The reactions of the molecular nitrogen doubly charged ion with neutral molecules of relevance to planetary ionospheres

Diatomic dications (e.g. C02+) have been known to exist for several decades and are believed to be important components of energised media. Molecular dications possess significant internal energy due to the Coulombic repulsion of their two positive charges, meaning that many possible reaction channels are available to dications in a collision with a neutral molecule. Modellers have recently predicted that N22+ is present in the ionosphere of Earth and Titan as well as the dications C>22+ and 02+ in the ionosphere of Earth and CC>22+ in the ionosphere of Mars. These recent predictions, of dications in planetary ionospheres, imply that dications, and processes involving dication-neutral collisions, may have more significance than previously thought in the upper atmospheres of planets. Therefore this thesis describes a study of the reactions between N2 dications and neutrals, potentially of relevance to the ionosphere of Earth and Titan. A position sensitive coincidence (PSCO) time-of flight (TOF) mass spectrometer is used to probe the reactivity, energetics and dynamics of the bimolecular reactions of N22 . Dication-neutrals reactions often result in a pair of singly charged ions. The PSCO experiment is used to collect these pairs of singly-charged ions in coincidence. From the position-sensitive data we extract the velocity vectors of the product ions, and if the reaction of interest involves the formation of a third, undetected, neutral species, its velocity can be determined via conservation of momentum. The electron transfer reactions between dications and neutrals have been well rationalized 2+ previously, so only the electron transfer reactions of N2 with Ne and NO are discussed in this thesis. This thesis concentrates on probing the less well rationalized, bond- forming reactions between dications and neutrals. The bond-forming reactions of N22+ with O2, CO2, H2O, C2H2, CH4, H2 and Ar have been investigated and discussed. Several new bond-forming reactions mechanisms are derived for example, the bond-forming reactions of N22+ with O2 proceed via a 'long' lived complex which dissociates via loss of a neutral and then charge separation, a mechanism which is also operating for one of the bond-forming reactions of N2 with CO2 and N2 with H2O. Additional bond-forming reactions are detected for N22+ with CO2 and H2O, which proceed via shorter lived collision complexes. The reactions of N22+ with C2H2, CH4, H2 and Ar all proceed via a variety of mechanisms involving short-lived collision complexes or H and electron stripping

Table1_Effects of dehydroabietic acid on nontarget lipidomics and proteomics of HepG2.XLSX

Objective: Studies of the effects of dehydroabietic acid on the multiomics of HepG2 hepatoma carcinoma cells are currently lacking. In this study, the molecular mechanism of the influence of dehydroabietic acid on HepG2 cells was disclosed by studying lipidomics and proteomics. Correlations among multiomics conjoint analysis results were verified.Methods: First, proteomics analysis of HepG2 cells was carried out using dehydroabietic acid. Differentially expressed proteins were screened and analyzed. Pathway enrichment analyses of differential proteins were compared, and the molecular mechanism was disclosed. Second, lipidomics analysis of HepG2 cells was conducted using dehydroabietic acid. The influence of dehydroabietic acid on HepG2 cells was determined on the lipid molecular level. Finally, a conjoint analysis of data related to differentially expressed proteins of ferroptosis and differentially changing lipid molecules was implemented.Results: A total of 260 upregulated and 961 downregulated proteins were screened in the proteomics analysis. The top five significantly enriched pathways included ferroptosis, oxidative phosphorylation, and protein processing in the endoplasmic reticulum. In the lipidomics analysis, 30 significantly differential metabolites with upregulated and downregulated expression were identified, and differentially expressed lipids were mainly related to the metabolism of glyceryl phosphatide. According to the comprehensive multiomics analysis results, real-time quantitative PCR and the enzyme-linked immunosorbent assay (ELISA), ACSL3 participated in cardiolipin metabolism.Conclusion: Dehydroabietic acid influences HepG2 cells through the above biological pathways.</p

Table4_Effects of dehydroabietic acid on nontarget lipidomics and proteomics of HepG2.XLSX

