Microsecond Time Range Research Articles

Structural dynamics of protein-protein association involved in the light-induced transition of Avena sativa LOV2 protein

The Light-oxygen-voltage-sensing domain (LOV) superfamily, found in enzymes and signal transduction proteins, plays a crucial role in converting light signals into structural signals, mediating various biological mechanisms. While time-resolved spectroscopic studies have revealed the dynamics of the LOV-domain chromophore’s electronic structures, understanding the structural changes in the protein moiety, particularly regarding light-induced dimerization, remains challenging. Here, we utilize time-resolved X-ray liquidography to capture the light-induced dimerization of Avena sativa LOV2. Our analysis unveils that dimerization occurs within milliseconds after the unfolding of the A’α and Jα helices in the microsecond time range. Notably, our findings suggest that protein-protein interactions (PPIs) among the β-scaffolds, mediated by helix unfolding, play a key role in dimerization. In this work, we offer structural insights into the dimerization of LOV2 proteins following structural changes in the A’α and Jα helices, as well as mechanistic insights into the protein-protein association process driven by PPIs.

Folding Kinetics and Volume Variation of the β-Hairpin Peptide Chignolin upon Ultrafast pH-Jumps.

In-depth characterization of fundamental folding steps of small model peptides is crucial for a better understanding of the folding mechanisms of more complex biomacromolecules. We have previously reported on the folding/unfolding kinetics of a model α-helix. Here, we study folding transitions in chignolin (GYDPETGTWG), a short β-hairpin peptide previously used as a model to study conformational changes in β-sheet proteins. Although previously suggested, until now, the role of the Tyr2-Trp9 interaction in the folding mechanism of chignolin was not clear. In the present work, pH-dependent conformational changes of chignolin were characterized by circular dichroism (CD), nuclear magnetic resonance (NMR), ultrafast pH-jump coupled with time-resolved photoacoustic calorimetry (TR-PAC), and molecular dynamics (MD) simulations. Taken together, our results present a comprehensive view of chignolin's folding kinetics upon local pH changes and the role of the Tyr2-Trp9 interaction in the folding process. CD data show that chignolin's β-hairpin formation displays a pH-dependent skew bell-shaped curve, with a maximum close to pH 6, and a large decrease in β-sheet content at alkaline pH. The β-hairpin structure is mainly stabilized by aromatic interactions between Tyr2 and Trp9 and CH-π interactions between Tyr2 and Pro4. Unfolding of chignolin at high pH demonstrates that protonation of Tyr2 is essential for the stability of the β-hairpin. Refolding studies were triggered by laser-induced pH-jumps and detected by TR-PAC. The refolding of chignolin from high pH, mainly due to the protonation of Tyr2, is characterized by a volume expansion (10.4 mL mol-1), independent of peptide concentration, in the microsecond time range (lifetime of 1.15 μs). At high pH, the presence of the deprotonated hydroxyl (tyrosinate) hinders the formation of the aromatic interaction between Tyr2 and Trp9 resulting in a more disorganized and dynamic tridimensional structure of the peptide. This was also confirmed by comparing MD simulations of chignolin under conditions mimicking neutral and high pH.

3-Ligated Phenothiazinyl-terephthalonitrile Dyads and Triads - Synthesis, Electronic Properties, Delayed Fluorescence and Electronic Structure.

The bromine-lithium exchange-borylation-Suzuki sequence efficiently furnishes phenothiazine-terephthalonitrile donor-acceptor dyads and triads in high yields. In contrast to most phenothiazine-acceptor conjugates the title compounds are ligated in p-position to the phenothiazine nitrogen atom. Moreover, the acceptors are either directed linked or ligated by an arylene bridge and p-anisyl N-substituents on the phenothiazine are chosen to lock the tricycle into an intra-configuration. Cyclic voltammetry reveals effects of bridging and ligation and N-substituent. Optical spectroscopy likewise displays similar band gaps, large Stokes shifts and substantial to high quantum yields in solution, in the solid state and in PMMA matrix. Time-resolved fluorescence spectroscopy indicates quite long fluorescence decay times in solution and emission components in the microsecond time range. TADF properties are further assessed by fluorescence increase in deoxygenated solution, gated emission spectroscopy and temperature-dependent determination of phosphorescence. The nature of the electronically excited states is investigated by DFT/MRCI. While for the directly ligated dyad a singlet-triplet energy gap [[EQUATION]] of 0.24 eV can be estimated and is consistently confirmed by quantum chemical calculations on the lowest energy conformer, even lower [[EQUATION]] of 0.029 and 0.008 eV are estimated for the investigated dyads and the triad in the solid state and in PMMA matrix.

