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1.
C-type Y2O3 ceramics (relative density ~94%) were prepared at 1500 °C for 2 hours with 1% wt. ZnO as sintering aid. The cell parameters of Y2O3 from Rietveld refinements are a = 10.6113(1) Å, V = 1194.8(1) Å3. The vibrational modes / lattice dynamics of Y2O3 were investigated using vibrational spectra (Raman and infrared reflection spectra) and first-principle (DFT) calculations. Eight of the 22 predicted first-order Raman modes and 12 of 16 predicted IR modes are observed and reliably assigned. For the observed vibrational modes, an excellent linearity (fexp = 1.023ftheo, R2 = 0.9999) between frequency from calculations (ftheo) and that from measurements (fexp) is observed. Accordingly, the corrected frequency (fcor) of vibrational modes, phonon band structure, and density of phonon states (DOPS) of Y2O3 are presented, in which, the frequency of phonons of Y2O3 is ≤625.2 cm−1 (wavelength ≥16.0 μm) with a gap of 30.6 cm−1 from 486.0 to 516.6 cm−1 (wavelength 20.6 - 19.4 μm) at room temperature. The modes with ftheo ≥292.5 cm−1 (fcor ≥299.2 cm−1) are dominated by the vibrations of O2− (light atom vibrations) and the vibrational modes with ftheo ≤239.0 cm−1 (fcor ≤244.5 cm−1) are dominated by the vibrations of both Y3+ and O2− (co-vibrations). The three modes Tu(7) at 301.6 cm−1, Tu(10) at 333.7 cm−1, and Tu(12) at 369.7 cm−1 of Y-O stretch vibrations dominate the phonon dielectric constant and dielectric loss of Y2O3 with more than 85% contributions.  相似文献   

2.
We use molecular dynamics simulations of a full atomistic Gō model to explore the impact of selected DE-loop mutations (D59P and W60C) on the folding space of protein human β2-microglobulin (Hβ2m), the causing agent of dialysis-related amyloidosis, a conformational disorder characterized by the deposition of insoluble amyloid fibrils in the osteoarticular system. Our simulations replicate the effect of mutations on the thermal stability that is observed in experiments in vitro. Furthermore, they predict the population of a partially folded state, with 60% of native internal free energy, which is akin to a molten globule. In the intermediate state, the solvent accessible surface area increases up to 40 times relative to the native state in 38% of the hydrophobic core residues, indicating that the identified species has aggregation potential. The intermediate state preserves the disulfide bond established between residue Cys25 and residue Cys80, which helps maintain the integrity of the core region, and is characterized by having two unstructured termini. The movements of the termini dominate the essential modes of the intermediate state, and exhibit the largest displacements in the D59P mutant, which is the most aggregation prone variant. PROPKA predictions of pKa suggest that the population of the intermediate state may be enhanced at acidic pH explaining the larger amyloidogenic potential observed in vitro at low pH for the WT protein and mutant forms.  相似文献   

3.
The excitation energy-dependent nature of Raman scattering spectrum, vibration, electronic or both, has been studied using different excitation sources on as-grown and annealed n- and p-type modulation-doped Ga1 − xInxNyAs1 − y/GaAs quantum well structures. The samples were grown by molecular beam technique with different N concentrations (y = 0%, 0.9%, 1.2%, 1.7%) at the same In concentration of 32%. Micro-Raman measurements have been carried out using 532 and 758 nm lines of diode lasers, and the 1064 nm line of the Nd-YAG laser has been used for Fourier transform-Raman scattering measurements. Raman scattering measurements with different excitation sources have revealed that the excitation energy is the decisive mechanism on the nature of the Raman scattering spectrum. When the excitation energy is close to the electronic band gap energy of any constituent semiconductor materials in the sample, electronic transition dominates the spectrum, leading to a very broad peak. In the condition that the excitation energy is much higher than the band gap energy, only vibrational modes contribute to the Raman scattering spectrum of the samples. Line shapes of the Raman scattering spectrum with the 785 and 1064 nm lines of lasers have been observed to be very broad peaks, whose absolute peak energy values are in good agreement with the ones obtained from photoluminescence measurements. On the other hand, Raman scattering spectrum with the 532 nm line has exhibited only vibrational modes. As a complementary tool of Raman scattering measurements with the excitation source of 532 nm, which shows weak vibrational transitions, attenuated total reflectance infrared spectroscopy has been also carried out. The results exhibited that the nature of the Raman scattering spectrum is strongly excitation energy-dependent, and with suitable excitation energy, electronic and/or vibrational transitions can be investigated.  相似文献   

