Energetic Characterization Research Articles

Carbamic acid and its dimer: A computational study.

A recent work by Marks et al. on the formation of carbamic acid in NH -CO interstellar ices pointed out its stability in the gas phase and the concomitant production of its dimer. Prompted by these results and the lack of information on these species, we have performed an accurate structural, energetic and spectroscopic investigation of carbamic acid and its dimer. For the former, the structural and spectroscopic characterization employed composite schemes based on coupled cluster (CC) calculations that account for the extrapolation to the complete basis set limit and core correlation effects. A first important outcome is the definitive confirmation of the nonplanarity of carbamic acid, then followed by an accurate estimate of its rotational and vibrational spectroscopy parameters. As far as the carbamic acid dimer is concerned, the investigation started from the identification of its most stable forms. For them, structure and vibrational properties have been evaluated using density functional theory, while a composite scheme rooted in CC theory has been employed for the energetic characterization. Our results allowed us to provide a better interpretation of the feature observed in the recent experiment mentioned above.

Physicochemical, steric, and energetic characterization of kaolinite based silicate nano-sheets as potential adsorbents for safranin basic dye: effect of exfoliation reagent and techniques.

Kaolinite was subjected to advanced exfoliation processes to form separated nano-silicate sheets (EXK) with enhanced physicochemical properties as adsorbents. This involved the incorporation of different exfoliating agents, urea (U/EXK), KNO3 (N/EXK), and CTAB (C/EXK), highlighting their impacts on their textural and surficial properties as adsorbents for safranin dye. The applied characterization techniques confirmed the higher exfoliating degree of C/EXK, followed by N/EXK and U/EXK. This appeared significantly in the determined surface area (55.7m2/g (C/EXK), 36.7m2/g (U/EXK), and 47.1m2/g (N/EXK)) and adsorption performances. The C/EXK structure displayed a better safranin uptake capacity (273.2mg/g) than N/EXK (231mg/g) and U/EXK (178.4mg/g). Beside the remarkable differences in textural properties, the advanced mathematical modeling and the corresponding steric and energetic parameters illustrate the mentioned uptake properties. The interface of C/EXK is highly saturated by active uptake sites (Nm = 158.8mg/g) as compared to N/EXK (109.3mg/g) and U/EXK (93.4mg/g), which is in agreement with the characterization findings and the expected higher exposure of siloxane groups. Each of these sites can be filled with four dye molecules using C/EXK and N/EXK, which implies the vertical orientation of these adsorbed ions and the effective operation of multi-molecular mechanisms. The energetic (ΔE < 40kJ/mol) and thermodynamic investigations indicate the spontaneous, physical, and exothermic uptake of safranin molecules by EXK particulates. These mechanisms might involve dipole bonding (2-29kJ/mol), electrostatic attraction (2-50kJ/mol), van der Waals forces (4-10kJ/mol), and hydrogen bonding (<30kJ/mol).

Advanced investigation of adsorption process of the five main responses of taste molecules onto the gerbil receptor sites (GCaMP3): Steric, molecular docking, and energy interpretations

In this research work, an adsorption phenomenon putatively in the process of taste at a molecular level for understanding the five principal tastes using experimental dose-gustatory responses on receptors sites of gerbil (GCaMP3). In order to perform theoretical interpretations of the experimental data of dose gustatory response curve were fitted with the single-layer physical model (PMM) for sucrose, cycloheximide, quinine and MSG. However, a two-layer with two-energies model for NaCl and citric acid. The modeling discussion indicated that all six molecules were linked with the gerbil receptor sites of tasting surface by a parallel and a no parallel orientations. In addition, the linking adsorption energies are ranged from 3.15 to 14.19 kJ/mol for all tasting molecules, which suggested that this process is performed by a reversible physical adsorption. These physico-chemical model parameters are utilized to determine the molar energy of adsorption for various taste-entities. By fitting the number of adsorbed molecules or molecular anchors per site, a stereographic and energetic characterization of interactions between six entities (sucrose, cycloheximide, MSG, citric acid, and NaCl) and the gerbil gustatory-receptor-sites is conducted. These distributions AED and PSD can be considered as a characterization of taste of not only not only not only of any gustatory entity but also a characterization of the gustatory receptor systems of the peripheric nerves. The docking computation between five gustatory molecules and the gerbil GCaMP3 cavity receptor sites is performed, showing a significant resemblance in the receptor-ligand detection process. Hence, the findings from docking confirm that the calculated binding affinities fell within the range of adsorption energies.

