Intermolecular Interactions in 3-Aminopropyltrimethoxysilane, N-Methyl-3-aminopropyltrimethoxysilane and 3-Aminopropyltriethoxysilane: Insights from Computational Spectroscopy.

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.

Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function.

Genes encoding subunits of the SWI/SNF or BAF ATP-dependent chromatin remodeling complex are among the most enriched for deleterious de novo mutations in intellectual disabilities and autism spectrum disorder, but the causative molecular pathways are not fully known 1,2 . Synaptic activity in neurons is critical for learning and memory and proper neural development 3 . Neural activity prompts calcium influx and transcription within minutes, facilitated in the nucleus by various transcription factors (TFs) and chromatin modifiers 4 . While BAF is required for activity-dependent developmental processes such as dendritic outgrowth 5-7 , the immediate molecular consequences of neural activity on BAF complexes and their functions are unknown. Here we mapped minute-scale biochemical consequences of neural activity, modeled by membrane depolarization of embryonic mouse primary cortical neurons, on BAF complexes. We used acute chemical perturbations of BAF ATPase activity and kinase signaling to define the activity-dependent effects on BAF complexes and activity-dependent BAF functions. Our studies found that BAF complexes change in subunit composition and are selectively phosphorylated within 10 minutes of depolarization. Increased levels of the core PBAF subunit Baf200/ Arid2 , uniquely containing an RFX-like DNA-binding domain, are concurrent with ATPase-dependent opening of chromatin at RFX/X-box motifs. Changes in BAF composition and phosphorylation lead to the regulation of chromatin accessibility for critical neurogenesis TFs. These biochemical effects are a convergent phenomenon downstream of multiple growth factor signaling pathways in mouse neurons and fibroblasts suggesting that BAF integrates signaling information from the membrane. In support of such a membrane-to-nucleus signaling cascade, we also identified a BAF-interacting kinase, Dclk2, whose inhibition attenuates BAF phosphorylation selectively. Our findings support a direct role of BAF complexes in responding to synaptic activity to regulate TF binding and transcription.

Can Chocolate Be Classified as an Ultra-Processed Food? A Short Review on Processing and Health Aspects to Help Answer This Question.

Chocolate is a confectionery product whose consumption has increased, particularly dark chocolate. Chocolate is produced with varying amounts of cocoa liquor (CL), cocoa butter (CB) and cocoa powder (CP). The main chocolate types are dark, milk and white. Processing steps for chocolate production are described, and nutritional compositions examined for benefits and risks to health. Chocolate processing comprises steps at farm level, initial industrial processing for production of CL, CB and CP (common for all chocolate types) and mixing with other ingredients (like milk and sugar differing according to chocolate type) for industrial chocolate processing. All chocolate types present similar processing levels, and none involve chemical processing. Nutritional profiles of chocolate products differ according to composition, e.g., dark chocolate contains more CL, and so a higher antioxidant capacity. Chocolate is an energy-dense food rich in bioactive compounds (polyphenols, alkaloids, amino acids). Studies have demonstrated benefits of moderate consumption in reducing cardiovascular risk and oxidative and inflammatory burden, improving cognitive functions, maintaining diversity in gut microbiota, among others. In our view, chocolate should not be classified as an ultra-processed food because of simple processing steps, limited ingredients, and being an important part of a healthy diet when consumed in moderation.

Structural Dynamics of Chloromethanes through Computational Spectroscopy: Combining INS and DFT.

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.

Vibrational Dynamics in crystalline 4-(dimethylamino) benzaldehyde: Inelastic Neutron Scattering and Periodic DFT Study.

The structure and dynamics of crystalline 4-(dimethylamino) benzaldehyde, 4DMAB, are assessed through INS spectroscopy combined with periodic DFT calculations. The excellent agreement between experimental and calculated spectra is the basis for a reliable assignment of INS bands. The external phonon modes of crystalline 4DMAB are quite well described by the simulated spectrum, as well as the modes involving low-frequency molecular vibrations. Crystal field splitting is predicted and observed for the modes assigned to the dimethylamino group. Concerning the torsional motion of methyl groups, four individual bands are identified and assigned to specific methyl groups in the asymmetric unit. The torsional frequencies of the four methyl groups in the asymmetric unit fall in a region of ca. 190 ± 20 cm-1, close to the range of values observed for methyl groups bonding to unsaturated carbon atoms. The hybridization state of the X atom in X-CH3 seems to play a key role in determining the methyl torsional frequency.

