Gas-Phase Anionic σ-Adduct (Trans)formations in Heteroaromatic Systems.
Ontology highlight
ABSTRACT:
SUBMITTER: Zimnicka M
PROVIDER: S-EPMC4475249 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Electrochemical systems suffer from poor management of evolving gas bubbles. Improved understanding of bubbles behavior helps to reduce overpotential, save energy and enhance the mass transfer during chemical reactions. This work investigates and reviews the gas bubbles hydrodynamics, behavior, and management in electrochemical cells. Although the rate of bubble growth over the electrode surface is well understood, there is no reliable prediction of bubbles break-off diameter from the electrode surface because of the complexity of bubbles motion near the electrode surface. Particle Image Velocimetry (PIV) and Laser Doppler Anemometry (LDA) are the most common experimental techniques to measure bubble dynamics. Although the PIV is faster than LDA, both techniques are considered expensive and time-consuming. This encourages adapting Computational Fluid Dynamics (CFD) methods as an alternative to study bubbles behavior. However, further development of CFD methods is required to include coalescence and break-up of bubbles for better understanding and accuracy. The disadvantages of CFD methods can be overcome by using hybrid methods. The behavior of bubbles in electrochemical systems is still a complex challenging topic which requires a better understanding of the gas bubbles hydrodynamics and their interactions with the electrode surface and bulk liquid, as well as between the bubbles itself.
| S-EPMC5935447 | biostudies-literature
Project description:Ion mobility-mass spectrometry (IM-MS) is often employed to look at the secondary, tertiary, and quaternary structures of naked peptides and proteins in the gas-phase. Recently, it has offered a unique glimpse into proline-containing peptides and their cis/trans Xxx-Pro isomers. An experimental "signature" has been identified wherein a proline-containing peptide has its Pro residues substituted with another amino acid and the presence or absence of conformations in the IM-MS spectra is observed. Despite the high probability that one could attribute these conformations to cis/trans isomers, it is also possible that cis/trans isomers are not the cause of the additional conformations in proline-containing peptides. However, the experimental evidence of such a system has not been demonstrated or reported. Herein, we present the IM-MS analysis of Neuropeptide Y's wild-type (WT) signal sequence and Leu7Pro (L7P) mutant. Although comparison of arrival times and collision cross-sections of [M + 4H](4+) ions yields the cis/trans "signature", molecular dynamics indicates that a cis-Pro7 is not very stable and that trans-Pro7 conformations of the same cross-section arise with equal frequency. We believe that this work further underscores the importance of theoretical calculations in IM-MS structural assignments.
| S-EPMC4972606 | biostudies-literature
Project description:Stacking interactions have been evaluated, employing computational methods, in dimers formed by analogous aliphatic and aromatic species of increasing size. Changes in stability as the systems become larger are mostly controlled by the balance of increasing repulsion and dispersion contributions, while electrostatics plays a secondary but relevant role. The interaction energy increases as the size of the system grows, but it does much faster in π-π dimers than in σ-π complexes and more remarkably than in σ-σ dimers. The main factor behind the larger stability of aromatic dimers compared to complexes containing aliphatic molecules is related to changes in the properties of the aromatic systems due to electron delocalization leading to larger dispersion contributions. Besides, an extra stabilization in π-π complexes is due to the softening of the repulsive wall in aromatic species that allows the molecules to come closer.