Oriented Insertion of ESR-Containing Hybrid Proteins in Proteoliposomes.

Microbial rhodopsins comprise a diverse family of retinal-containing membrane proteins that convert absorbed light energy to transmembrane ion transport or sensory signals. Incorporation of these proteins in proteoliposomes allows their properties to be studied in a native-like environment; however, unidirectional protein orientation in the artificial membranes is rarely observed. We aimed to obtain proteoliposomes with unidirectional orientation using a proton-pumping retinal protein from Exiguobacterium sibiricum, ESR, as a model. Three ESR hybrids with soluble protein domains (mCherry or thioredoxin at the C-terminus and Caf1M chaperone at the N-terminus) were obtained and characterized. The photocycle of the hybrid proteins incorporated in proteoliposomes demonstrated a higher pKa of the M state accumulation compared to that of the wild-type ESR. Large negative electrogenic phases and an increase in the relative amplitude of kinetic components in the microsecond time range in the kinetics of membrane potential generation of ESR-Cherry and ESR-Trx indicate a decrease in the efficiency of transmembrane proton transport. On the contrary, Caf-ESR demonstrates a native-like kinetics of membrane potential generation and the corresponding electrogenic stages. Our experiments show that the hybrid with Caf1M promotes the unidirectional orientation of ESR in proteoliposomes.

Unveiling charge dynamics of visible light absorbing oxysulfide for efficient overall water splitting

Oxysulfide semiconductor, Y2Ti2O5S2, has recently discovered its exciting potential for visible-light-induced overall water splitting, and therefore, imperatively requires the probing of unknown fundamental charge loss pathways to engineer the photoactivity enhancement. Herein, transient diffuse reflectance spectroscopy measurements are coupled with theoretical calculations to unveil the nanosecond to microsecond time range dynamics of the photogenerated charge carriers. In early nanosecond range, the pump-fluence-dependent decay dynamics of the absorption signal is originated from the bimolecular recombination of mobile charge carriers, in contrast, the power-law decay kinetics in late microsecond range is dominated by hole detrapping from exponential tail trap states of valence band. A well-calibrated theoretical model estimates various efficiency limiting material parameters like recombination rate constant, n-type doping density and tail-states parameters. Compared to metal oxides, longer effective carrier lifetime ~6 ns is demonstrated. Different design routes are proposed to realize efficiency beyond 10% for commercial solar-to-hydrogen production from oxysulfide photocatalysts.

Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation

The electrostatic interaction of RNA with its aqueous environment is most relevant for defining macromolecular structure and biological function. The attractive interaction of phosphate groups in the RNA backbone with ions in the water environment leads to the accumulation of positively charged ions in the first few hydration layers around RNA. Electrostatics of this ion atmosphere and the resulting ion concentration profiles have been described by solutions of the nonlinear Poisson-Boltzmann equation and atomistic molecular dynamics (MD) simulations. Much less is known on contact pairs of RNA phosphate groups with ions at the RNA surface, regarding their abundance, molecular geometry, and role in defining RNA structure. Here, we present a combined theoretical and experimental study of interactions of a short RNA duplex with magnesium (Mg2+) ions. MD simulations covering a microsecond time range give detailed hydration geometries as well as electrostatics and spatial arrangements of phosphate-Mg2+ pairs, including both pairs in direct contact and separated by a single water layer. The theoretical predictions are benchmarked by linear infrared absorption and nonlinear two-dimensional infrared spectra of the asymmetric phosphate stretch vibration which probes both local interaction geometries and electric fields. Contact pairs of phosphate groups and Mg2+ ions are identified via their impact on the vibrational frequency position and line shape. A quantitative analysis of infrared spectra for a range of Mg2+-excess concentrations and comparison with fluorescence titration measurements shows that on average 20–30% of the Mg2+ ions interacting with the RNA duplex form contact pairs. The experimental and MD results are in good agreement. In contrast, calculations based on the nonlinear Poisson-Boltzmann equation fail in describing the ion arrangement, molecular electrostatic potential, and local electric field strengths correctly. Our results underline the importance of local electric field mapping and molecular-level simulations to correctly account for the electrostatics at the RNA-water interface.