New Insights on the Vibrational Dynamics of 2-Methoxy-, 4-Methoxy- and 4-Ethoxy-Benzaldehyde from INS Spectra and Periodic DFT Calculations.

The dynamics of 2-methoxybenzaldehyde, 4-methoxybenzaldehyde, and 4-ethoxybenzaldehyde in the solid state are assessed through INS spectroscopy combined with periodic DFT calculations. In the absence of experimental data for 4-ethoxybenzaldehyde, a tentative crystal structure, based on its similarity with 4-methoxybenzaldehyde, is considered and evaluated. The excellent agreement between calculated and experimental spectra allows a confident assignment of the vibrational modes. Several spectral features in the INS spectra are unambiguously assigned and torsional potential barriers for the methyl groups are derived from experimental frequencies. The intramolecular nature of the potential energy barrier for methyl rotation about O-CH3 bonds compares with the one reported for torsion about saturated C-CH3 bonds. On the other hand, the intermolecular contribution to the potential energy barrier may represent 1/3 of the barrier height in these systems.

Biodegradability in aquatic system of thin materials based on chitosan, PBAT and HDPE polymers: Respirometric and physical-chemical analysis.

Biodegradation tests of chitosan (CH), polybutylene adipate terephthalate (PBAT) and high density polyethylene (HDPE) polymers were carried out using the standard OECD 301D guidelines. The results showed that the CH samples biodegraded faster than those of PBAT. Photographs registered exhibited the complete or partial disintegration of the samples, and a more opaque color was observed with the increase of biodegradation. FTIR analysis showed some changes in the intensity of the typical bands of the HDPE sample. The presence of P. nitroreducens bacteria was revealed on the PBAT sample surface by SEM studies. Additionally, a clear increase in elastic modulus (EM) and tensile strength (TS) values were observed in PBAT and HDPE samples on day 3, which decreased significantly at the end of the study. Furthermore, an increase in the crystallinity of the HDPE sample was observed on day 28.

Characterization of whey protein-based films incorporated with natamycin and nanoemulsion of α-tocopherol.

Food packaging materials are commonly derived from petroleum that increases global contamination; this raises the interest to evaluate raw material from renewable sources such as whey protein for the development of packaging materials, especially to produce active films. This research aimed to evaluate whey protein-based film properties when natamycin, nanoemulsioned α-tocopherol, or both were added. An oil-in-water (O/W) nanoemulsion of antioxidant (α-tocopherol) was prepared by microfluidization technique. Four films were prepared with different levels of natamycin and nanoemulsified α-tocopherol and were characterized in terms of physicochemical, mechanical, optical-properties, water vapor barrier, FTIR, microstructure, antioxidant and antimicrobial activity. The natamycin, nanoemulsified α-tocopherol, or both did not modify the moisture content of the films. Moreover lead to a significant reduction of tensile strength and elastic modulus, while presenting growth in the elongation at break. Film opacity, the total color difference, the UV-Vis light barrier, and the water vapor permeability values increased when compounds were incorporated into the film. The microstructure studies showed uniformly distributed porosity throughout the films. The addition of nanoemulsioned α-tocopherol into whey protein-based films provoked antioxidant activity and the addition of natamycin produced films with effectivity against C. albicans, P. chrysogenum, and S. cerevisiae, allowing develop a material appropriate for use as active food packaging.

Understanding the Structure and Dynamics of Nanocellulose-Based Composites with Neutral and ionic Poly(methacrylate) Derivatives using Inelastic Neutron Scattering and DFT Calculations.

