Structural Dynamics-Us最新文献

The desorption of a carbon monoxide molecule from a Ru(0001) surface was studied by means of X-ray Absorption Spectra (XAS) computed with Transition Potential (TP-DFT) and Time Dependent (TD-DFT) DFT methods. By unraveling the evolution of the CO electronic structure upon desorption, we observed that at 2.3 Å from the surface, the CO molecule has already predominantly gas-phase character. While C 1s XAS is quite insensitive to changes in the C-O bond length, the O 1s excitation is very sensitive with the π* coming down in energy upon CO bond stretching, which competes with the increase in orbital energy due to the repulsive interaction with the metallic surface. We show in a systematic way that the TP-DFT method can describe the XAS rather well at the endpoints (chemisorbed and gas phase) but is affected by artificial charge transfer and/or incorrect spin treatment in the transition region in cases like CO, where there are low-lying π* orbitals and large exchange interactions between the core 1s and valence-acceptor π* orbitals. As an alternative, we demonstrate by comparing with experimental data that a linear response approach using TD-DFT employing common exchange-correlation functionals and finite-size clusters can yield a good description of the spectral evolution of the 1s → π* transition with correct spin and gas-to-chemisorbed chemical shifts in good agreement with experiment.

In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn₄CaO₅ cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn₄CaO₅ cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn₄CaO₅ cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ_1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 10¹⁵ to 5 × 10¹⁷ W/cm² at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.

Quantitative knowledge of electron-phonon coupling is important for many applications as well as for the fundamental understanding of nonequilibrium relaxation processes. Time-resolved diffraction provides direct access to this knowledge through its sensitivity to laser-induced lattice dynamics. Here, we present an approach for analyzing time-resolved polycrystalline diffraction data. A two-step routine is used to minimize the number of time-dependent fit parameters. The lattice dynamics are extracted by finding the best fit to the full transient diffraction pattern rather than by analyzing transient changes of individual Debye-Scherrer rings. We apply this approach to platinum, an important component of novel photocatalytic and spintronic applications, for which a large variation of literature values exists for the electron-phonon coupling parameter $G_{\text{ep}}$ . Based on the extracted evolution of the atomic mean squared displacement and using a two-temperature model, we obtain $G_{\text{ep}}=(3.9\pm 0.2)\times {10}^{17}\frac{W}{m^{3}K}$ (statistical error). We find that at least up to an absorbed energy density of 124 J/cm³, $G_{\text{ep}}$ is not fluence-dependent. Our results for the lattice dynamics of platinum provide insights into electron-phonon coupling and phonon thermalization and constitute a basis for quantitative descriptions of platinum-based heterostructures in nonequilibrium conditions.

The dynamics of proteins that are associated with their function typically occur on the microsecond timescale, orders of magnitude faster than the time resolution of cryo-electron microscopy. We have recently introduced a novel approach to time-resolved cryo-electron microscopy that affords microsecond time resolution. It involves melting a cryo sample with a heating laser, so as to allow dynamics of the proteins to briefly occur in the liquid phase. When the laser is turned off, the sample rapidly revitrifies, trapping the particles in their transient configurations. Precise control of the temperature evolution of the sample is crucial for such an approach to succeed. Here, we provide a detailed characterization of the heat transfer occurring under laser irradiation as well as the associated phase behavior of the cryo sample. While areas close to the laser focus undergo melting and revitrification, surrounding regions crystallize. In situ observations of these phase changes therefore provide a convenient approach for assessing the temperature reached in each melting and revitrification experiment and for adjusting the heating laser power on the fly.

