustness for protein-protein complexes owing to improved ergodic sampling. We are confident that the strategy presented in this study will have a broad range of applications, helping us understand recognition-association phenomena in the areas of physical, biological, and medicinal chemistry.

Water treatment by cavitation: Understanding it at a single bubble - bacterial cell level

Cavitation is a potentially useful phenomenon accompanied by extreme conditions, which is one of the reasons for its increased use in a variety of applications, such as surface cleaning, enhanced chemistry, and water treatment. Yet, we are still not able to answer many fundamental questions related to efficacy and effectiveness of cavitation treatment, such as: “Can single bubbles destroy contaminants?” and “What precisely is the mechanism behind bubble's cleaning power?”. For these reasons, the present paper addresses cavitation as a tool for eradication and removal of wall-bound bacteria at a fundamental level of a single microbubble and a bacterial cell. We present a method to study bubble-bacteria interaction on a nano- to microscale resolution in both space and time. The method allows for accurate and fast positioning of a single microbubble above the individual wall-bound bacterial cell with optical tweezers and triggering of a violent microscale cavitation event, which either results in mechanical removal or destruction of the bacterial cell. Results on E. coli bacteria show that only cells in the immediate vicinity of the microbubble are affected, and that a very high likelihood of cell detachment and cell death exists for cells located directly under the center of a bubble. Further details behind near-wall microbubble dynamics are revealed by numerical simulations, which demonstrate that a water jet resulting from a near-wall bubble implosion is the primary mechanism of wall-bound cell damage. The results suggest that peak hydrodynamic forces as high as 0.8 μN and 1.2 μN are required to achieve consistent E. coli bacterial cell detachment or death with high frequency mechanical perturbations on a nano- to microsecond time scale. Understanding of the cavitation phenomenon at a fundamental level of a single bubble will enable further optimization of novel water treatment and surface cleaning technologies to provide more efficient and chemical-free processes.

Abstract 2737: A gene therapy with a novel PD-L1 inhibitory peptide secretory gene inhibits the growth of colon carcinoma in mice

Abstract In the United States, colorectal cancer (CRC) is the second leading cause of cancer-related death in both sexes. Immune checkpoint blockade therapy (ICBT) has emerged as a powerful new tool for cancer therapy. However, only CRCs associated with microsatellite instability (MSI) or DNA mismatch repair gene defects (dMMR, ~15% of all CRCs) are sensitive to this therapy. This poor sensitivity to ICBT is either due to poor tumor infiltration of functional T cells or T cell exhaustion. To overcome this, we investigated a combination treatment with an oncolytic virus and an immune checkpoint inhibitor (ICI). Because tumor cell oncolysis generates neoantigens and increases tumor immunogenicity, T cell infiltration into the tumor tissue will be increased and the efficacy of ICBT will be enhanced. Accordingly, local immune checkpoint inhibition coupled with oncolysis may be an ideal ICBT. In the present study, a novel peptide that interferes with the PD-1/PD-L1 immune checkpoint pathway, termed PD-L1 inhibitory peptide 3 (PD-L1ip3), was computationally designed, experimentally validated for its specific binding to PD-L1, and evaluated for its antitumor effects in cell culture and in a mouse colon carcinoma syngeneic murine model. Fourteen candidate peptide sequences were generated using the PinaColada algorithm and the x-ray structure of the PD-1:PD-L1 complex and screened in molecular dynamics simulations on the microsecond timescale. Two were chosen for experimental testing, wherein the peptide denoted PD-L1ip3 showed a binding affinity for PD-L1 in the micromolar range. In cell culture studies, treatment with PD-L1ip3, but not a similar peptide with a scrambled sequence, substantially increased death of CT26 colon carcinoma cells when co-cultured with murine CD8+ T cells primed by antigens from CT26 cells. In immunocompetent mice, growth of CT26 tumor cells transduced with the PD-L1ip3 gene by an adenovirus vector was significantly slower than that of un-transduced CT26 cells. This tumor growth attenuation was further enhanced by cotreatment with the peptide form of PD-L1ip3. The present study suggests that this peptide can stimulate host antitumor immunity via a blockade of the PD-1/PD-L1 pathway, thereby increasing CD8+ T cell-induced death of colon carcinoma cells. The tumor site-specific inhibition of PD-L1 by an adenovirus carrying the PD-L1ip3 gene, together with direct peptide treatment, may be used as a local immune checkpoint blockade therapy to inhibit colon carcinoma growth. This research was supported by Kansas State University Johnson Cancer Research center (MT), K-INBRE Scholar Award (MB), National Cancer Institute (MT, JC) and the National Science Foundation (JC). Citation Format: Susumu Ishiguro, Deepa Upreti, Molly Bassette, E. R. Azhagiya Singam, Ravindra Thakkar, Mayme Loyd, Makoto Inui, Jeffrey Comer, Masaaki Tamura. A gene therapy with a novel PD-L1 inhibitory peptide secretory gene inhibits the growth of colon carcinoma in mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2737.