OC fault diagnosis of multilevel inverter using SVM technique and detection algorithm

The Open Circuit (OC) faults occurring in switches of Multilevel Converters (MLC) may lead to undesirable operation of the converter. Therefore, fault detection and its localization in minimum time are necessary. This paper focuses on the fast fault detection algorithm based on the two samples technique and the fault localization algorithm using the Entropy of Wavelet Packets (EWP) as a feature. The EWP feature is used to classify and localize the OC faults in Insulated Gate Bipolar Transistors (IGBTs) of three-phase, three-level inverter using Support Vector Machine (SVM) based fault classification algorithm. The proposed technique can detect the fault in single IGBT and multiple IGBTs in a lesser time range of microseconds to 0.33 ms. It gives better performance and accuracy (99.70%) than previously proposed SVM algorithms, as the EWP-based feature extraction process used in this paper is simple and accurate with a less computational burden.

Sapphire α−Al2O3 puzzle: Joint μSR and density functional theory study

Sapphire $(\ensuremath{\alpha}\text{\ensuremath{-}}{\mathrm{Al}}_{2}{\mathrm{O}}_{3})$ has been investigated by the muon spin rotation $(\ensuremath{\mu}\mathrm{SR})$ method in several experiments in the past. The main $\ensuremath{\mu}\mathrm{SR}$ component is a diamagnetic-like signal with a fast relaxation. Because of this diamagnetic-like behavior, the signal was assigned to either positively charged muonium $({\mathrm{Mu}}^{+})$ or negatively charged muonium $({\mathrm{Mu}}^{\ensuremath{-}})$, but neither of the two assignments was satisfactory (the so-called ``sapphire puzzle''). We have proposed that the signal is due to a weakly paramagnetic muonium configuration (transition state) which is formed during the reaction of muonium with the host lattice. In the present paper, we report new experimental data on ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$ and discuss these and earlier data in the ${\mathrm{Mu}}^{\ensuremath{-}}$ and in the transition state model. Calculations based on density functional theory were also performed with detailed findings on the energetics of the different muonium configurations and their migration energies. We conclude that the transition state model is more plausible than the ${\mathrm{Mu}}^{\ensuremath{-}}$ model, but the ${\mathrm{Mu}}^{\ensuremath{-}}$ interpretation cannot be excluded completely. In addition, the evidence is presented that the bare muon performs local motion but no long-range diffusion below room temperature in the microsecond time range.

RDX-Al and PETN-Al composites’ glow spectral kinetics at the explosion initiated with laser pulse

Glow spectral kinetics of cyclotrimethylenetrinitramine (RDX) and pentaerythritol tetranitrate (PETN) based composites containing aluminum nanoparticles (average diameter 100 nm) caused by explosion stimulated by neodymium laser pulse (1064 nm, 14 ns) have been studied for the first time with nanosecond temporal resolution. The experiments have been performed in the conditions of gas-dynamic relaxation hindrance. The aluminum nanoparticles, as well as the surrounding shell of the RDX and PETN, are heated during the pulse. If the laser pulse energy density is higher than the critical one, the fluorescence, whose typical relaxation time is 50 ns, appears and spectral maximum is blue-shifted with elevating the energy density of the laser pulse. The fluorescence is related to NO2● formed in the radical dissociation of RDX and PETN molecules stimulated by rapid heating in the aluminum nanoparticles explosive environment. The following exothermal decomposition reaction leads to a sample explosion in the microsecond time range. The emission spectrum of the explosion products is a thermal one with temperatures 3500 K and 3400 K for RDX-Al and PETN-Al relatively, which has been estimated using spectral pyrometry approach.