Energetic Azoxy‐Coupled Tetrazoles

ABSTRACTAzoxy coupling of 5‐amino‐1‐methyl‐tetrazole, 5‐amino‐2‐methyl‐tetrazole, and 5‐amino‐1‐methoxy‐tetrazole was performed by reacting each with various oxidants. These reactions revealed aqueous Oxone to be the most facile system for yielding the azoxy couple for the previously mentioned tetrazoles. Chemical and structural characterization of each novel azoxy‐coupled tetrazole was conducted with 1H NMR, 13C NMR, HRMS, and single‐crystal x‐ray diffraction. Energetic characterization was evaluated by analysis of each compounds' single crystal x‐ray diffraction density, impact sensitivity, friction sensitivity, and decomposition temperature. All compounds were found to be very sensitive to impact and friction stimuli.

Theoretical study of a putative adsorption mechanism of arginine and glutamate on goldfish 5.24 and zebrafish Z06: Statistical physics modeling, thermodynamic study, and docking simulation

An adsorption phenomenon putatively involved in the sense of smell of arginine and glutamate amino acids in the goldfish olfactory receptor 5.24 and the zebrafish olfactory receptor Z06 was applied in this study to deeply interpret and characterize the olfaction process at a molecular level. As a result, the experimental concentration-olfactory response curves were adjusted using the mono-layer model with one energy (MLM1E). On the one hand, the physicochemical parameters involved in the chosen model were utilized to microscopically investigate the four olfactory systems. Indeed, the two amino acids were adsorbed via a non-parallel configuration, and the process of adsorption was multi-molecular. The molar adsorption energies, which ranged from 22.09 to 35.97 kJ/mol, could be utilized to define the energetic interaction types between the investigated amino acids and the two tested fish olfactory receptors. The size and adsorption energy heterogeneity of 5.24 and Z06 binding pockets were measured by estimating the pocket site size distributions or PSDs (stereographic characterization) and the adsorption energy distributions or AEDs (energetic characterization). On the other hand, these physicochemical parameters could also be applied to macroscopically investigate the four olfactory systems. Hence, three thermodynamic functions including the adsorption entropy Sa, the internal energy Eint, and the Gibbs free energy G were computed in order to investigate the disorder, the exothermicity, and the spontaneity of the studied systems, respectively. The docking modeling analysis of arginine and glutamate amino acids with goldfish 5.24 and zebrafish Z06 revealed simulated binding energies that closely matched the average adsorption energies (peaks of AEDs). These affinities corresponded to the adsorption energy bands known as olfactory bands or spectrums of vibration modes.

Microscopic and macroscopic analysis of hexavalent chromium adsorption on polypyrrole-polyaniline@rice husk ash adsorbent using statistical physics modeling

This paper contributed with new findings to understand and characterize a heavy metal adsorption on a composite adsorbent. The synthesized polypyrrole–polyaniline@rice husk ash (PPY–PANI@RHA) was prepared and used as an adsorbent for the removal of hexavalent chromium Cr(VI). The adsorption isotherms of Cr(VI) ions on PPY–PANI@RHA were experimentally determined at pH 2, and at different adsorption temperatures (293, 303, and 313 K). Multi-layer model developed using statistical physics formalism was applied to theoretically analyze and characterize the different interactions and ion exchanges during the adsorption process for the elimination of this toxic metal from aqueous solutions, and to attribute new physicochemical interpretation of the process of adsorption. The physicochemical structures and properties of the synthesized PPY–PANI@RHA were characterized via Fourier transform infrared spectroscopy (FTIR). Fitting findings showed that the mechanism of adsorption of Cr(VI) on PPY–PANI@RHA was a multi-ionic mechanism, where one binding site may be occupied by one and two ions. It may also be noticed that the temperature augmentation generated the activation of more functional groups of the composite adsorbent, facilitating the interactions of metal ions with the binding sites and the access to smaller pore. The energetic characterization suggested that the mechanism of adsorption of the investigated systems was exothermic and Cr(VI) ions were physisorbed on PPY-PANI@RHA surface via electrostatic interaction, reduction of Cr(VI) to Cr(III), hydrogen bonding, and ion exchange. Overall, the utilization of the theory of statistical physics provided fruitful and profounder analysis of the adsorption mechanism. The estimation of the pore size distribution (PSD) of the polypyrrole-polyaniline@rice husk ash using the statistical physics approach was considered stereographic characterization of the adsorbent (here PPY–PANI@RHA was globally a meso-porous adsorbent). Lastly, the mechanism of Cr(VI) removal from wastewater using PPY-PANI@RHA as adsorbent was macroscopically investigated via the estimation of three thermodynamic functions.