Understanding Precatalyst Activation and Speciation in Manganese-Catalyzed C-H Bond Functionalization Reactions.

An investigation into species formed following precatalyst activation in Mn-catalyzed C-H bond functionalization reactions is reported. Time-resolved infrared spectroscopy demonstrates that light-induced CO dissociation from precatalysts [Mn(C^N)(CO)4] (C^N = cyclometalated 2-phenylpyridine (1a), cyclometalated 1,1-bis(4-methoxyphenyl)methanimine (1b)) in a toluene solution of 2-phenylpyridine (2a) or 1,1-bis(4-methoxyphenyl)methanimine (2b) results in the initial formation of solvent complexes fac-[Mn(C^N)(CO)3(toluene)]. Subsequent solvent substitution on a nanosecond time scale then yields fac-[Mn(C^N)(CO)3(κ1-(N)-2a)] and fac-[Mn(C^N)(CO)3(κ1-(N)-2b)], respectively. When the experiments are performed in the presence of phenylacetylene, the initial formation of fac-[Mn(C^N)(CO)3(toluene)] is followed by a competitive substitution reaction to give fac-[Mn(C^N)(CO)3(2)] and fac-[Mn(C^N)(CO)3(η2-PhC2H)]. The fate of the reaction mixture depends on the nature of the nitrogen-containing substrate used. In the case of 2-phenylpyridine, migratory insertion of the alkyne into the Mn-C bond occurs, and fac-[Mn(C^N)(CO)3(κ1-(N)-2a)] remains unchanged. In contrast, when 2b is used, substitution of the η2-bound phenylacetylene by 2b occurs on a microsecond time scale, and fac-[Mn(C^N)(CO)3(κ1-(N)-2b)] is the sole product from the reaction. Calculations with density functional theory indicate that this difference in behavior may be correlated with the different affinities of 2a and 2b for the manganese. This study therefore demonstrates that speciation immediately following precatalyst activation is a kinetically controlled event. The most dominant species in the reaction mixture (the solvent) initially binds to the metal. The subsequent substitution of the metal-bound solvent is also kinetically controlled (on a ns time scale) prior to the thermodynamic distribution of products being obtained.

Charge Dynamics of a CuO Thin Film on Picosecond to Microsecond Timescales Revealed by Transient Absorption Spectroscopy.