4.
Endo-1,4-β-xylanase (EC 3.2.1.8) is the enzyme from Ruminococcus albus 8 (R. albus 8) (Xyn10A), and catalyzes the degradation of arabinoxylan, which is a major cell wall non-starch polysaccharide of cereals. The crystallographic structure of Xyn10A is still unknown. For this reason, we report a computer-assisted homology study conducted to build its three-dimensional structure based on the known sequence of amino acids of this enzyme. In this study, the best similarity was found with the Clostridium thermocellum (C. thermocellum) N-terminal endo-1,4-β-d-xylanase 10 b. Following the 100 ns molecular dynamics (MD) simulation, a reliable model was obtained for further studies. Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) methods were used for the substrate xylotetraose having the reactive sugar, which was bound in the −1 subsite of Xyn10A in the 4C1 (chair) and 2SO (skew boat) ground state conformations. According to the simulations and free energy analysis, Xyn10A binds the substrate with the −1 sugar in the 2SO conformation 39.27 kcal·mol−1 tighter than the substrate with the sugar in the 4C1 conformation. According to the Xyn10A-2SO Xylotetraose (X4(sb) interaction energies, the most important subsite for the substrate binding is subsite −1. The results of this study indicate that the substrate is bound in a skew boat conformation with Xyn10A and the −1 sugar subsite proceeds from the 4C1 conformation through 2SO to the transition state. MM-PBSA free energy analysis indicates that Asn187 and Trp344 in subsite −1 may an important residue for substrate binding. Our findings provide fundamental knowledge that may contribute to further enhancement of enzyme performance through molecular engineering.  相似文献   

5.
Cyanobacteriochromes (CBCRs) are promising optogenetic tools for their diverse absorption properties with a single compact cofactor-binding domain. We previously uncovered the ultrafast reversible photoswitching dynamics of a red/green photoreceptor AnPixJg2, which binds phycocyanobilin (PCB) that is unavailable in mammalian cells. Biliverdin (BV) is a mammalian cofactor with a similar structure to PCB but exhibits redder absorption. To improve the AnPixJg2 feasibility in mammalian applications, AnPixJg2_BV4 with only four mutations has been engineered to incorporate BV. Herein, we implemented femtosecond transient absorption (fs-TA) and ground state femtosecond stimulated Raman spectroscopy (GS-FSRS) to uncover transient electronic dynamics on molecular time scales and key structural motions responsible for the photoconversion of AnPixJg2_BV4 with PCB (Bpcb) and BV (Bbv) cofactors in comparison with the parent AnPixJg2 (Apcb). Bpcb adopts the same photoconversion scheme as Apcb, while BV4 mutations create a less bulky environment around the cofactor D ring that promotes a faster twist. The engineered Bbv employs a reversible clockwise/counterclockwise photoswitching that requires a two-step twist on ~5 and 35 picosecond (ps) time scales. The primary forward Pfr → Po transition displays equal amplitude weights between the two processes before reaching a conical intersection. In contrast, the primary reverse Po → Pfr transition shows a 2:1 weight ratio of the ~35 ps over 5 ps component, implying notable changes to the D-ring-twisting pathway. Moreover, we performed pre-resonance GS-FSRS and quantum calculations to identify the Bbv vibrational marker bands at ~659,797, and 1225 cm−1. These modes reveal a stronger H-bonding network around the BV cofactor A ring with BV4 mutations, corroborating the D-ring-dominant reversible photoswitching pathway in the excited state. Implementation of BV4 mutations in other PCB-binding GAF domains like AnPixJg4, AM1_1870g3, and NpF2164g5 could promote similar efficient reversible photoswitching for more directional bioimaging and optogenetic applications, and inspire other bioengineering advances.  相似文献   