Crystal structure and characterization of monascin from the extracts of Monascus purpureus-fermented rice.

We present a novel solid form of monascin, an azaphilonoid derivative extracted from Monascus purpureus-fermented rice. The crystal structure, C21H26O5, was characterized by single-crystal X-ray diffraction and belongs to the orthorhombic space group P212121. To gain insight into the electronic properties of the short contacts in the crystalline state of monascin, we utilized the Experimental Library of Multipolar Atom Model 2 (ELMAM2) database to transfer the electron density of monascin in its crystalline state. Hirshfeld surface analysis, fingerprint analysis, electronic properties and energetic characterization reveal that intermolecular C-H...O hydrogen bonds play a crucial role in the noncovalent bonding interactions by connecting molecules into two- and three-dimensional networks. The molecular electrostatic potential (MEP) map of the monascin molecule demonstrates that negatively charged regions located at four O atoms are favoured binding sites for more positively charged amino acid residues during molecular recognition. In addition, powder X-ray diffraction confirms that no transformation occurs during the crystallization of monascin.

Extracting binding energies and binding modes from biomolecular simulations of fragment binding to endothiapepsin.

Fragment-based drug discovery (FBDD) aims to discover a set of small binding fragments that may be subsequently linked together. Therefore, in-depth knowledge of the individual fragments' structural and energetic binding properties is essential. In addition to experimental techniques, the direct simulation of fragment binding by molecular dynamics (MD) simulations became popular to characterize fragment binding. However, former studies showed that long simulation times and high computational demands per fragment are needed, which limits applicability in FBDD. Here, we performed short, unbiased MD simulations of direct fragment binding to endothiapepsin, a well-characterized model system of pepsin-like aspartic proteases. To evaluate the strengths and limitations of short MD simulations for the structural and energetic characterization of fragment binding, we predicted the fragments' absolute free energies and binding poses based on the direct simulations of fragment binding and compared the predictions to experimental data. The predicted absolute free energies are in fair agreement with the experiment. Combining the MD data with binding mode predictions from molecular docking approaches helped to correctly identify the most promising fragments for further chemical optimization. Importantly, all computations and predictions were done within 5 days, suggesting that MD simulations may become a viable tool in FBDD projects.

Colored cotton crop wastes valorization through pyrolysis: a study of energetic characterization and analytical Py-GC/MS

The present work aimed to study different parts of colored cotton waste through energetic characterization and analytical flash pyrolysis. Stalks and bolls of BRS cotton cultivars from Sementes do Brasil (Green, Ruby, Topaz and Jade) were studied, using white cotton (BRS 286) as a comparison. The energetic potential of biomass was evaluated by bulk density, High Heating Value (HHV), proximate and ultimate analysis, compositional and thermogravimetric analysis (TGA). Pyrolysis was performed in a micro-pyrolyzer and the products were identified by gas chromatography and mass spectroscopy (Py-GC/MS). The results indicated a significant energetic potential, suggesting that can be used as an alternative energy source for thermochemical processes. The results of conventional pyrolysis indicated the presence of oxygenated compounds of different organic groups: aldehydes, ketones, phenols, furans and ethers, characteristic of the decomposition of lignocellulosic materials. Light organic acids in the C1-C4 range stood out the most, followed by phenols that appeared in a considerable proportion. Finally, it is concluded that the energy potential and pyrolysis products of the different parts (stalks and bolls) of colored cotton waste can be used to generate bioenergy and various chemical compounds of plant origin from green chemistry.