Understanding the mechanism of charge dynamics in photocatalysts is the key to design and optimize more efficient materials for renewable energy applications. In this study, the charge dynamics of a CuO thin film are unraveled via transient absorption spectroscopy (TAS) on the picosecond to microsecond timescale for three different excitation energies, i.e., above, near, and below the band gap, to explore the role of incoherent broadband light sources. The shape of the ps-TAS spectra changes with the delay time, while that of the ns-TAS spectra is invariant for all the excitation energies. Regardless of the excitations, three time constants, τ1 ∼ 0.34-0.59 ps, τ2 ∼ 162-175 ns, and τ3 ∼ 2.5-3.3 μs, are resolved, indicating the dominating charge dynamics at very different timescales. Based on these observations, the UV-vis absorption spectrum, and previous findings in the literature, a compelling transition energy diagram is proposed. Two conduction bands and two defect (deep and shallow) states dominate the initial photo-induced electron transitions, and a sub-valence band energy state is involved in the subsequent transient absorption. By solving the rate equations for the pump-induced population dynamics and implementing the assumed Lorentzian absorption spectral shape between two energy states, the TAS spectra are modeled which capture the main spectral and time-dependent features for t > 1 ps. By further considering the contributions from free-electron absorption during very early delay times, the modeled spectra reproduce the experimental spectra very well over the entire time range and under different excitation conditions.

Site-specific protein backbone deuterium 2Hα quadrupolar patterns by proton-detected quadruple-resonance 3D 2HαcαNH MAS NMR spectroscopy

A novel deuterium-excited and proton-detected quadruple-resonance three-dimensional (3D) 2HαcαNH MAS nuclear magnetic resonance (NMR) method is presented to obtain site-specific 2Hα deuterium quadrupolar couplings from protein backbone, as an extension to the 2D version of the experiment reported earlier. Proton-detection results in high sensitivity compared to the heteronuclei detection methods. Utilizing four independent radiofrequency (RF) channels (quadruple-resonance), we managed to excite the 2Hα, then transfer deuterium polarization to its attached Cα, followed by polarization transfers to the neighboring backbone nitrogen and then to the amide proton for detection. This experiment results in an easy to interpret HSQC-like 2D 1H–15N fingerprint NMR spectrum, which contains site-specific deuterium quadrupolar patterns in the indirect third dimension. Provided that four-channel NMR probe technology is available, the setup of the 2HαcαNH experiment is relatively straightforward, by using low power deuterium excitation and polarization transfer schemes we have been developing. To our knowledge, this is the first demonstration of a quadruple-resonance MAS NMR experiment to link 2Hα quadrupolar couplings to proton-detection, extending our previous triple-resonance demonstrations. Distortion-free excitation and polarization transfer of ∼160–170 kHz 2Hα quadrupolar coupling were presented by using a deuterium RF strength of ∼20 kHz. From these 2Hα patterns, an average backbone order parameter of S = 0.92 was determined on a deuterated SH3 sample, with an average η = 0.22. These indicate that SH3 backbone represents sizable dynamics in the microsecond timescale where the 2Hα lineshape is sensitive. Moreover, site-specific 2Hα T1 relaxation times were obtained for a proof of concept. This 3D 2HαcαNH NMR experiment has the potential to determine structure and dynamics of perdeuterated proteins by utilizing deuterium as a novel reporter.

5-Deazaalloxazine as photosensitizer of singlet oxygen and potential redox-sensitive agent

Flavins are a unique class of compounds that combine the features of singlet oxygen generators and redox-dependent fluorophores. From a broad family of flavin derivatives, deazaalloxazines are significantly underdeveloped from the point of view of photophysical properties. Herein, we report photophysics of 5-deazaalloxazine (1a) in water, acetonitrile, and some other solvents. In particular, triplet excited states of 1a in water and in acetonitrile were investigated using ultraviolet–visible (UV–Vis) transient absorption spectroscopy. The measured triplet lifetimes for 1a were all on the microsecond time scale (≈ 60 μs) in deoxygenated solutions. The quantum yield of S1 → T1 intersystem crossing for 1a in water was 0.43 based on T1 energy transfer from 1a to indicaxanthin (5) acting as acceptor and on comparative actinometric measurements using benzophenone (6). 1a was an efficient photosensitizer for singlet oxygen in aerated solutions, with quantum yields of singlet oxygen in methanol of about 0.76, compared to acetonitrile ~ 0.74, dichloromethane ~ 0.64 and 1,2-dichloroethane ~ 0.54. Significantly lower singlet oxygen quantum yields were obtained in water and deuterated water (ФΔ ~ 0.42 and 0.44, respectively). Human red blood cells (RBC) were used as a cell model to study the antioxidant capacity in vitro and cytotoxic activity of 1a. Fluorescence-lifetime imaging microscopy (FLIM) data were analyzed by fluorescence lifetime parameters and distribution for different parts of the emission spectrum. Comparison of multidimensional fluorescent properties of RBC under physiological-like and oxidative-stress conditions in the presence and absence of 1a suggests its dual activity as probe and singlet-oxygen generator and opens up a pathway for using FLIM to analyze complex intracellular behavior of flavin-like compounds. These new data on structure–property relationship contribute to the body of information required for a rational design of flavin-based tools for future biological and biochemical applications.Graphical abstract