6.
We have successfully prepared α-Fe2O3 nanospheres by solvothermal method using 2-butanone and water mixture solvent for the first time, which were about 100 nm in diameter and composed of very small nanoparticles. The as-prepared samples were characterized using X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. The results showed that the product was α-Fe2O3 nanosphere, and the temperature was an important factor on the formation of α-Fe2O3 nanospheres.  相似文献   

7.
The interaction of CO with ceria under conditions typically used to measure the oxygen storage capacity (OSC) of automotive three way catalysts (TWC) has been investigated by in situ Raman spectroscopy. During exposure of the ceria to CO at 623 K vibrational bands at 1582–1600 and 1331–1340 cm−1 appeared; these bands increased with increasing time of exposure to CO. The band positions are consistent with phonon modes of carbon; however, assignment to carboxylate species or carbonate species cannot be excluded. Subsequent exposure to O2 at room temperature resulted in a decrease in the intensities of the 1582–1600 and 1331–1340 cm−1 bands by more than 90%. As well, exposure to O2 at room temperature also resulted in the appearance of Raman modes characteristic of formate and peroxide surface species. The mechanism by which formate forms upon room temperature O2 exposure is discussed in the context of the assignment of the 1582–1600 and 1331–1340 cm−1 bands to carbon phonon modes which result from the disproportionation of CO on reduced ceria.  相似文献   

8.
Mechanical cues are employed to promote stem cell differentiation and functional tissue formation in tissue engineering and regenerative medicine. We have developed a Magnetic Force Bioreactor (MFB) that delivers highly targeted local forces to cells at a pico-newton level, utilizing magnetic micro- and nano-particles to target cell surface receptors. In this study, we investigated the effects of magnetically targeting and actuating specific two mechanical-sensitive cell membrane receptors—platelet-derived growth factor receptor α (PDGFRα) and integrin ανβ3. It was found that a higher mineral-to-matrix ratio was obtained after three weeks of magneto-mechanical stimulation coupled with osteogenic medium culture by initially targeting PDGFRα compared with targeting integrin ανβ3 and non-treated controls. Moreover, different initiation sites caused a differentiated response profile when using a 2-day-lagged magneto-mechanical stimulation over culture periods of 7 and 12 days). However, both resulted in statistically higher osteogenic marker genes expression compared with immediate magneto-mechanical stimulation. These results provide insights into important parameters for designing appropriate protocols for ex vivo induced bone formation via magneto-mechanical actuation.  相似文献   

9.
The non-adiabatic dynamics of furan excited in the ππ* state (S2 in the Franck–Condon geometry) was studied using non-adiabatic molecular dynamics simulations in connection with an ensemble density functional method. The time-resolved photoelectron spectra were theoretically simulated in a wide range of electron binding energies that covered the valence as well as the core electrons. The dynamics of the decay (rise) of the photoelectron signal were compared with the excited-state population dynamics. It was observed that the photoelectron signal decay parameters at certain electron binding energies displayed a good correlation with the events occurring during the excited-state dynamics. Thus, the time profile of the photoelectron intensity of the K-shell electrons of oxygen (decay constant of 34 ± 3 fs) showed a reasonable correlation with the time of passage through conical intersections with the ground state (47 ± 2 fs). The ground-state recovery constant of the photoelectron signal (121 ± 30 fs) was in good agreement with the theoretically obtained excited-state lifetime (93 ± 9 fs), as well as with the experimentally estimated recovery time constant (ca. 110 fs). Hence, it is proposed to complement the traditional TRPES observations with the trXPS (or trNEXAFS) measurements to obtain more reliable estimates of the most mechanistically important events during the excited-state dynamics.  相似文献   

