Search Results (21)

In addition to investigations of the three-dimensional protein structure, information on the dynamical properties of proteins is indispensable for an understanding of protein function in general. Correlations between protein dynamics and function are typically anticipated when both molecular mobility and function are concurrently affected under specific temperatures or hydration conditions. In contrast, excitation energy transfer within the major photosynthetic light-harvesting complex II (LHC II) presents an atypical case, as it remains fully operational even at cryogenic temperatures, primarily depending on the interactions between electronic states and involving harmonic protein vibrations only. This review summarizes recent work on vibrational and conformational protein dynamics of LHC II and directly relates these findings to its light-harvesting function. In addition, we give a comprehensive introduction into the use of neutron spectroscopy and molecular dynamics simulations to investigate the protein dynamics of photosynthetic protein complexes in solution, which is information complementary to that obtained by protein crystallography. Full article

In this work, a computational spectroscopy approach was used to provide a complete assignment of the inelastic neutron scattering spectra of three title alkoxysilane derivatives—3-aminopropyltrimethoxysilane (APTS), N-methyl-3-aminopropyltrimethoxysilane (MAPTS), and 3-aminopropyltriethoxysilane (APTES). The simulated spectra obtained from density functional theory (DFT) calculations exhibit a remarkable match with the experimental spectra. The description of the experimental band profiles improves as the number of molecules considered in the theoretical model increases, from monomers to trimers. This highlights the significance of incorporating non-covalent interactions, encompassing classical NH···N, N–H···O, as well as C–H···N and C–H···O hydrogen bond contacts, to achieve a comprehensive understanding of the system. A distinct scenario emerges when considering optical vibrational techniques, infrared and Raman spectroscopy. In these instances, the monomer model provides a reasonable description of the experimental spectra, and no substantial alterations are observed in the simulated spectra when employing dimer and trimer models. This observation underscores the distinctive ability of neutron spectroscopy in combination with DFT calculations in assessing the structure and dynamics of molecular materials. Full article

A boron-rich boron–carbide material (B_4+δC) was synthesized by spark plasma sintering of a ball-milled mixture of high-purity boron powder and graphitic carbon at a pressure of 7 MPa and a temperature of 1930 °C. This high-pressure, high-temperature synthesized material was recovered and characterized by X-ray diffraction, X-ray photoelectron spectroscopy, Raman spectroscopy, Vickers hardness measurements, and thermal oxidation studies. The X-ray diffraction studies revealed a single-phase rhombohedral structure (space group R-3m) with lattice parameters in hexagonal representation as a = 5.609 ± 0.007 Å and c = 12.082 ± 0.02 Å. The experimental lattice parameters result in a value of δ = 0.55, or the composition of the synthesized compound as B_4.55C. The high-resolution scans of boron binding energy reveal the existence of a B-C bond at 188.5 eV. Raman spectroscopy reveals the existence of a 386 cm⁻¹ vibrational mode representative of C-B-B linear chain formation due to excess boron in the lattice. The measured Vickers microhardness at a load of 200 gf shows a high hardness value of 33.8 ± 2.3 GPa. Thermal gravimetric studies on B_4.55C were conducted at a temperature of 1300 °C in a compressed dry air environment, and its behavior is compared to other high-temperature ceramic materials such as high-entropy transition metal boride. The high neutron absorption cross section, high melting point, high mechanical strength, and thermal oxidation resistance make this material ideal for applications in extreme environments. Full article

The behavior of brucite over wide ranges of temperatures and pressures is of great interest for fundamental geochemistry and geophysics. Brucite layers and their octahedral Mg(OH)₆ structural units constitute an important structural part of layered dense magnesium hydrous silicates (DMHS), which play a major role in mineral equilibria controlling water balance in the subduction zones of the upper mantle. The ClayFF force field was originally developed for atomistic computer simulations of clays and other layered minerals and their hydrated interfaces. The crystallographic parameters of brucite at 25 °C and 1 bar were used, among several others, to develop the original ClayFF parametrization. Its new recent modification, ClayFF-MOH, can more accurately account for the bending of Mg–O–H angles in the brucite structure, and it was used here to test the applicability of this simple classical model over very wide ranges of temperature and pressure well beyond the range of its original implementation (up to 600 °C and 15 GPa). The pressure and temperature dependencies of brucite crystallographic parameters, the compressibility of the crystal lattice, the coefficients of thermal expansion, and the vibrational spectra were calculated in a series of classical molecular dynamics simulations using the ClayFF-MOH model and compared with a diverse set of available experimental data, including X-ray diffractometry, neutron scattering, IR and Raman spectroscopy. These new results demonstrated that ClayFF-MOH, as simple and approximate as it is, can be quite accurate in predicting many mineral properties at subduction zone conditions, which greatly expands the area of its applicability. Full article