Action spectroscopy of spin forbidden states in the gas phase: A powerful probe for large non-luminescent molecules.

Triplet action spectra of two similar copper porphyrins, copper tetraphenylporphyrin (CuTPP) and copper octaethylporphyrin (CuOEP), have been studied in the gas phase at low temperatures in the absence of external perturbations by using a resonant pump and a 193 nm probe, ionizing the 3ππ* orbital localized on the porphyrin cycle. The molecules were prepared by laser desorption in a disk source, then cooled in a helium supersonic expansion, and finally excited in the Q band system (S1 ← S0). This type of experiment allows the spectroscopic characterization of large non-luminescent molecules in the absence of solvent perturbations. The two copper porphyrins exhibit a broad electronic origin Q00 absorption spectrum, partly caused by the short lifetime of the excited (S1) state. The two porphyrins differ strongly with a strong Q00 band for CuOEP and a weak one for CuTPP, in agreement with the Gouterman four-orbital model. The two molecules exhibit different solvent shifts: CuOEP is blue shifted in non-polar solvents owing to its alkyl substituents, while CuTPP is red shifted as for regular transitions to ππ* orbitals. The decay dynamics of the triplet state exhibit a collision-free lifetime of 70 ± 7 ns for CuTPP atop a microsecond decay. This non-exponential decay can be viewed as evidence of time evolution of two states combining the state with spin 1 borne by the porphyrin ring and that by the Cu atom 12. Therefore, this method allows solvent-free spectrodynamics of large molecules in a short microsecond time range.

Effect of spin-orbit interaction on recombination luminescence of dye in films of halogen-containing derivative poly-N-epoxypropylcarbazole

A photoluminescence kinetics of a cationic polymethine dye in composite polymer films based on halogen-containing derivatives poly-N-epoxypropylcarbazole (PEPC) has been studied. The observed luminescence kinetics is formed by the fluorescence of the dye and recombination luminescence associated with the formation and recombination of electron-hole pairs (EHP). It was shown, that measuring the external magnetic field effect on the kinetics of dye luminescence in a wide time range made it possible to determine the characteristic times of the recombination processes with the involvement of EHP formed from singlet and triplet excited electronic states of the dye molecules and main channels of electron energy transformation in composite films. An enhancement of the spin-orbit interaction in polymers with different heavy atoms leads to an increase in a value of the magnetic effect (g(B)) in the nanosecond time range and to a decrease in g(B) value in the microsecond time range.

Flow analysis of a shock wave at pulse ionization: Riemann problem implementation

An experimental study of the plasma-gas dynamic fluid formed after pulse ionization of the gas flow with a plane shock wave with Mach number 2.2–4.8 is carried out. Nanosecond volume discharge with UV preionization was switched on when the shock moved in a tube channel test section. Energy input occurs in the low-pressure gas volume separated by the shock surface within a time less than 200–300 ns; a single shock wave breaks into three discontinuities in accordance with the 1D Riemann problem solution. The initial (plasma-dynamic) stage of the flow in the nanosecond time range is visualized by glow recording; the supersonic gas processes in the microsecond time range are recorded using high-speed shadow imaging. Quantitative information about the dynamics of the shocks and contact surface (plots of horizontal distance) was obtained within time up to 25 µs. A region with an increased gas-discharge plasma glow intensity, after the discharge electric current termination, was recorded in the time interval from 0.3 to 1.5 µs; it was explained by a jump in gas temperature and density between the new shock wave and the contact discontinuity.

