Physicochemical properties calculated using DFT method and changes of 5-methyluridine hemihydrate crystals at high temperatures.

5-methyluridine hemihydrate (5 mU) single crystals were synthesized by the slow solvent evaporation method. The physicochemical properties, such as frontier molecular orbitals, global reactivity indices and vibrational were computationally studied through density functional theory (DFT). In addition, structural, vibrational, and thermal properties were obtained by powder X-ray diffraction (PXRD), Raman spectroscopy, thermogravimetric (TG) analysis and differential scanning calorimetry (DSC). PXRD evaluated the structural behavior of 5 mU crystal in the temperature range of 300-460 K. The high-temperature PXRD results suggested that the crystal undergoes two dehydration processes, being a first occurring from the orthorhombic structure (P21212) to triclinic (P1), in which the water losses occurred around 380 K. A second dehydration triggers the change from the triclinic structure to monoclinic (P21) within the 420-435 K temperature range. Furthermore, after this temperature, the anhydrous 5 mU suffers a melting process near 460 K, which is remarkably characterized as an irreversible process. Raman spectroscopy was carried out to identify the vibrational modes linked to the water molecule and the noticeable changes in these bands due to high-temperature effects around 380 K and 410 K. Indeed, changes on Raman bands, such as intensity inversion, the disappearance of bands associated with the hydrogen bonds formed from the water molecules and uracil group, and the ribose group were observed. Finally, this study provided details on the structural and vibrational changes caused by the dehydration of 5 mU crystals and the importance of hydrogen bonds for understanding the intermolecular interactions of the 5 mU, a methylated nucleoside with important biological functions.

High pressure Raman spectra and DFT calculation of glyphosate.

Glyphosate, N-(phosphonomethyl)glycine, (C3H8NO5P), was obtained through the method of slow evaporation method from aqueous solution and its structure analyzed through X-ray diffraction and the Rietveld method. The normal modes of the crystal were investigated using Raman spectroscopy and Density Functional Theory to obtain the assignment of most of the normal modes in the spectral range between 3070 and 45 cm-1. The crystal was compressed to high pressure through a diamond anvil cell, up to 6.2 GPa. From the behavior of the modes corresponding to both internal modes and lattice modes it was possible to discovery two phase transitions undergone by glyphosate, one between 0.97 and 1.5 GPa and other in the pressure interval 4.29-4.63 GPa. The analysis of the Raman spectra also indicates a certain disorder and conformational changes of the molecules in the unit cell at high pressure. Additionally, the phase transitions revealed to be reversible, with no cracking of the sample in the compression - decompression run.

Response to comment on 'Hydrogen bonds in crystalline d-alanine: diffraction and spectroscopic evidence for differences between enantiomers'.

A response is given to comments by Bürgi & Macchi [IUCrJ (2018), 5, 654-657] about Belo et al. [IUCrJ (2018), 5, 6-12.].

Raman studies of nanocomposites catalysts: temperature and pressure effects of CeAl, CeMn and NiAl oxides.

High temperature and pressure effects on the physicochemical properties of binary oxides catalysts were investigated. The nanocomposites catalysts comprising of CeAl, CeMn and NiAl were characterized through various physicochemical techniques. A study of the temperature and pressure induced phenomena monitored by Raman spectroscopy was proposed and discussed. Spectral modifications of the Raman modes belonging to the CeMn suggest structural changes in the solid due to the MnO2 phase oxidation with increasing temperature. The thermal expansion and lattice anharmonicity effects were observed on CeMn due to lack of stability of the lattice vacancies. The CeAl and NiAl composites presented crystallographic stability at low temperatures however, undertake a phase transformation of NiO/Al2O3 into NiAl2O4, mostly without any deformation in its structure with increasing the temperature. It was also inferred that the binary oxides are more stables in comparison with monoxides. Detailed pressure-dependent Raman measurements of the T2g phonon mode of CeMn and NiAl revealed that the pressure contributes to modify bonds length and reduces the particles sizes of the solids. On the contrary, high pressure on CeAl sample improved the stability with addition of Al2O3 in the CeO2 lattice. The results then suggest a good stability of CeAl and NiAl composite catalysts at high pressure and low temperature and show how to prospect of tuning the catalysis for surface reactions entirely through in situ spectroscopic investigations means.