The crystal and magnetic structures of van der Waals layered ferromagnet Cr${\mathrm{Br}}_3$ were studied using X-ray powder diffraction and neutron powder diffraction at pressures up to 23 GPa at ambient temperature and up to 2.8 GPa in the temperature range 6–300 K, respectively. The vibration spectra of Cr${\mathrm{Br}}_3$ were studied using Raman spectroscopy at pressures up to 23 GPa at ambient temperature. The anomalous pressure behavior of structural parameters and vibrational modes was observed, associated with a gradual isostructural phase transition in the pressure range 2.5–7 GPa. The Curie temperature T_C reduced rapidly with a pressure coefficient $d{T}_C/dP=-4.1\left(4\right)$ K/GPa. A full suppression of the ferromagnetic state was expected at P_C~8.4 GPa, where onset of the antiferromagnetic spin arrangement or magnetically disordered state may take place. Anomalies in Raman spectra at P~15 GPa point to another possible phase transformation in Cr${\mathrm{Br}}_3$, which may be related to the proximity of metallization of this van der Waals ferromagnet. Full article

Since the initial assessment four decades ago of zirconium diberyllide, ZrBe₂, as a potential hydride-forming intermetallic for hydrogen-storage applications, structural and dynamical studies to date have been chiefly limited to the hydride composition, ZrBe₂H_1.5, which exists as a single-phase disordered hydride with hexagonal P6/mmm symmetry that undergoes hydrogen sublattice ordering below ~200 K (~235–250 K for ZrBe₂D_1.5). It is desirable from both fundamental and technological viewpoints to have a more complete understanding of the ZrBe₂H_x phase diagram. In the present study, both neutron powder diffraction and neutron vibrational spectroscopy measurements of ZrBe₂H_x at lower hydrogen contents (x < 1.5) indicate that at least two other ordered phases exist at low temperatures, coinciding with respective nominal x values of 1 and 0.67. Compared to ZrBe₂H_1.5, these more-hydrogen-dilute phases possess different structural symmetries (orthorhombic) with different H-sublattice orderings and undergo much-higher-temperature order-disorder transitions at ≈ 460 K (x = 1) and ≈ 490 K (x = 0.67) to the characteristic H-disordered hexagonal P6/mmm structure associated with ZrBe₂H_1.5. Full article

In this work, the structural dynamics of the chloromethanes CCl₄, CHCl₃ and CH₂Cl₂ were evaluated through a computational spectroscopy approach by comparing experimental inelastic neutron scattering (INS) spectra with the corresponding simulated spectra obtained from periodic DFT calculations. The overall excellent agreement between experimental and calculated spectra allows a confident assignment of the vibrational features, including not only the molecular fundamental modes but also lattice and combination modes. In particular, an impressive overtone sequence for CHCl₃ is fully described by the simulated INS spectrum. In the CCl₄ spectrum, the splitting of the ν3 mode at ca. 765–790 cm⁻¹ is discussed on the basis of the Fermi resonance vs. crystal splitting controversy. Full article

The Museo Egizio’s collection contains 200 precious and unique leather artifacts belonging to different historical periods. The materials used during the tanning and curing procedures affect the chemical and elemental composition of the surface of the samples as well as their preservation status, specifically through the hydration level within the bulk. Here we provide an experimental characterization of a series of samples from Museo Egizio that document an extensive denaturation phenomenon (gelatinization), by combining non-destructive techniques including surface probes (X-ray fluorescence, Raman scattering, and scanning electron microscopy enhanced by X-ray energy spectroscopy) and neutron-based bulk techniques (inelastic and deep-inelastic neutron scattering). Results show partial dehydration of the samples in the bulk, affecting the morphology of their surface, the presence of potassium alum, and iron oxides, as well as phosphates and hydroxides related to the tanning and curing procedures. Finally, we briefly discuss the need for a versatile and adaptable software package that is capable of combining quantitative analyses with complementary techniques including morphological, elemental, and chemical composition. Full article