Dynamics of water and other small molecules confined in nanoporous materials is one of the current topics in condensed matter physics. One popular host material is a benzenedicarboxylate-bridging metal (III) complex abbreviated to MIL-53, whose chemical formula is M(OH)[C₆H₂(CO₂)₂R₂] where M = Cr, Al, Fe and R = H, OH, NH₂, COOH. These materials absorb not only water but also ammonia molecules. We have measured the quasi-elastic neutron scattering of MIL-53(Fe)-(COOH)₂·2H₂O and MIL-53(Fe)-(COOH)₂·3NH₃ which have full guest occupancy and exhibit the highest proton conductivity in the MIL-53 family. In a wide relaxation time region (τ = 10^-12-10^-8 s), two relaxations with Arrhenius temperature dependence were found in each sample. It is of interest that their activation energies are smaller than those of bulk H₂O and NH₃ liquids. The momentum transfer dependence of the relaxation time and the temperature dependence of the relaxation intensity suggest that the proton conduction is due to the Grotthuss mechanism with thermally excited H₂O and NH₃ molecules.

A systemic investigation of the terahertz (THz) transmission of La_0.67Ca_0.33MnO₃ film on the (001)-oriented NdGaO₃ substrate under external magnetic field and low temperature have been performed. The significant THz absorption difference between the out-of-plane and the in-plane magnetic field direction is observed, which is consistent with the electrical transport measurement using the standard four-probe technique. Furthermore, we find that the complex THz conductivities can be reproduced in terms of the Drude Smith equation as the magnetic field is perpendicular to the film plane, whereas it deviates from this model when the in-plane magnetic field is applied. We suggest that such anisotropies in THz transport dynamics have close correspondences with the phase separation and anisotropic magnetoresistance effects in the perovskite-structured manganites. Our work demonstrates that the THz time-domain spectroscopy (TDS) can be an effective non-contact method for studying the magneto-transport properties of the perovskite-structured manganites.

Here we report the vibrational spectra of deprotonated serine calculated from the classical molecular dynamics (MD) simulations and thermostated ring-polymer molecular dynamics (TRPMD) simulation with third-order density-functional tight-binding. In our earlier study [Inakollu and Yu, "A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function," J. Comput. Chem. 39, 2067 (2018)] of deprotonated serine, we observed a significant difference in the vibrational spectra with the classical MD simulations compared to the infrared multiple photon dissociation spectra. It was postulated that this is due to neglecting the nuclear quantum effects (NQEs). In this work, NQEs are considered in spectral calculation using the TRPMD simulations. With the help of potential of mean force calculations, the conformational space of deprotonated serine is analyzed and used to understand the difference in the spectra of classical MD and TRPMD simulations at 298.15 and 100 K. The high-frequency vibrational bands in the spectra are characterized using Fourier transform localized vibrational mode (FT-ν_N AC) and interatomic distance histograms. At room temperature, the quantum effects are less significant, and the free energy profiles in the classical MD and the TRPMD simulations are very similar. However, the hydrogen bond between the hydroxyl-carboxyl bond is slightly stronger in TRPMD simulations. At 100 K, the quantum effects are more prominent, especially in the 2600-3600 cm^-1, and the free energy profile slightly differs between the classical MD and TRPMD simulations. Using the FT-ν_N AC and the interatomic distance histograms, the high-frequency vibrational bands are discussed in detail.

Recent research indicates that graphene oxide (GO) nanosheets can be used to regulate ice formation by controlling critical ice nucleus growth in water at supercooling temperatures. In addition, the study of ice formation mechanisms regulated by GO nanosheets, a good model system for antifreeze proteins (AFPs), will shed light on how AFPs regulate ice formation in nature. In this work, time-resolved small-angle x-ray scattering (TR-SAXS) and quasi-elastic neutron scattering (QENS) experiments were carried out to investigate the structural and dynamical mechanisms of ice formation regulated by GO nanosheets. Strikingly, a transient intermediate state was observed in TR-SAXS experiments that only exists in the aqueous dispersions with a larger GO size (11 nm). This serves as evidence that the size of GO is critical for regulating ice formation. Elastic neutron scattering results indicate that ice is formed in all samples and thermal hysteresis occurs in GO aqueous dispersions in both H₂O and D₂O. The structural and dynamics information about water molecules in GO, extracted from QENS, reveals different dynamical behaviors of water molecules in GO aqueous dispersions when approaching the ice formation temperature.

[This corrects the article DOI: 10.1063/4.0000046.].