Bacterial nanocellulose (BC)-based composites containing poly(2-hydroxyethyl methacrylate) (PHEMA), poly(methacroylcholine chloride) (PMACC) or poly(methacroylcholine hydroxide) (PMACH) were characterized by inelastic neutron scattering (INS) spectroscopy, combined with DFT (density functional theory) calculations of model systems. A reasonable match between calculated and experimental spectral lines and their intensities was used to support the vibrational assignment of the observed bands and to validate the possible structures. The differences between the spectra of the nanocomposites and the pure precursors indicate that interactions between the components are stronger for the ionic poly(methacrylate) derivatives than for the neutral counterpart. Displaced anions interact differently with cellulose chains, due to the different ability to compete with the O-H···O hydrogen bonds in cellulose. Hence, the INS is an adequate technique to delve deeper into the structure and dynamics of nanocellulose-based composites, confirming that they are true nanocomposite materials instead of simple mixtures of totally independent domains.

Disintegrability under composting conditions of films based on gelatin, chitosan and/or sodium caseinate containing boldo-of-Chile leafs extract.

Biodegradable films based on pure gelatin (GEL100), chitosan (CH100) and sodium caseinate (SCas100), and gelatin-chitosan (GEL50:CH50) and gelatin­sodium caseinate (GEL50:SCas50) blends, without or with boldo-of-Chile leafs extract (BoC) were studied. The solubility in water (%) of all the pure films was analyzed. Moreover, the disintegration process was evaluated throughout the mass loss (%), structural (FTIR) changes and visual analyses of films up to 5 days of composting conditions. The Boltzmann function allowed obtaining the half-maximal disintegration time (t50) of all the films. Only Scas100 films exhibited complete solubility in water, compared to the other films (P < 0.05). At day 1, SCas100 + B film exhibited total mass loss, meanwhile for the other film samples this parameter varied between 47.9 ± 3.0% (CH100 + B) and 6.8 ± 1.3% (GEL100 + B) (P < 0.05). FTIR analysis showed some changes in the intensity of the typical bands of the pure or blended films. Photographs registered exhibited the complete disintegration of all films into 5 days. Finally, Boltzmann equation displayed that pure SCas100 film disintegrated in the shortest time (0.500 days), and GEL50:CH50 blended film in the longest time (1.766 days). In conclusion, the results of this work show an appropriate and complete disintegration of all studied films in composting conditions.

What a difference a methyl group makes - probing choline-urea molecular interactions through urea structure modification.

There is a lack of fundamental knowledge on deep eutectic solvents, even for the most extensively studied mixtures, such as the mixture of cholinium chloride and urea, which prevents a judicious choice of components to prepare new solvents. The objective of this work is to study and understand the fundamental interactions between cholinium chloride and urea that lead to the experimentally observed melting temperature depression. To do so, the structure of urea was strategically and progressively modified, in order to block certain interaction centres, and the solid-liquid equilibrium data of each new binary system was experimentally measured. Using this approach, it was concluded that the most important interaction between cholinium chloride and urea occurs through hydrogen bonding between the chloride anion and the amine groups. Any blockage of these groups severely hampers the melting point depression effect. Raman spectroscopy and DFT calculations were utilized to study in more detail this hydrogen bonding and its nuances.

Understanding the vibrational spectra of crystalline isoniazid: Raman, IR and INS spectroscopy and solid-state DFT study.

This work presents a comprehensive spectroscopic analysis of crystalline isoniazid, one of the main drugs in tuberculosis chemotherapy, using a blend of spectroscopic and computational methods. Mid- and far-infrared, Raman, and inelastic neutron scattering spectroscopies, with contribution of isotopic substitution are combined with discrete and periodic DFT quantum chemical calculations. This combined approach successfully reproduces the whole spectral range, allowing a sound assignment of all the vibrational bands. Previous misassignments have been corrected and several spectral features of isoniazid crystal are reported for the first time. Virtues and limitations of the computational approach (periodic and discrete) are also discussed in light of the present state-of-the-art in the field.

Identification of microplastics using Raman spectroscopy: Latest developments and future prospects.