10.
Although all forms of dynamical behaviour of a protein under allosteric interaction with effectors are predicted, little evidence of ultrafast dynamics in the interaction has been reported. Here, we demonstrate the efficacy of a combined approach involving picosecond‐resolved FRET and polarisation‐gated fluorescence for the exploration of ultrafast dynamics in the allosteric interaction of the Gal repressor (GalR) protein dimer with DNA operator sequences OE and OI. FRET from the single tryptophan residue to a covalently attached probe IAEDANS at a cysteine residue in the C‐terminal domain of GalR shows structural perturbation and conformational dynamics during allosteric interaction. Polarisation‐gated fluorescence spectroscopy of IAEDANS and another probe (FITC) covalently attached to the operator directly revealed the essential dynamics for cooperativity in the protein–protein interaction. The ultrafast resonance energy transfer from IAEDANS in the protein to FITC also revealed different dynamic flexibility in the allosteric interaction. An attempt was made to correlate the dynamic changes in the protein dimers with OE and OI with the consequent protein–protein interaction (tetramerisation) to form a DNA loop encompassing the promoter segment.  相似文献   

11.
J.-L Sauvajol  L Alvarez 《Carbon》2002,40(10):1697-1714
We review recent and original results on the vibrational properties of single wall carbon nanotubes (SWNT). We especially focus on calculations and experiments performed on nanotube bundles. So far, the main technique for probing the dynamics has been Raman spectroscopy. Here, we discuss: (i) the relation between frequency of the A1g radial breathing mode and nanotube diameter, (ii) the origin of resonance and the consequences on the profile and intensity of the Raman lines, and (iii) the assignment and resonant behaviour of the Raman lines between 700 and 1000 cm−1. Recently, inelastic neutron scattering techniques (INS) were shown to be effective tools to probe the vibrational density of states of SWNT. We review the INS results and focus on the study of low frequency excitations, especially libration-twist modes and acoustic modes. Both Raman and INS results are analysed in the light of calculations performed in a valence force field model taking into account van der Waals intertubes interactions in the bundles.  相似文献   

12.
Ultrafast hole carrier relaxation dynamics in CuO nanowires have been investigated using transient absorption spectroscopy. Following femtosecond pulse excitation in a non-collinear pump-probe configuration, a combination of non-degenerate transmission and reflection measurements reveal initial ultrafast state filling dynamics independent of the probing photon energy. This behavior is attributed to the occupation of states by photo-generated carriers in the intrinsic hole region of the p-type CuO nanowires located near the top of the valence band. Intensity measurements indicate an upper fluence threshold of 40 μJ/cm2 where carrier relaxation is mainly governed by the hole dynamics. The fast relaxation of the photo-generated carriers was determined to follow a double exponential decay with time constants of 0.4 ps and 2.1 ps. Furthermore, time-correlated single photon counting measurements provide evidence of three exponential relaxation channels on the nanosecond timescale.  相似文献   

13.
Infrared (IR) and Raman spectroscopic features of silicate glasses are often interpreted based on the analogy with those of smaller molecules, molecular clusters, or crystalline counterparts; this study tests the accuracy and validity of these widely cited peak assignment schemes by comparing vibrational spectral features with bond parameters of the glass network created by molecular dynamics (MD) simulations. A series of sodium silicate glasses with compositions of [Na2O]x[Al2O3]2[SiO2]98−x with x = 7, 12, 17, and 22 were synthesized and analyzed with IR and Raman. A silica glass substrate and a crystalline quartz were also analyzed for comparison. Glass structures with the same compositions were generated with MD simulations using three types of potentials: fixed partial charge pairwise (Teter), partial diffuse charge potential (MGFF), and bond order-based charge transfer potential (ReaxFF). The comparison of simulated and experimental IR spectra showed that, among these three potentials tested, ReaxFF reproduces the concentration dependence of spectral features closest to the experimentally observed trend. Thus, the bond length and angle distributions as well as Si–Qn species and ring size distributions of silica and sodium silicate glasses were obtained from ReaxFF-MD simulations and further compared with the peak assignment or deconvolution schemes—which have been widely used since 1970s and 1980s—(a) correlation between the IR peak position in the Si–O stretch region (1050-1120 cm−1) and the Si–O–Si bond angle; (b) deconvolution of the Raman bands in the Si–O stretch region with the Qn speciation; and (c) assignment of the Raman bands in the 420-600 cm−1 region to the bending modes of (SiO)n rings with different sizes (typically, n = 3-6). The comparisons showed that none of these widely used methods is congruent with the bond parameters or structures of silicate glass networks produced via ReaxFF-MD simulations. This finding invokes that the adequacy of these spectral interpretation methods must be questioned. Alternative interpretations are proposed, which are to be tested independently in future studies.  相似文献   