| S-EPMC6645327 | biostudies-literature
Project description:MGAS315 is a wild type strain. RNA isolated in exponential phase and stationary phase were compared Keywords: Growth phase comparison
2007-06-28 | GSE5179 | GEO
Project description:A complex fracture network is generally generated during the hydraulic fracturing treatment in shale gas reservoirs. Numerous efforts have been made to model the flow behavior of such fracture networks. However, it is still challenging to predict the impacts of various gas transport mechanisms on well performance with arbitrary fracture geometry in a computationally efficient manner. We develop a robust and comprehensive model for real gas transport in shales with complex non-planar fracture network. Contributions of gas transport mechanisms and fracture complexity to well productivity and rate transient behavior are systematically analyzed. The major findings are: simple planar fracture can overestimate gas production than non-planar fracture due to less fracture interference. A "hump" that occurs in the transition period and formation linear flow with a slope less than 1/2 can infer the appearance of natural fractures. The sharpness of the "hump" can indicate the complexity and irregularity of the fracture networks. Gas flow mechanisms can extend the transition flow period. The gas desorption could make the "hump" more profound. The Knudsen diffusion and slippage effect play a dominant role in the later production time. Maximizing the fracture complexity through generating large connected networks is an effective way to increase shale gas production.
| S-EPMC5098178 | biostudies-literature
Project description:Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. Here, we generated the first manually curated genome-scale metabolic reconstruction for three Methanothermobacter spp.. We investigated differences in growth performance and gas consumption/production of three wild-type strains and one genetically engineered strain in two independent quadruplicate chemostat bioreactor experiments: 1) with molecular hydrogen and carbon dioxide; and 2) with sodium formate. In the first experiment, we found the highest methane production rate for Methanothermobacter thermautotrophicus ΔH, while Methanothermobacter marburgensis Marburg reached the highest biomass growth rate. We collected statistically reliable transcriptomics and proteomics data sets from these steady-state bioreactors, which we integrated within our genome-scale metabolic models. The implementation of an pan-model that contains combined reactions from all three microbes allowed us to perform an interspecies comparison of the complete omics data set. While the observed differences in the growth behavior cannot be fully explained, the comparison enabled us to identify crucial differences in growth-related pathways, such as formate anabolism. In the second experiment, we found stable growth with a M. thermautotrophicus ΔH plasmid-carrying strain on formate with similar performance parameters compared to wild-type Methanothermobacter thermautotrophicus Z-245. The results of the two studies demonstrate the advantages of an integrative approach using fermentation and omics data with genome-scale modeling for the investigation of lesser studied metabolisms, and the biotechnological potential of Methanothermobacter spp. as production platform hosts.
2022-12-31 | GSE218145 | GEO
Project description:Organic acids play a key role in central metabolic functions of organisms, are crucial for understanding regulatory processes and are ubiquitous inside the cell. Therefore, quantification of these compounds provides a valuable approach for studying dynamics of metabolic processes, in particular when the organism faces changing environmental conditions. However, the extraction and analysis of organic acids can be challenging and validated methods available in this field are limited. In this study, we developed a method for the extraction and quantification of organic acids from microbial samples based on solid-phase extraction on a strong anionic exchange cartridge and gas chromatographic-mass spectrometric analysis. Full method validation was conducted to determine quality parameters of the new method. Recoveries for 12 of the 15 aromatic and aliphatic acids were between 100 and 111% and detection limits between 3 and 272 ng/mL. The ranges for the regression coefficients and process standard deviations for these compound classes were 0.9874-0.9994 and 0.04-0.69 μg/mL, respectively. Limitations were encountered when targeting aliphatic acids with hydroxy, oxo or enol ester functions. Finally, we demonstrated the applicability of the method on cell extracts of the bacterium Escherichia coli and the dinoflagellate Prorocentrum minimum. Graphical abstract.