Widespread microplastic pollution is raising growing concerns as to its detrimental effects upon living organisms. A realistic risk assessment must stand on representative data on the abundance, size distribution and chemical composition of microplastics. Raman microscopy is an indispensable tool for the analysis of very small microplastics (<20 µm). Still, its use is far from widespread, in part due to drawbacks such as long measurement time and proneness to spectral distortion induced by fluorescence. This review discusses each drawback followed by a showcase of interesting and easily available solutions that contribute to faster and better identification of microplastics using Raman spectroscopy. Among discussed topics are: enhanced signal quality with better detectors and spectrum processing; automated particle selection for faster Raman mapping; comprehensive reference libraries for successful spectral matching. A last section introduces non-conventional Raman techniques (non-linear Raman, hyperspectral imaging, standoff Raman) which permit more advanced applications such as real-time Raman detection and imaging of microplastics.

RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway.

Removal of damaged mitochondria is orchestrated by a pathway involving the PINK1 kinase and the PARKIN ubiquitin ligase. Ubiquitin chains assembled by PARKIN on the mitochondrial outer membrane recruit autophagy cargo receptors in complexes with TBK1 protein kinase. While TBK1 is known to phosphorylate cargo receptors to promote ubiquitin binding, it is unknown whether TBK1 phosphorylates other proteins to promote mitophagy. Using global quantitative proteomics, we identified S72 in RAB7A, a RAB previously linked with mitophagy, as a dynamic target of TBK1 upon mitochondrial depolarization. TBK1 directly phosphorylates RAB7AS72, but not several other RABs known to be phosphorylated on the homologous residue by LRRK2, in vitro, and this modification requires PARKIN activity in vivo. Interaction proteomics using nonphosphorylatable and phosphomimetic RAB7A mutants revealed loss of association of RAB7AS72E with RAB GDP dissociation inhibitor and increased association with the DENN domain-containing heterodimer FLCN-FNIP1. FLCN-FNIP1 is recruited to damaged mitochondria, and this process is inhibited in cells expressing RAB7AS72A. Moreover, nonphosphorylatable RAB7A failed to support efficient mitophagy, as well as recruitment of ATG9A-positive vesicles to damaged mitochondria. These data reveal a novel function for TBK1 in mitophagy, which parallels that of LRRK2-mediated phosphorylation of the homologous site in distinct RABs to control membrane trafficking.

Conformational and vibrational reassessment of solid paracetamol.

This work provides an answer to the urge for a more detailed and accurate knowledge of the vibrational spectrum of the widely used analgesic/antipyretic drug commonly known as paracetamol. A comprehensive spectroscopic analysis - including infrared, Raman, and inelastic neutron scattering (INS) - is combined with a computational approach which takes account for the effects of intermolecular interactions in the solid state. This allows a full reassessment of the vibrational assignments for Paracetamol, thus preventing the propagation of incorrect data analysis and misassignments already found in the literature. In particular, the vibrational modes involving the hydrogen-bonded NH and OH groups are correctly reallocated to bands shifted by up to 300cm-1 relatively to previous assignments.

Characterization of a polyhydroxyalkanoate obtained from pineapple peel waste using Ralsthonia eutropha.

Agro-industrial waste can be the production source of biopolymers such as polyhydroxyalkanoates. The aim of this study was to produce and characterize Polyhydroxyalkanoates produced from pineapple peel waste fermentation processes. The methodology includes different pineapple peel waste fermentation conditions. The produced biopolymer was characterized using FTIR, GC-MS and NMR. The best fermentation condition for biopolymer production was obtained using pH 9, Carbon/Nitrogen 11, carbon/phosphorus 6 and fermentation time of 60h. FTIR analyzes showed PHB group characteristics, such as OH, CH and CO. In addition, GC-MS showed two monomers with 4 and 8 carbons, referred to PHB and PHBHV. H(1) NMR analysis showed 0.88-0.97 and 5.27ppm signals, corresponding to CH3 and CH, respectively. In conclusion, polyhydroxyalkanoate production from pineapple peels waste is an alternative for the treatment of waste generated in Colombia's fruit industry.

New In Vitro Studies on the Bioprofile of Genista tenera Antihyperglycemic Extract.