Molecular modelling of DNA cytosine methylation

Epigenetic modifications are significant processes controlling gene expression. Since their discovery by C. H. Waddington, several multisubject research proceeded and allowed investigation of how biochemical regulations can influence gene transcription. The main epigenetic modification is DNA methylation. This catalytic process of attaching methyl groups to nucleobases (mostly cytosine) is fundamental for the regulation of gene expression and chromatin accessibility. Methylated parts of the genome, which are mostly gene promoters and enhancers, are silenced due to specific biological mechanisms. Scientists postulate that aberrant DNA methylation and other epigenetic modifications can contribute to the development of diverse pathologies such as Alzheimer's disease, epilepsy, Schizophrenia, tumorigenesis, and atherosclerosis. Due to these discoveries, it is important to characterize in detail the mechanism of epigenetic modifications to develop new possible ways of treatment. In this work, we presented complex studies of DNA methylation mechanism including dynamic and energetic analysis of the reaction system. A cluster chemical approach was used to model the active site of enzyme catalyzing methylation - DNMT1 (DNA methyltransferase 1). The created model was subjected to quantum chemical calculations. Geometry optimization was performed with ADF software, providing an energetic characterization of the studied process. Dynamic properties of the enzyme model were described due to molecular dynamics (MD) procedures performed with CP2K software. MD calculations were focused on the observation and description of proton transfer between glutamate acid and cytosine, which is considered the main enzyme-substrate interaction leading to the creation of 5-methylcytosine 5mC (product of the studied reaction) and covalent bonding between enzymes cysteine and nucleobase. This research provides a comprehensive understanding of the DNA methylation mechanism and may contribute to the invention of new drugs and modern ways of treatment.

Synthesis and Energetic Characterization of Borane-Amines on High-Nitrogen Heterocycles.

Borane-amines have garnered attention over the last several decades in a variety of applications, ranging from hydrogen storage materials to hypergolic fuel systems. An investigation into the synthesis of borane-amines with high-nitrogen content heterocycles was undertaken in this work. Borane-amines were formed by the reaction of BH3·Me2S in tetrahydrofuran (THF) with the requisite nitrogen-containing heterocycle and isolated by placing the crude reaction mixture in hexanes to precipitate the product. X-ray crystallography, thermogravimetric analysis (TGA), high resolution mass spectroscopy (HRMS), 1H NMR, 13C NMR, and 11B NMR were utilized for product characterization, while impact and friction sensitivity testing were conducted to identify sensitivity in the synthesized compounds. Most isolated borane-amines, except one, were found to decompose in the atmosphere and were more sensitive to mechanical stimuli than their starting materials; however, all synthesized compounds were found to be hypergolic in the presence of white fuming nitric acid (WFNA).

Energetic and dynamic characterization of pollutant dispersion in varied building layouts through an augmented analysis procedure

This work presents a post-data analysis procedure, namely, proper orthogonal decomposition (POD)–dynamic mode decomposition (DMD)–discrete Fourier transform analysis, for evaluating the dominant features of the flow fields from both energetic and dynamic perspectives. The large-eddy simulation (LES) was first employed to reproduce the flow field surrounding three types of building layouts. Subsequently, both POD and DMD were conducted according to LES simulation results. The extracted modes were classified into three types based on the POD and DMD: Type-1 mode: energetically and dynamically significant mode, Type-2 mode: energetically significant and dynamically insignificant mode, and Type-3 mode: energetically insignificant and dynamically significant mode. The findings indicate that Type-1 mode governs the primary velocity field and the predominant vortex patterns observed at the rear of the building arrays, as the reduction of inter-building widths leads to a shorter flow separation region. Type-2 mode is characterized by the presence of small-scale vortices and the high turbulent kinetic energy region, which periodically triggers pollutant increase in the vicinity of structures. Type-3 mode demonstrates a minimal energetic influence on the flow field; nevertheless, it significantly contributes to the consistent build-up of pollutants within the far-wake region. The present study also investigates the predominant coherent structures of flow fields concerning various building layouts and highlights the influence of passage widths on the efficiency of pollutant removal. This comprehensive analysis enables a systematic exploration of flow patterns within various building layouts, offering potential solutions for pollutant dispersion challenges in metropolitan areas.

Unveiling structural and energetic characterization of the emissive RNA alphabet anchored in the methylthieno[3,4-d]pyrimidine heterocycle core.