14.
Solutions of hydrogen-capped polyynes were prepared by laser ablation of graphite powder in n-hexane and subjected to size separation by high-performance liquid chromatography. Solutions of size-selected polyynes CnH2 (n = 8–16) were investigated by normal Raman (NR) and surface-enhanced Raman scattering (SERS) spectroscopy. A main band appearing in the 2000–2200 cm−1 region of the NR spectra showed a systematic downward shift as the chain length increased. The observed NR bands were assigned to Raman-active CC stretching vibrational modes by comparison with calculations based on density functional theory. Raman bands observed in SERS spectra were very broad and located at frequencies lower than the NR bands. A systematic band shift with increasing chain length was also observed for one of the bands. This band was thus assigned to a counterpart of the strong band in the NR spectra. These results made it possible to assign the origins of previously reported SERS bands of mixed polyyne solutions.  相似文献   

15.
The isothermal structural properties, equation of state, and vibrational dynamics of 2MNT were studied under high‐pressure using synchrotron XRD and optical Raman and IR microspectroscopy. Analysis of the XRD patterns revealed no indication of a phase transition to near 15 GPa and the pressure‐volume isotherm remained smooth to 15 GPa. Near 15 GPa, significant sample damage was observed from the X‐ray beam which precluded the acquisition of patterns above this pressure. XRD and Raman spectroscopic measurements showed the monoclinic ambient condition phase of 2MNT remains the dominant phase to near 20 GPa, although a shift of the NO2 IR active vibrational modes to lower frequencies suggested a subtle geometry modification not reflected in the XRD data.  相似文献   

16.
Direct inhibition of tumor necrosis factor-alpha (TNF-α) action is considered a promising way to prevent or treat TNF-α-associated diseases. The trimeric form of TNF-α binds to its receptor (TNFR) and activates the downstream signaling pathway. The interaction of TNF-α with molecular-grade dimethyl sulfoxide (DMSO) in an equal volumetric ratio renders TNF-α inert, in this state, TNF-α fails to activate TNFR. Here, we aimed to examine the inhibition of TNF-α function by various concentrations of DMSO. Its higher concentration led to stronger attenuation of TNF-α-induced cytokine secretion by fibroblasts, and of their death. We found that this inhibition was mediated by a perturbation in the formation of the functional TNF-α trimer. Molecular dynamics simulations revealed a transient interaction between DMSO molecules and the central hydrophobic cavity of the TNF-α homodimer, indicating that a brief interaction of DMSO with the TNF-α homodimer may disrupt the formation of the functional homotrimer. We also found that the sensitizing effect of actinomycin D on TNF-α-induced cell death depends upon the timing of these treatments and on the cell type. This study will help to select an appropriate concentration of DMSO as a working solvent for the screening of water-insoluble TNF-α inhibitors.  相似文献   