Hydrogen bonds in crystalline d-alanine: diffraction and spectroscopic evidence for differences between enantiomers.

Enantiomeric amino acids have specific physiological functions in complex biological systems. Systematic studies focusing on the solid-state properties of d-amino acids are, however, still limited. To shed light on this field, structural and spectroscopic studies of d-alanine using neutron powder diffraction, polarized Raman scattering and ab initio calculations of harmonic vibrational frequencies were carried out. Clear changes in the number of vibrational modes are observed as a function of temperature, which can be directly connected to variations of the N-D bond lengths. These results reveal dissimilarities in the structural properties of d-alanine compared with l-alanine.

Pressure-induced phase transition and fracture in α-MoO3 nanoribbons.

MoO3 nanoribbons were studied under different pressure conditions ranging from 0 to 21GPa at room temperature. The effect of the applied pressure on the spectroscopic and morphologic properties of the MoO3 nanoribbons was investigated by means of Raman spectroscopy and scanning electron microscopy techniques. The pressure dependent Raman spectra of the MoO3 nanoribbons indicate that a structural phase transition occurs at 5GPa from the orthorhombic α-MoO3 phase (Pbnm) to the monoclinic MoO3-II phase (P21/m), which remains stable up to 21GPa. Such phase transformation occurs at considerably lower pressure than the critical pressure for α-MoO3 microcrystals (12GPa). We suggested that the applanate morphology combined with the presence of crystalline defects in the sample play an important role in the phase transition of the MoO3 nanoribbons. Frequencies and linewidths of the Raman bands as a function of pressure also suggest a pressure-induced morphological change and the decreasing of the nanocrystal size. The observed spectroscopic changes are supported by electron microscopy images, which clearly show a pressure-induced morphologic change in MoO3 nanoribbons.

Raman evidence for pressure-induced formation of diamondene.

Despite the advanced stage of diamond thin-film technology, with applications ranging from superconductivity to biosensing, the realization of a stable and atomically thick two-dimensional diamond material, named here as diamondene, is still forthcoming. Adding to the outstanding properties of its bulk and thin-film counterparts, diamondene is predicted to be a ferromagnetic semiconductor with spin polarized bands. Here, we provide spectroscopic evidence for the formation of diamondene by performing Raman spectroscopy of double-layer graphene under high pressure. The results are explained in terms of a breakdown in the Kohn anomaly associated with the finite size of the remaining graphene sites surrounded by the diamondene matrix. Ab initio calculations and molecular dynamics simulations are employed to clarify the mechanism of diamondene formation, which requires two or more layers of graphene subjected to high pressures in the presence of specific chemical groups such as hydroxyl groups or hydrogens.The synthesis of two-dimensional diamond is the ultimate goal of diamond thin-film technology. Here, the authors perform Raman spectroscopy of bilayer graphene under pressure, and obtain spectroscopic evidence of formation of diamondene, an atomically thin form of diamond.

Large-field electron imaging and X-ray elemental mapping unveil the morphology, structure, and fractal features of a Cretaceous fossil at the centimeter scale.

We used here a scanning electron microscopy approach that detected backscattered electrons (BSEs) and X-rays (from ionization processes) along a large-field (LF) scan, applied on a Cretaceous fossil of a shrimp (area ∼280 mm(2)) from the Araripe Sedimentary Basin. High-definition LF images from BSEs and X-rays were essentially generated by assembling thousands of magnified images that covered the whole area of the fossil, thus unveiling morphological and compositional aspects at length scales from micrometers to centimeters. Morphological features of the shrimp such as pleopods, pereopods, and antennae located at near-surface layers (undetected by photography techniques) were unveiled in detail by LF BSE images and in calcium and phosphorus elemental maps (mineralized as hydroxyapatite). LF elemental maps for zinc and sulfur indicated a rare fossilization event observed for the first time in fossils from the Araripe Sedimentary Basin: the mineralization of zinc sulfide interfacing to hydroxyapatite in the fossil. Finally, a dimensional analysis of the phosphorus map led to an important finding: the existence of a fractal characteristic (D = 1.63) for the hydroxyapatite-matrix interface, a result of physical-geological events occurring with spatial scale invariance on the specimen, over millions of years.