(Invited) Triplet Energy Transfer at Interfaces between Molecules and Perovskite or Metal Chalcogenide Nanostructures

The movement of energy and charge at nanoscale interfaces between organics and inorganics could enable novel schemes for photoconversion. We have been exploring ligand exchange and functionalization for nanoscale semiconductors with tunable properties. Lead chalcogenide quantum dots (QDs) have near-infrared band gaps that are ideal for solar harvesting and can be tuned to resonance with molecular ligands that harbor triplet excitons. Photoexcitation of either ligand or QD sets in motion energy transfer processes that have kinetics defined by nanocrystal band gap, triplet energy, and the arrangement and distance of molecules on the QD surface. Energy or charge transfer on a ps timescale can inhibit production of triplets by singlet fission, but strategies for enhancing the singlet fission rate or isolating the molecules from direct contact with the QD surface are being studied to circumvent this problem. In CsPbBr3 nanocrystals, ligand exchange with pentacene derivatives produces complementary absorption spectra for organic and inorganic components. Excitation of the strongly absorbing nanocrystal leads to energy transfer to the pentacene singlet, which undergoes fast singlet fission. The yield of triplets compared to absorbed photons is greater 100%, and the triplet lifetime is into the microsecond time range. Further dependence on the preparation conditions of the system (e.g., solution vs. film) is being explored. Other investigations have involved incorporating specialized molecules for attachment to transition metal dichalcogenides (TMDCs). The focus is on producing a uniform layer of bound molecules on the planar surfaces and understanding the interplay between interfacial charge-transfer and other photophysical properties like singlet fission.

Supplemental data for Blood platelets contain tumor-derived RNA biomarkers

We report on the growth mechanism of spherical silicon nanocrystals in a remote expanding Ar plasma using a time-modulated SiH4 gas injection in the microsecond time range. Under identical time-modulation parameters, we varied the local density of the SiH4 gas by changing its stagnation pressure on the injection line over the range of 0.1–2.0 bar. We observed that nanocrystals were synthesized in a size range from ∼2 to ∼50 nm with monocrystalline morphology. Smaller nanocrystals (∼2–6 nm) with narrower size distributions and with higher number densities were synthesized with an increase of the SiH4 gas-phase density. We related this observation to the rapid depletion of the number density of the molecules, ions, and radicals in the plasma during nanocrystal growth, which can primarily occur via nucleation with no significant subsequent coagulation. In addition, in our remote plasma environment, rapid cooling of the gas in the particle growth zone from ∼1500 to ∼400 K significantly reduces the coalescence...

Photoinduced Charge-Transfer Dynamics in WO3/BiVO4 Photoanodes Probed through Midinfrared Transient Absorption Spectroscopy.

The dynamics of photopromoted electrons in BiVO4, WO3, and WO3/BiVO4 heterojunction electrodes has been directly probed by transient absorption (TA) midinfrared (mid-IR) spectroscopy in the picosecond to microsecond time range. By comparison of the dynamics recorded with the two individual oxides at 2050 cm-1 with that of the heterojunction system after excitation at different wavelengths, electron-transfer processes between selectively excited BiVO4 and WO3 have been directly tracked for the first time. These results support the charge carrier interactions which were previously hypothesized by probing the BiVO4 hole dynamics through TA spectroscopy in the visible range. Nanosecond mid-IR TA experiments confirmed that charge carrier separation occurs in WO3/BiVO4 electrodes under visible-light excitation, persisting up to the microsecond time scale.

Structure of the CoI Intermediate of a Cobalt Pentapyridyl Catalyst for Hydrogen Evolution Revealed by Time-Resolved X-ray Spectroscopy.

Cobalt polypyridyls are highly efficient water-stable molecular catalysts for hydrogen evolution. The catalytic mechanism explaining their activity is under debate and the main question is the nature of the involvement of pyridyls in the proton transfer: the pentapyridyl ligand, acting as a pentadentate ligand, can provide stability to the catalyst or one of the pyridines can be involved in the proton transfer. Time-resolved Co K-edge X-ray absorption spectroscopy in the microsecond time range indicates that, for the [CoII (aPPy)] catalyst (aPPy=di([2,2'-bipyridin]-6-yl)(pyridin-2-yl)methanol), the pendant pyridine dissociates from the cobalt in the intermediate CoI state. This opens the possibility for pyridinium to act as an intramolecular proton donor. In the resting state, the catalyst returns to the original six-coordinate high-spin CoII state with a pentapyridyl and one water molecule coordinating to the metal center. Such a bifunctional role of the polypyridyl ligands can be exploited during further optimization of the catalyst.