The wavelengths of neutrons available at neutron scattering facilities are comparable with intra- and inter-molecular distances, while their energies are comparable with molecular vibrational energies, making such neutrons highly suitable for studies of molecular-level dynamics. The unmistakable trend in neutron spectroscopy has been towards measurements of systems of greater complexity. Several decades of studies of dynamics using neutron scattering have witnessed a progression from measurements of solids to liquids to protein complexes and biomembranes, which may exhibit properties characteristic of both solids and liquids. Over the last two decades, the frontier of complexity amenable to neutron spectroscopy studies has reached the level of cells. Considering this a baseline for neutron spectroscopy of systems of the utmost biological complexity, we briefly review what has been learned to date from neutron scattering studies at the cellular level and then discuss in more detail the recent strides into neutron spectroscopy of tissues and whole multicellular organisms. Full article

Biochar (BCR) was obtained from the pyrolysis of a palm-oil-empty fruit bunch at 773 K for 2 h and used as a catalyst for the hydrodeoxygenation (HDO) of guaiacol (GUA) as a bio-oil model compound. Brunauer–Emmet–Teller surface area analysis, NH₃ and CO₂-temperature-programmed desorption, scanning electron microscope–dispersive X-ray spectroscopy, CHN analysis and X-ray fluorescence spectroscopy suggested that macroporous and mesoporous structures were formed in BCR with a co-presence of hydrophilic and hydrophobic sites and acid–base behavior. A combination of infrared, Raman and inelastic neutron scattering (INS) was carried out to achieve a complete vibrational assignment of BCR. The CH–OH ratio in BCR is ~5, showing that the hydroxyl functional groups are a minority species. There was no evidence for any aromatic C–H stretch modes in the infrared, but they are clearly seen in the INS and are the majority species, with a ratio of sp³–CH:sp²–CH of 1:1.3. The hydrogen bound to sp²–C is largely present as isolated C–H bonds, rather than adjacent C–H bonds. The Raman spectrum shows the characteristic G band (ideal graphitic lattice) and three D bands (disordered graphitic lattice, amorphous carbon, and defective graphitic lattice) of sp² carbons. Adsorbed water in BCR is present as disordered layers on the surface rather than trapped in voids in the material and could be removed easily by drying prior to catalysis. Catalytic testing demonstrated that BCR was able to catalyze the HDO of GUA, yielding phenol and cresols as the major products. Phenol was produced both from the direct demethoxylation of GUA, as well as through the demethylation pathway via the formation of catechol as the intermediate followed by deoxygenation. Full article

In this article, a novel method of simultaneous carborane- and gadolinium-containing compounds as efficient agents for neutron capture therapy (NCT) delivery via magnetic nanocarriers is presented. The presence of both Gd and B increases the efficiency of NCT and using nanocarriers enhances selectivity. These factors make NCT not only efficient, but also safe. Superparamagnetic Fe₃O₄ nanoparticles were treated with silane and then the polyelectrolytic layer was formed for further immobilization of NCT agents. Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), energy dispersive X-ray (EDX), ultraviolet–visible (UV-Vis) and Mössbauer spectroscopies, dynamic light scattering (DLS), scanning electron microscopy (SEM), vibrating-sample magnetometry (VSM) were applied for the characterization of the chemical and element composition, structure, morphology and magnetic properties of nanocarriers. The cytotoxicity effect was evaluated on different cell lines: BxPC-3, PC-3 MCF-7, HepG2 and L929, human skin fibroblasts as normal cells. average size of nanoparticles is 110 nm; magnetization at 1T and coercivity is 43.1 emu/g and 8.1, respectively; the amount of B is 0.077 mg/g and the amount of Gd is 0.632 mg/g. Successful immobilization of NCT agents, their low cytotoxicity against normal cells and selective cytotoxicity against cancer cells as well as the superparamagnetic properties of nanocarriers were confirmed by analyses above. Full article

The new complex of N,N-Dimethylglycine (DMG) with chloranilic acid (CLA) was synthesized and examined for thermal, structural, and dynamical properties. The structure of the reaction product between DMG and CLA was investigated in a deuterated dimethyl sulfoxide (DMSO-d6) solution and in the solid state by Nuclear Magnetic Resonance (NMR) (Cross Polarization Magic Angle Spinning-CPMAS NMR). The formation of the 1:1 complex of CLA and DMG in the DMSO solution was also confirmed by diffusion measurement. X-ray single crystal diffraction results revealed that the N,N-dimethylglycine–chloranilic acid (DMG⁺–CLA⁻) complex crystallizes in the centrosymmetric triclinic P-1 space group. The X-ray diffraction and NMR spectroscopy show the presence of the protonated form of N,N-dimethylglycine and the deprotonated form of chloranilic acid molecules. The vibrational properties of the co-crystal were investigated by the use of neutron (INS), infrared (IR), and Raman (RS) spectroscopies, as well as the density functional theory (DFT) with periodic boundary conditions. From the band shape analysis of the N–CH₃ bending vibration, we can conclude that the CH₃ groups perform fast (τ_R ≈ 10⁻¹¹ to 10^‒13 s) reorientational motions down to a temperature of 140 K, with activation energy at ca. 6.7 kJ mol⁻¹. X-ray diffraction and IR investigations confirm the presence of a strong N⁺–H···O⁻ hydrogen bond in the studied co-crystal. Full article