This study presents a comprehensive theoretical exploration of the fluorescent non-natural emissive nucleobases- mthA, mthG, mthC, and mthU derived from the methylthieno[3,4-d]pyrimidine heterocycle. Our calculations, aligning with experimental findings, reveal that these non-natural bases exert minimal influence on the geometry of classical Watson-Crick base pairs within an RNA duplex, maintaining H-bonding akin to natural bases. In terms of energy, the impact of the modified bases, but for mthG, is also found to be little significant. We delved into an in-depth analysis of the photophysical properties of these non-natural bases. This investigation unveiled a correlation between their absorption/emission peaks and the substantial impact of the modification on the energy levels of the highest unoccupied molecular orbitals (HOMO) and the lowest unoccupied molecular orbital (LUMO). Notably, this alteration in energy levels resulted in a significant reduction of the HOMO-LUMO gap, from approximately 5.4-5.5 eV in the natural bases, to roughly 3.9-4.7 eV in the modified bases. This shift led to a consequential change in absorption and emission spectra towards longer wavelengths, elucidating their bathochromic shift.

Isomerism of : Accurate structural, energetic, and spectroscopic characterization.

A recent work [Ye et al. Mon. Not. R. Astron. Soc. 2023, 525, 1158] on the gas-phase formation of t-HC(O)SH, already detected in the interstellar medium, pointed out that the trans form of HC(S)OH is a potential candidate for astronomical observations. Prompted by these results, the family of isomers has been investigated from an energetic point of view using a double-hybrid density functional in combination with a partially augmented triple-zeta basis set. This preliminary study showed that the most stable species of the family are the cis and trans forms of HC(O)SH and HC(S)OH. For their structural and spectroscopic characterization, a composite scheme based on coupled cluster (CC) calculations that incorporates up to the quadruple excitations and accounts for the extrapolation to the complete basis set limit and core correlation effects has been employed. This approach opens to the prediction of rotational constants with an accuracy of 0.1%. A hybrid scheme, based on harmonic frequencies computed using the CC singles, doubles and a perturbative treatment of triples method (CCSD(T)) in conjunction with a quadruple-zeta basis set, allowed us to obtain fundamental vibrational frequencies with a mean absolute error of about 1%.

Spectroelectrochemical Characterization of Energetics in Type I vs Quasi-Type II Heterojunctions in CdSe@CdS Nanorod Films

Spectroelectrochemical Characterization of Energetics in Type I vs Quasi-Type II Heterojunctions in CdSe@CdS Nanorod Films

Membrane Tubulation with a Biomembrane Force Probe.

Tubulation is a common cellular process involving the formation of membrane tubes ranging from 50 nm to 1 µm in diameter. These tubes facilitate intercompartmental connections, material transport within cells and content exchange between cells. The high curvature of these tubes makes them specific targets for proteins that sense local geometry. In vitro, similar tubes have been created by pulling on the membranes of giant unilamellar vesicles. Optical tweezers and micromanipulation are typically used in these experiments, involving the manipulation of a GUV with a micropipette and a streptavidin-coated bead trapped in optical tweezers. The interaction forms streptavidin/biotin bonds, leading to tube formation. Here, we propose a cost-effective alternative using only micromanipulation techniques, replacing optical tweezers with a Biomembrane Force Probe (BFP). The BFP, employing a biotinylated erythrocyte as a nanospring, allows for the controlled measurement of forces ranging from 1 pN to 1 nN. The BFP has been widely used to study molecular interactions in cellular processes, extending beyond its original purpose. We outline the experimental setup, tube formation and characterization of tube dimensions and energetics, and discuss the advantages and limitations of this approach in studying membrane tubulation.

Quantitative investigations of Zebrafish olfactory receptor ORA1 responsiveness to three pheromones: Microscopic and macroscopic characterizations via an advanced statistical physics treatment