Excited-State Intramolecular Proton Transfer in Salicylidene-α-Hydroxy Carboxylate Derivatives: Direct Detection of the Triplet Excited State of the cis-Keto Tautomer.

Excited-state intramolecular hydrogen transfer on the triplet surface of salicylideneaniline derivatives has received much less attention than the corresponding ultrafast process on the singlet surface. To enhance the understanding of this triplet reactivity, the photochemical properties of a series of salicylidene-α-hydroxy acid salts with different substituents on the phenol moiety (1-3) were characterized. UV/vis absorption and phosphorescence measurements in ethanol revealed that 1-3 exist as both enol and keto tautomers, with the enol form being predominant. Irradiation of 1 at 310 nm in ethanol glass (77 K) yielded an absorption band with a λmax at ∼405 nm, which was assigned to the trans-keto tautomer (trans-1K). In contrast, laser flash photolysis of 1-3 in methanol or acetonitrile resulted in a transient absorption with λmax at 440-460 nm. This transient, which decayed on the microsecond timescale and was significantly shorter lived in methanol than in acetonitrile, was assigned to the triplet excited state (T1) of the cis-keto tautomer (cis-1K-3K) and residual absorption of trans-1K-3K by comparison with TD-DFT calculations. The assignment of the T1 of cis-1K was further supported by quenching studies with anthracene and 2,5-dimethyl-2,4-hexadiene. Laser flash photolysis of 1 in the temperature range of 173-293 K gave an activation barrier of 6.7 kcal/mol for the decay of the T1 of cis-1K. In contrast, the calculated activation barrier for cis-1K to undergo a 1,5-H atom shift to reform 1 was smaller, indicating that intersystem crossing of the T1 of cis-1K is the rate-determining step in the regeneration of 1.

Stellar prospects for FRB gravitational lensing

ABSTRACTGravitational lensing of fast radio bursts (FRBs) offers an exciting avenue for several cosmological applications. However, it is not yet clear how many such events future surveys will detect nor how to optimally find them. We use the known properties of FRBs to forecast detection rates of gravitational lensing on delay time-scales from microseconds to years, corresponding to lens masses spanning 15 orders of magnitude. We highlight the role of the FRB redshift distribution on our ability to observe gravitational lensing. We consider cosmological lensing of FRBs by stars in foreground galaxies and show that strong stellar lensing will dominate on microsecond time-scales. Upcoming surveys such as DSA-2000 and CHORD will constrain the fraction of dark matter in compact objects (e.g. primordial black holes) and may detect millilensing events from intermediate mass black holes (IMBHs) or small dark matter halos. Coherent all-sky monitors will be able to detect longer-duration lensing events from massive galaxies, in addition to short time-scale lensing. Finally, we propose a new application of FRB gravitational lensing that will measure directly the circumgalactic medium of intervening galaxies.