A shortage in the supply of ³He used for thermal neutron detector makes researchers to find ³He alternatives for developing new neutron detectors. Here, we prepared a neutron-sensitive composite liposome with tributyl borate and encapsulating with Fe₃O₄@oleic acid nanoparticles (Fe₃O₄@OA NPs), methylene blue (MB), or anti-albumin from bovine serum (anti-BSA). The tributyl borate compound was characterized by Fourier transform infrared spectroscopy (FT-IR). In addition, the morphology, element compositions, and magnetic properties of the composite liposome were investigated with transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDS), and vibrating sample magnetometer (VSM), respectively. The results indicated that a typical ellipsoidal magnetic liposome structure was obtained, and the lengths of the minor axis and major axis were 49 ± 1 nm and 87 ± 3 nm, respectively. Under thermal neutron irradiation, the structure of composite liposome was destroyed, and encapsulated reporter molecules were released, which was detected by ultraviolet–visible (UV–vis) spectroscopy and surface plasmon resonance (SPR) technology. The response of this sensor based on a destructive assay shows a good correlation with neutron doses. Besides, the sensor has a neutron to gamma-ray rejection ratio of 1568 at a thermal neutron flux rate of 135.6 n/cm²·s, which makes it a promising alternative to ³He. Full article

Conformational and polymorphic states in the nitro-derivative of o-hydroxy acetophenone have been studied by experimental and theoretical methods. The potential energy curves for the rotation of the nitro group and isomerization of the hydroxyl group have been calculated by density functional theory (DFT) to estimate the barriers of the conformational changes. Two polymorphic forms of the studied compound were obtained by the slow and fast evaporation of polar and non-polar solutions, respectively. Both of the polymorphs were investigated by Infrared-Red (IR) and Raman spectroscopy, Incoherent Inelastic Neutron Scattering (IINS), X-ray diffraction, nuclear quadrupole resonance spectroscopy (NQR), differential scanning calorimetry (DSC) and density functional theory (DFT) methods. In one of the polymorphs, the existence of a phase transition was shown. The position of the nitro group and its impact on the crystal cell of the studied compound were analyzed. The conformational equilibrium determined by the reorientation of the hydroxyl group was observed under argon matrix isolation. An analysis of vibrational spectra was achieved for the interpretation of conformational equilibrium. The infrared spectra were measured in a wide temperature range to reveal the spectral bands that were the most sensitive to the phase transition and conformational equilibrium. The results showed the interrelations between intramolecular processes and macroscopic phenomena in the studied compound. Full article

Extra virgin olive oil (EVOO) is defined as a functional food as it contains numerous phenolic components with well-recognized health-beneficial properties, such as high antioxidant and anti-inflammatory capacity. These characteristics depend on their structural/conformational behavior, which is largely determined by intra- and intermolecular H-bond interactions. While the vibrational dynamics of isolated compounds have been studied in a number of recent investigations, their signal in a real-life sample of EVOO is overwhelmed by the major constituent acids. Here, we provide a full characterization of the vibrational spectroscopic signal from commercially available EVOO samples using Inelastic Neutron Scattering (INS) and Raman spectroscopies. The spectra are dominated by CH₂ vibrations, especially at about 750 cm⁻¹ and 1300 cm⁻¹. By comparison with the spectra from hydroxytyrosol and other minor phenolic compounds, we show that the best regions in which to look for the structure–activity information related to the minor polar compounds is at 675 and 1200 cm⁻¹ for hydroxytyrosol, and around 450 cm⁻¹ for all minor polar compounds used as reference, especially if a selectively deuterated sample is available. The regional origin of the EVOO samples investigated appears to be related to the different amount of phenolic esters versus acids as reflected by the relative intensities of the peaks at 1655 and 1747 cm⁻¹. Full article