In this work, an adsorption phenomenon putatively involved in the olfactory sense of phenylacetic acid, 4-chlorophenylacetic acid, and 4-methoxyphenylacetic acid pheromones in the Zebrafish olfactory receptor ORA1 was a helpful mechanism in interpreting and characterizing the olfaction process at a molecular level. Hence, the experimental dose-olfactory response curves were fitted by applying the one-layer adsorption model with a single energy (1LM1E). On one hand, the different parameters introduced in the selected model were used to microscopically study the three olfactory systems. Indeed, the fitting results showed that phenylacetic acid displayed the greatest maximum olfactory response at saturation, due to the effect of functional groups at the R4 position. The three pheromones were docked via a non-parallel orientation and the adsorption process was a multi-molecular mechanism. The sizes of different binding pockets of ORA1 were determined through the estimation of the olfactory receptor site size distributions (stereographic characterization). The estimated adsorption energies, ranging from 17.340 to 21.332 kJ/mol, can be used to describe the energetic interactions between the studied pheromones and the Zebrafish ORA1 binding pockets. The spectrums of the adsorption energy distributions of phenylacetic acid, 4-chlorophenylacetic acid, and 4-methoxyphenylacetic acid, which were spread out from 10 to 32.5 kJ/mol, 5 to 30 kJ/mol, and 10 to 32.5 kJ/mol, respectively, was determined to estimate the corresponding olfactory bands (energetic characterization). On the other hand, three thermodynamic functions were estimated in order to macroscopically study the three olfactory systems.

Synthesis, Structure, and Energetic Characteristics of Perovskite Photocatalyst SrTiO3: an Experimental and DFT Study

SrTiO3-based photocatalysts have become widely used due to their excellent properties such as high thermal stability, photocorrosion resistance, and stable structure that can be modified by doping and making composites. In this work, SrTiO3 powder was prepared from Sr(NO3)2 and TiO2 precursors by a simple chemical precipitation method followed by calcination. It was determined that calcination at 900 °C followed by treatment in nitric acid solution produced cubic SrTiO3 particles without the presence of any impurities. In addition, structural, morphology, and energetic characterization using experimental and theoretical aspects are presented. Within the framework of density functional theory, the electronic properties of SrTiO3 have been investigated in the Quantum ESPRESSO software package using the PBE functional under the generalized gradient approximation (GGA). The band structure and density of states were obtained, and the width of the bandgap was determined.

Structural and energetic characterization of silica-alumina gels for adsorption processes

The surface chemistry of silica-alumina gels is largely determined by number and type of silanol groups present. However, until now the influence of different silanol groups on adsorption processes is largely unknown. The aim of this study is to develop a method for an energetic characterization of silica-alumina gels by combining data measured by nuclear magnetic resonance (NMR), thermogravimetric analysis (TGA) and adsorption calorimetry. The silica-alumina gels used for the studies are systematically modified by pretreating at temperatures between 200 °C and 1000 °C. To quantify number and distribution of silanol groups, complementary data from 29Si-NMR and 1H NMR and thermogravimetric measurements is combined. Adsorption measurements with the adsorptives cyclopentane (nonpolar) and pyrrolidine (polar molecule capable of hydrogen bonding) provide further information. Based on the adsorption isotherms and load-dependent heats of adsorption, it is shown that number and distribution of silanol groups have little effect on the adsorption of cyclopentane. In contrast, different energy levels are found for the heat of adsorption of pyrrolidine at ∼106 kJ mol−1, ∼95 kJ mol−1, ∼87 kJ mol−1, and ∼80 kJ mol−1 depending on pretreatment temperature. Based on the combination of all data, a model is proposed to assign the identified energy levels of adsorption to different silanol groups.

Modeling and assessing the potential of the Boqueirão channel for tidal exploration

Exploring the energy potential of the oceans is a promising alternative to produce clean energy with a reduced environmental impact. Brazil has a significant tidal potential, particularly in the coastal region of the north, which covers the states of Amapá, Pará and Maranhão. The Boqueirão Channel, located in São Marcos Bay in Maranhão, is recognized for its wide tidal variability and strong tidal currents, which shows it has a significant tidal potential. This article examines the energetic characterization of this estuary in terms of tidal currents. Based on measurements taken in situ using an Acoustic Doppler Current Profiler and a Conductivity, Temperature and Depth sensor, the area is modeled in Delft3D software, with velocity results adjusted and validated to allow accurate representation of tidal currents. The theoretical potential of an area of 1.5 km2, considering a hydrokinetic turbine with diffuser, was estimated at 85.75 GWh. The results obtained are compared with those in the literature. Taking into account the available area and the physical constraints of the channel, it is possible to estimate a Levelized Cost of Energy - LCOE of 0.185 $kWh−1 for the projected hydrokinetic farm.