Spectroscopic analysis and X-ray diffraction of trunk fossils from the Parnaíba Basin, Northeast Brazil.

The Parnaiba Sedimentary Basin is of the Paleozoic age and is located in Northeast Brazil, covering the states of Piauí, Maranhão and Tocantins and a small part of Ceará and Pará. In this work we applied several chemical analytical techniques to characterize trunk fossils found in the Parnaíba Sedimentary Basin, collected from four different sites, and discuss their fossilization process. We performed a study of the trunk fossils through X-ray diffraction, energy dispersive spectroscopy, infrared and Raman spectroscopy. The analysis allow us to identify the different compositions which are present in the trunk fossils: kaolinite (Al2Si2O5(OH)4), hematite (Fe2O3) and quartz (SiO2). Based in these results we were able to identify that the main fossilization mechanism of the trunk fossil was silicification. Furthermore, through Raman spectroscopy, we have observed the presence of carbonaceous materials in the Permian fossils, as evidenced by the D and G Raman bands. The relative intensities and bandwidths of the D and G bands indicated that the carbon has a low crystallinity. Thus, most of trunk fossils analyzed were permineralized and not petrified, because there is the presence of carbon that characterizes the partial decomposition of the organic matter in some trunks.

Temperature and high pressure effects on the structural features of catalytic nanocomposites oxides by Raman spectroscopy.

Structural characterizations of nanostructured oxides were studied by X-ray diffraction (XRD), Raman and infrared spectroscopy. The oxides catalysts namely, SnO2, ZrO2, CeO2, MnOx, Al2O3 and TiO2 were prepared by a nanocasting route and the effect of the temperature and pressure on the stability of the solids was evaluated. Raman spectra showed that ZrO2 and TiO2 exhibited phase transitions at moderate temperatures whereas CeO2, SnO2 and MnOx had an effective creation of defects in their structures upon annealing at elevated temperatures. The results suggested also that the effect of the temperature on the particles growth is related to the type of oxide. In this regard, phase transition by up to 600°C accelerated the sintering of ZrO2 and CeO2 grains compared to TiO2, SnO2 and MnOx counterparts. Under hydrostatic pressures lower than 10GPa, rutile TiO2 and tetragonal ZrO2 exhibited pressure induced phase transition whereas CeO2 and SnO2 were stable at pressures close to 15GPa. The experiments revealed that the nanostructured SnO2 oxide exhibited stable performance at relatively high temperatures without phase transition or sintering, being suitable to be used as catalysts in the range of temperature and pressure studied.

Synthesis and antibacterial activity of a new derivative of the Meldrun acid: 2,2-dimethyl-5-(4H-1,2,4-triazol-4-ylaminomethylene)-1,3-dioxane-4,6-dione (C9H10N4O4).

The discovery of new substances with proven antimicrobial activity is the current study goal of various researchers. Usage of synthetic products has grown considerably in the past few years due to processing agility, and capability of going through previous chemical modifications in order to enhance its biological activity. Widespread careless use of antimicrobials has made the number of resistant microorganisms rise significantly, thus demanding more efficient drugs to fight them. One of these synthetic candidates for this purpose is the substance 2,2-Dimethyl-5-(4H-1,2,4-triazol-4-ylaminomethylene)-1,3-dioxane-4,6-dione (C9H10N4O4), aminomethylene derivative from Meldrum's acid. This substance, alone and in association with common antibiotics, were evaluated in vitro for antimicrobial activity, and had their minimum inhibitory concentration (MIC) towards Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 10536 and Pseudomonas aeruginosa ATCC 15442, as well as multiresistant strains Escherichia coli 27, Staphylococcus aureus 358 and Pseudomonas aeruginosa 03 determined. The antimicrobial modulation action tests of the aminoglycosides with C9H10N4O4 were performed according to the microdilution method, and resulted in observation of a positive synergic effect.

Molecular flexibility and structural instabilities in crystalline l-methionine.