The inhibition of α-glucosidase and glucose-6-phosphatase, two enzymes involved in the carbohydrate metabolism, is an important target to control glycaemia on individuals with type 2 diabetes. In this work we report for the first time the inhibition of both enzymes by the antihyperglycemic n-butanol extract from Genista tenera (Fabaceae). This extract decreased α-glucosidase and glucose-6-phosphatase activities to 0.97 and 80.25 %, respectively, being more effective than acarbose, and phlorizin, the positive controls, which reduced enzymes activities only to 17.39 and 96.06 %. Once inflammation and oxidative stress are related to diabetic impairments, the anti-inflammatory activity of the extract was also evaluated, through its inhibitory activity over COX-1 enzyme (47.5 % inhibition). Moreover, after induction of oxidative stress by UV radiation, the viability of irradiated rat liver hepatoma cells exposed to the extract was significantly higher (67.82 %) than that promoted by ascorbic acid, the positive control (45.05 %). In addition, the stability of the extract under gastrointestinal conditions was evaluated by HPLC-DAD-ESI-MS/MS. Flavonoid diglycosides were identified as the main constituents of the extract, and no alterations in the chemical composition nor in the antioxidant activity were observed after in vitro digestion with artificial gastric and pancreatic juices.

1,3,5-Tris(bromomethyl)benzene.

The asymmetric unit of the title compound, C(9)H(9)Br(3), is composed of a single molecule. Two bromo substituents are located on one side of the plane of the aromatic ring and the third is on the opposite side, with the molecular unit exhibiting an approximate noncrystallographic C(s) point group. The crystal structure is rich in Br...Br, CH(2)···Br and CH···π weak intermolecular contacts which mediate the crystal packing of individual molecules. These interactions promote a red-shift of a handful of vibrational modes (associated with the pendant -CH(2)Br groups) compared with values from theoretical density functional theory (DFT) calculations.

Hydrogen-bond dynamics of C-H...O interactions: the chloroform...acetone case.

Spectroscopic evidence for C-H...O hydrogen bonding in chloroform...acetone [Cl(3)CH...O=C(CH(3))(2)] mixtures was obtained from vibrational inelastic neutron scattering (INS) spectra. Comparison between the INS spectra of pure samples and their binary mixtures reveals the presence of new bands at about 82, 130 and 170 cm(-1). Assignment of the 82 cm(-1) band to the nuO...H anti-translational mode is considered and discussed. In addition, the betaC-H mode of CHCl(3) at 1242 cm(-1) is split in the spectra of the mixtures, and the high-wavenumber component is assigned to the hydrogen-bonded complex. The plot of the integrated intensity of this component shows a maximum for x=0.5, in agreement with the 1:1 stoichiometry of the chloroformacetone complex, with a calculated complexation constant of 0.15 dm(3) mol(-1). Results also show that the complex behaves as an independent entity, that is, despite being weak, such interactions play a key role in supramolecular chemistry.

Potential of Amaranthus cruentus BRS Alegria in the production of flour, starch and protein concentrate: chemical, thermal and rheological characterization.

BACKGROUND: Amaranth is a little-known culture in Brazilian agriculture. Amaranthus cruentus BRS Alegria was the first cultivar recommended by Embrapa for the soil of the Brazilian scrubland. In order to evaluate the potential of this species in the production of flour, starch and protein concentrates, the latter products were obtained from A. cruentus BRS Alegria seeds, characterized and compared with the products obtained from the A. caudatus species cultivated in its soil of origin. RESULTS: The seeds of A. cruentus BRS Alegria furnished high-purity starch and flour with significant content of starch, proteins, and lipids. The starch and flour of this species presented higher gelatinization temperatures and formed stronger gels upon cooling compared with those obtained from the A. caudatus species. This is due to their greater amylose content and a difference in the composition of the more important fatty acids, such as stearic, oleic and linoleic acids, which indicates that they have greater heat stability. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and differential scanning calorimetry revealed the presence of albumins, globulins, glutelins and prolamins in the protein concentrate, which was obtained as a byproduct of starch production. CONCLUSION: Amaranthus cruentus BRS Alegria has potential application in the production of flour, starch and protein concentrates, with interesting characteristics for use as food ingredients.