| S-EPMC7533261 | biostudies-literature
Project description:Three-coordinate Ph BOX Me2 ZnR (Ph BOX Me2 =phenyl-(4,4-dimethyl-oxazolinato; R=Me: 2 a, Et: 2 b) catalyzes the dehydrocoupling of primary or secondary silanes and alcohols to give silyl ethers and hydrogen, with high turnover numbers (TON; up to 107 ) under solvent-free conditions. Primary and secondary silanes react with small, medium, and large alcohols to give various degrees of substitution, from mono- to tri-alkoxylation, whereas tri-substituted silanes do not react with MeOH under these conditions. The effect of coordinative unsaturation on the behavior of the Zn catalyst is revealed through a dramatic variation of both rate law and experimental rate constants, which depend on the concentrations of both the alcohol and hydrosilane reactants. That is, the catalyst adapts its mechanism to access the most facile and efficient conversion. In particular, either alcohol or hydrosilane binds to the open coordination site on the Ph BOX Me2 ZnOR catalyst to form a Ph BOX Me2 ZnOR(HOR) complex under one set of conditions or an unprecedented σ-adduct Ph BOX Me2 ZnOR(H-SiR'3 ) under other conditions. Saturation kinetics provide evidence for the latter species, in support of the hypothesis that σ-bond metathesis reactions involving four-centered electrocyclic 2σ-2σ transition states are preceded by σ-adducts.
| S-EPMC8362191 | biostudies-literature
Project description:Septic systems are potentially a significant source of greenhouse gases (GHGs). The present study investigated GHGs from the blackwater septic systems that are widely used especially in low- and middle-income countries. Ten blackwater septic tanks in Hanoi, Vietnam, were investigated using the floating chamber method. The average methane and carbon dioxide emission rates measured at the first compartment (65% of total capacity) of the septic tanks were 11.92 and 20.24 g/cap/day, respectively, whereas nitrous oxide emission was negligible. Methane emission rate was significantly correlated with septage oxidation-reduction potential (ORP) (R = -0.67, p = 0.034), chemical oxygen demand mass (R = 0.78, p = 0.007), and biochemical oxygen demand mass (R = 0.78, p = 0.008), whereas it was not significantly correlated with water temperature (R = 0.26, p = 0.47) and dissolved oxygen (R = -0.59, p = 0.075) within the limited range: 30.6-31.7 °C and 0.03-0.34 mg-O2/L. The methane emission rates from septic tanks accumulating septage for >5 years were significantly higher than those at 0-5 years (p = 0.016). These results suggest that lower ORP and higher biodegradable carbon mass, in association with longer septage storage periods are key conditions for methane emissions. To the best of our knowledge, this is the first study to characterize GHG emissions from septic systems.
| S-EPMC7818654 | biostudies-literature
Project description:Theoretical determinations of absorption cross sections (σ) in the gas phase and molar extinction coefficients (ε) in condensed phases (water solution, interfaces or surfaces, protein or nucleic acids embeddings, etc.) are of interest when rates of photochemical processes, J = ∫ ϕ(λ) σ(λ) I(λ) dλ, are needed, where ϕ(λ) and I(λ) are the quantum yield of the process and the irradiance of the light source, respectively, as functions of the wavelength λ. Efficient computational strategies based on single-reference quantum-chemistry methods have been developed enabling determinations of line shapes or, in some cases, achieving rovibrational resolution. Developments are however lacking for strongly correlated problems, with many excited states, high-order excitations, and/or near degeneracies between states of the same and different spin multiplicities. In this work, we define and compare the performance of distinct computational strategies using multiconfigurational quantum chemistry, nuclear sampling of the chromophore (by means of molecular dynamics, ab initio molecular dynamics, or Wigner sampling), and conformational and statistical sampling of the environment (by means of molecular dynamics). A new mathematical approach revisiting previous absolute orientation algorithms is also developed to improve alignments of geometries. These approaches are benchmarked through the nπ* band of acrolein not only in the gas phase and water solution but also in a gas-phase/water interface, a common situation for instance in atmospheric chemistry. Subsequently, the best strategy is used to compute the absorption band for the adduct formed upon addition of an OH radical to the C6 position of uracil and compared with the available experimental data. Overall, quantum Wigner sampling of the chromophore with molecular dynamics sampling of the environment with CASPT2 electronic-structure determinations arise as a powerful methodology to predict meaningful σ(λ) and ε(λ) band line shapes with accurate absolute intensities.
| S-EPMC8444339 | biostudies-literature