We have investigated the dynamics in polycrystalline samples of l-methionine related to the structural transition at about 307K by incoherent inelastic and quasielastic neutron scattering, X-ray powder diffraction as well as ab-initio calculations. l-Methionine is a sulfur amino acid which can be considered a derivative of alanine with the alanine R-group CH3 exchanged by CH3S(CH2)2. Using X-ray powder diffraction we have observed at ~190K an anomalous drop of the c-lattice parameter and an abrupt change of the ß-monoclinic angle that could be correlated to the anomalies observed in previous specific heat measurements. Distinct changes in the quasielastic region of the neutron spectra are interpreted as being due to the onset and slowing-down of reorientational motions of the CH3-S group, are clearly distinguished above 130K in crystalline l-methionine. Large-amplitude motions observed at low frequencies are also activated above 275K, while other well-defined vibrations are damped. The ensemble of our results suggests that the crystalline structure of l-methionine is dynamically highly disordered above 275K, and such disorder can be linked to the flexibility of the molecular thiol-ether group.

Structure-property relations in crystalline L-leucine obtained from calorimetry, X-rays, neutron and Raman scattering.

We have studied the amino acid L-leucine (LEU) using inelastic neutron scattering, X-rays and neutron diffraction, calorimetry and Raman scattering as a function of temperature, focusing on the relationship between the local dynamics of the NH(3), CH(3), CH(2) and CO(2) moieties and the molecular structure of LEU. Calorimetric and diffraction data evidenced two novel phase transitions at about 150 K (T(1)) and 275 K (T(2)). The dynamical susceptibility function, obtained from the inelastic neutron scattering results, shows a re-distribution of the intensity of the vibrational bands that can be directly correlated with the phase transitions observed at T(1) and T(2), as well as with the already reported phase transition at T(3) = 353 K. Through the analysis of the Raman modes, the new structural arrangement observed below T(1) was related to conformational modifications of the CH and CH(3) groups, while the behavior of the N-H stretching vibration, ν(NH(3)), gave insight into the intermolecular N-H…O interactions. The observation of changes in the translational symmetry in the crystalline lattice, as well as anharmonic dynamics, allows for localized motions in LEU.

Raman and neutron scattering study of partially deuterated L-alanine: evidence of a solid-solid phase transition.

Raman and neutron experiments using specific isotope labeling were combined in order to study the dynamics and structure of L-alanine. Inelastic neutron and Raman scattering data of C(2)H(4)(ND(2))CO(2)D are discussed in relation to the doubling of the lattice parameter a observed by means of neutron powder diffraction in C(2)D(4) (NH(2))CO(2)H. The major changes accompanying the phase transition are found in the vibrational frequencies involving the torsional vibration tau(CO(2)(-)), which is clearly affected by the hydrogen bonds between the protons of the ammonium group and the oxygen atoms of the carboxylate group. At lower temperatures the rearrangement of identifiable hydrogen bonds induces changes in the bending vibration delta(ND(3)), confirming some orientational disorder.

Structural isotopic effects in the smallest chiral amino acid: observation of a structural phase transition in fully deuterated alanine.

A first study of possible changes instigated by deuteration in amino acids was carried out using neutron diffraction, inelastic neutron scattering, and Raman scattering in l-alanine, C2H4(NH2)COOH. Careful analysis of the structural parameters shows that deuteration of l-alanine engenders significant geometric changes as a function of temperature, which can be directly related to the observation of new lattice vibration modes in the Raman spectra. The combination of the experimental data suggests that C2D4(ND2)COOD undergoes a structural phase transition (or a structural rearrangement) at about 170 K. Considering that this particular amino acid is a hydrogen-bonded system with short hydrogen bonds (O...H approximately 1.8 A), we evoke the Ubbelohde effect to conclude that substitution of hydrogen for deuterium gives rise to changes in the hydrogen-bonding interactions. The structural differences suggest distinct relative stabilities for the hydrogenous and deuterated l-alanine.

New crystals in the lithium sulfate family.

The preparation and structures of caesium lithium sulfate, Cs(1.15)Li(2.85)(SO(4))(2), and caesium lithium rubidium sulfate, Cs(0.90)Li(2.88)Rb(0.22)(SO(4))(2), are described and discussed in the context of simple and double sulfate polymorphism. The latter structure is related to the former through the substitution of Rb for Cs. In both crystals, the sulfate ions occupy two non-equivalent sites, but the ions are disordered in Cs(1.15)Li(2.85)(SO(4))(2).