Slow spin tunneling in the paramagnetic phase of the pyrochlore Nd2Sn2O7

The insulating pyrochlore compound Nd2Sn2O7 has been shown to undergo a second order magnetic phase transition at Tc ~ 0.91 K to a noncoplanar all-in--all-out magnetic structure of the Nd3+ magnetic moments. An anomalously slow paramagnetic spin dynamics has been evidenced from neutron backscattering and muon spin relaxation (muSR). In the case of muSR this has been revealed through the strong effect of a 50 mT longitudinal field on the spin-lattice relaxation rate. Here, motivated by a recent successful work performed for Yb2Ti2O7 and Yb2Sn2O7, analyzing the shape of the muSR longitudinal polarization function, we substantiate the existence of extremely slow paramagnetic spin dynamics in the microsecond time range for Nd2Sn2O7. Between 1.7 and 7 K, this time scale is temperature independent. This suggests a double spin-flip tunneling relaxation mechanism to be at play, probably involving spin substructures such as tetrahedra. Unexpectedly, the standard deviation of the field distribution at the muon site increases as the system is cooled. This exotic spin dynamics is in sharp contrast with the dynamics above 100 K which is driven by the Orbach relaxation mechanism involving single Nd3+ magnetic moments.

Laser Initiation of PETN containing Nickel Inclusions

The spectral and kinetic characteristics of pentaerythritol tetranitrate (PETN) containing nickel nanoparticles glow initiated by laser pulses was studied with high temporal resolution. It was shown that glow which is chemiluminescence arises as a result of chemical reaction initiation. We suggest that the glow is concerned on excited nitrogen dioxide NO2 luminescence. The reaction propagation leads to the explosion in the microsecond time range that is accompanied by thermal glow of the reaction products with temperature T=4300 K.

Microsecond X-ray Absorption Spectroscopy Identification of Co(I) Intermediates in Cobaloxime-Catalyzed Hydrogen Evolution.

Rational development of efficient photocatalytic systems for hydrogen production requires understanding the catalytic mechanism and detailed information about the structure of intermediates in the catalytic cycle. We demonstrate how time-resolved X-ray absorption spectroscopy in the microsecond time range can be used to identify such intermediates and to determine their local geometric structure. This method was used to obtain the solution structure of the Co(I) intermediate of cobaloxime, which is a non-noble metal catalyst for solar hydrogen production from water. Distances between cobalt and the nearest ligands including two solvent molecules and displacement of the cobalt atom out of plane formed by the planar ligands have been determined. Combining in situ X-ray absorption and UV/Vis data, we demonstrate how slight modification of the catalyst structure can lead to the formation of a catalytically inactive Co(I) state under similar conditions. Possible deactivation mechanisms are discussed.

Structural basis and dynamics of multidrug recognition in a minimal bacterial multidrug resistance system.

TipA is a transcriptional regulator found in diverse bacteria. It constitutes a minimal autoregulated multidrug resistance system against numerous thiopeptide antibiotics. Here we report the structures of its drug-binding domain TipAS in complexes with promothiocin A and nosiheptide, and a model of the thiostrepton complex. Drug binding induces a large transition from a partially unfolded to a globin-like structure. The structures rationalize the mechanism of promiscuous, yet specific, drug recognition: (i) a four-ring motif present in all known TipA-inducing antibiotics is recognized specifically by conserved TipAS amino acids; and (ii) the variable part of the antibiotic is accommodated within a flexible cleft that rigidifies upon drug binding. Remarkably, the identified four-ring motif is also the major interacting part of the antibiotic with the ribosome. Hence the TipA multidrug resistance mechanism is directed against the same chemical motif that inhibits protein synthesis. The observed identity of chemical motifs responsible for antibiotic function and resistance may be a general principle and could help to better define new leads for antibiotics.