Structural and dynamic properties of the YTH domain in complex with N6‐methyladenosine RNA studied by accelerated molecular dynamics simulations

BackgroundN6‐methyl adenosine (m6A) modifications of mRNA and long non‐coding RNA (lncRNAs) are known to play a significant role in regulation of gene expression and organismal development. Besides writer and eraser proteins of this dynamic modification, the YT521‐B homology (YTH) domain can recognize the modification involved in numerous cellular processes. The function of proteins containing YTH domain and its binding mode with N6‐Methyladenosine RNA has attracted considerable attention. However, the structural and dynamic characteristics of the YTH domain in complex with m6A RNA is still unknown.MethodThis work presents results of accelerated molecular dynamics (aMD) simulations at the timescale of microseconds. Principal component analysis (PCA), molecular mechanics generalized Born surface area (MM/GBSA) calculations, contact analysis and contact‐based principal component analysis (conPCA) provide new insights into structure and dynamics of the YTH‐RNA complex.ResultsThe aMD simulations indicate that the recognition loop has a larger movement away from the binding pocket in the YTH‐A3 RNA than that in the YTH‐m6A3 RNA. In aMD trajectories of the apo YTH, there is a significant close‐open transition of the recognition loop, that is to say, the apo YTH can take both the closed and open structure. We have found that the YTH domain binds more favorably to the methylated RNA than the non‐methylated RNA. The per‐residue free energy decomposition and conPCA suggest that hydrophobic residues including W380, L383‐V385, W431‐P434, M437, and M441‐L442, may play important roles in favorable binding of the m6A RNA to the YTH domain, which is also supported by aMD simulations of a double mutated system (L383A/M437A).ConclusionThe results are in good agreement with higher structural stability of the YTH‐m6A RNA than that of the YTH‐A3 RNA. The addition of a methylation group on A3 can enhance its binding to the hydrophobic pocket in the YTH domain. Our simulations support a ‘conformational selection’ mechanism between the YTH‐RNA binding. This work may aid in our understanding of the structural and dynamic characteristics of the YTH protein in complex with the methylated RNA.

Understanding Excited-State Relaxation in 1,3-Bis(N-carbazolyl)benzene, a Host Material for Organic Light-Emitting Diodes

We present a detailed spectroscopic study of 1,3-bis(N-carbazolyl)benzene (mCP), a prototypical host material for blue emitters in organic light-emitting diodes, using time-resolved emission and ultrafast transient absorption spectroscopy. Upon photoexcitation, mCP dissolved in tetrahydrofuran and mCP dispersed at low number density in poly(methyl methacrylate) (PMMA) films show a monoexponential emission decay in the range 6–7 ns. Transient absorption experiments detect the formation of the T1 triplet state from S1 with a quantum yield of ca. 20%, a band maximum at 450 nm, and a lifetime on the microsecond time scale. The strong spectral overlap of S1 stimulated emission and S1 excited state absorption suggests that S1–S1 singlet–singlet annihilation (SSA) based on Förster resonance energy transfer (FRET) should be feasible at high mCP concentrations in mCP:PMMA and neat mCP films. At these concentrations, the intensity of the mCP emission is strongly quenched and the spectra show a dramatic change exhibiting monomer, aggregate, and excimer emission bands. The small Stokes shift and thus the good overlap of the absorption and emission spectra of mCP open up the possibility for efficient diffusive S1 singlet hopping in neat mCP films by means of a multi-step homo-FRET mechanism involving S1 and the respective S0 nearest neighbor. Fluence-dependent transient absorption measurements find pronounced S1–S1 SSA. Kinetic modeling suggests a bimolecular diffusive SSA mechanism with a rate constant kdiff of 1.40 × 10–8 cm3 s–1. In contrast, modeling based on direct S1–S1 FRET results in an unrealistically large Förster radius of 17 nm. These experiments therefore suggest that mCP molecules in S1 efficiently diffuse through the mCP film by multi-step homo-FRET and annihilate upon approaching a critical distance to another mCP molecule in S1. Finally, we find clear spectral evidence for vibrationally hot mCP molecules (S0*) in the transient absorption spectra of neat mCP thin films, which cool down on a time scale from nanoseconds to microseconds.