17.
Brush-like α-Fe2O3–ZnO heterostructures were synthesized through a sputtering ZnO seed-assisted hydrothermal growth method. The resulting heterostructures consisted of α-Fe2O3 rod templates and ZnO branched crystals with an average diameter of approximately 12 nm and length of 25 nm. The gas-sensing results demonstrated that the α-Fe2O3–ZnO heterostructure-based sensor exhibited excellent sensitivity, selectivity, and stability toward low-concentration NO2 gas at an optimal temperature of 300 °C. The α-Fe2O3–ZnO sensor, in particular, demonstrated substantially higher sensitivity compared with pristine α-Fe2O3, along with faster response and recovery speeds under similar test conditions. An appropriate material synergic effect accounts for the considerable enhancement in the NO2 gas-sensing performance of the α-Fe2O3–ZnO heterostructures.  相似文献   

18.
Transition-metal (TM)-doped diluted magnetic oxides (DMOs) have attracted attention from both experimental and theoretical points of view due to their potential use in spintronics towards new nanostructured devices and new technologies. In the present work, we study the magnetic properties of Sn0.96TM0.04O2 and Sn0.96TM0.04O1.98(VO)0.02, where TM = Fe and Co, focusing in particular in the role played by the presence of O vacancies nearby the TM. The calculated total energy as a function of the total magnetic moment per cell shows a magnetic metastability, corresponding to a ground state, respectively, with 2 and 1 μB/cell, for Fe and Co. Two metastable states, with 0 and 4 μB/cell were found for Fe, and a single value, 3 μB/cell, for Co. The spin-crossover energies (ES) were calculated. The values are ES0/2 = 107 meV and ES4/2 = 25 meV for Fe. For Co, ES3/1 = 36 meV. By creating O vacancies close to the TM site, we show that the metastablity and ES change. For iron, a new state appears, and the state with zero magnetic moment disappears. The ground state is 4 μB/cell instead of 2 μB/cell, and the energy ES2/4 is 30 meV. For cobalt, the ground state is then found with 3 μB/cell and the metastable state with 1 μB/cell. The spin-crossover energy ES1/3 is 21 meV. Our results suggest that these materials may be used in devices for spintronic applications that require different magnetization states.  相似文献   

19.
S100B is an astrocytic extracellular Ca2+-binding protein implicated in Alzheimer’s disease, whose role as a holdase-type chaperone delaying Aβ42 aggregation and toxicity was recently uncovered. Here, we employ computational biology approaches to dissect the structural details and dynamics of the interaction between S100B and Aβ42. Driven by previous structural data, we used the Aβ25–35 segment, which recapitulates key aspects of S100B activity, as a starting guide for the analysis. We used Haddock to establish a preferred binding mode, which was studied with the full length Aβ using long (1 μs) molecular dynamics (MD) simulations to investigate the structural dynamics and obtain representative interaction complexes. From the analysis, Aβ-Lys28 emerged as a key candidate for stabilizing interactions with the S100B binding cleft, in particular involving a triad composed of Met79, Thr82 and Glu86. Binding constant calculations concluded that coulombic interactions, presumably implicating the Lys28(Aβ)/Glu86(S100B) pair, are very relevant for the holdase-type chaperone activity. To confirm this experimentally, we examined the inhibitory effect of S100B over Aβ aggregation at high ionic strength. In agreement with the computational predictions, we observed that electrostatic perturbation of the Aβ-S100B interaction decreases anti-aggregation activity. Altogether, these findings unveil features relevant in the definition of selectivity of the S100B chaperone, with implications in Alzheimer’s disease.  相似文献   

20.
2D β-Ga2O3 flakes on a continuous 2D graphene film were prepared by a one-step chemical vapor deposition on liquid gallium surface. The composite was characterized by optical microscopy, scanning electron microscopy, Raman spectroscopy, energy dispersive spectroscopy, and X-ray photoelectron spectroscopy (XPS). The experimental results indicate that Ga2O3 flakes grew on the surface of graphene film during the cooling process. In particular, tenfold enhancement of graphene Raman scattering signal was detected on Ga2O3 flakes, and XPS indicates the C-O bonding between graphene and Ga2O3. The mechanism of Raman enhancement was discussed. The 2D Ga2O3-2D graphene structure may possess potential applications.  相似文献   

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