Objective: Studies of the effects of dehydroabietic acid on the multiomics of HepG2 hepatoma carcinoma cells are currently lacking. In this study, the molecular mechanism of the influence of dehydroabietic acid on HepG2 cells was disclosed by studying lipidomics and proteomics. Correlations among multiomics conjoint analysis results were verified.Methods: First, proteomics analysis of HepG2 cells was carried out using dehydroabietic acid. Differentially expressed proteins were screened and analyzed. Pathway enrichment analyses of differential proteins were compared, and the molecular mechanism was disclosed. Second, lipidomics analysis of HepG2 cells was conducted using dehydroabietic acid. The influence of dehydroabietic acid on HepG2 cells was determined on the lipid molecular level. Finally, a conjoint analysis of data related to differentially expressed proteins of ferroptosis and differentially changing lipid molecules was implemented.Results: A total of 260 upregulated and 961 downregulated proteins were screened in the proteomics analysis. The top five significantly enriched pathways included ferroptosis, oxidative phosphorylation, and protein processing in the endoplasmic reticulum. In the lipidomics analysis, 30 significantly differential metabolites with upregulated and downregulated expression were identified, and differentially expressed lipids were mainly related to the metabolism of glyceryl phosphatide. According to the comprehensive multiomics analysis results, real-time quantitative PCR and the enzyme-linked immunosorbent assay (ELISA), ACSL3 participated in cardiolipin metabolism.Conclusion: Dehydroabietic acid influences HepG2 cells through the above biological pathways.</p

Table2_Effects of dehydroabietic acid on nontarget lipidomics and proteomics of HepG2.XLSX

Objective: Studies of the effects of dehydroabietic acid on the multiomics of HepG2 hepatoma carcinoma cells are currently lacking. In this study, the molecular mechanism of the influence of dehydroabietic acid on HepG2 cells was disclosed by studying lipidomics and proteomics. Correlations among multiomics conjoint analysis results were verified.Methods: First, proteomics analysis of HepG2 cells was carried out using dehydroabietic acid. Differentially expressed proteins were screened and analyzed. Pathway enrichment analyses of differential proteins were compared, and the molecular mechanism was disclosed. Second, lipidomics analysis of HepG2 cells was conducted using dehydroabietic acid. The influence of dehydroabietic acid on HepG2 cells was determined on the lipid molecular level. Finally, a conjoint analysis of data related to differentially expressed proteins of ferroptosis and differentially changing lipid molecules was implemented.Results: A total of 260 upregulated and 961 downregulated proteins were screened in the proteomics analysis. The top five significantly enriched pathways included ferroptosis, oxidative phosphorylation, and protein processing in the endoplasmic reticulum. In the lipidomics analysis, 30 significantly differential metabolites with upregulated and downregulated expression were identified, and differentially expressed lipids were mainly related to the metabolism of glyceryl phosphatide. According to the comprehensive multiomics analysis results, real-time quantitative PCR and the enzyme-linked immunosorbent assay (ELISA), ACSL3 participated in cardiolipin metabolism.Conclusion: Dehydroabietic acid influences HepG2 cells through the above biological pathways.</p

Table3_Effects of dehydroabietic acid on nontarget lipidomics and proteomics of HepG2.XLSX

Objective: Studies of the effects of dehydroabietic acid on the multiomics of HepG2 hepatoma carcinoma cells are currently lacking. In this study, the molecular mechanism of the influence of dehydroabietic acid on HepG2 cells was disclosed by studying lipidomics and proteomics. Correlations among multiomics conjoint analysis results were verified.Methods: First, proteomics analysis of HepG2 cells was carried out using dehydroabietic acid. Differentially expressed proteins were screened and analyzed. Pathway enrichment analyses of differential proteins were compared, and the molecular mechanism was disclosed. Second, lipidomics analysis of HepG2 cells was conducted using dehydroabietic acid. The influence of dehydroabietic acid on HepG2 cells was determined on the lipid molecular level. Finally, a conjoint analysis of data related to differentially expressed proteins of ferroptosis and differentially changing lipid molecules was implemented.Results: A total of 260 upregulated and 961 downregulated proteins were screened in the proteomics analysis. The top five significantly enriched pathways included ferroptosis, oxidative phosphorylation, and protein processing in the endoplasmic reticulum. In the lipidomics analysis, 30 significantly differential metabolites with upregulated and downregulated expression were identified, and differentially expressed lipids were mainly related to the metabolism of glyceryl phosphatide. According to the comprehensive multiomics analysis results, real-time quantitative PCR and the enzyme-linked immunosorbent assay (ELISA), ACSL3 participated in cardiolipin metabolism.Conclusion: Dehydroabietic acid influences HepG2 cells through the above biological pathways.</p

Correlations and Predictions of p<i>K</i>_a Values of Fluorophenols and Bromophenols Using Hydrogen-Bonded Complexes with Ammonia

Density functional theory calculations have been preformed on a series of the hydrogen-bonded fluorophenol−ammonia and bromophenol−ammonia complexes. Intermolecular and intramolecular properties, particularly those related to hydrogen bonding, have been carefully analyzed. Several properties, such as the bond length and stretching frequency of the hydroxyl group, the hydrogen bond length and binding energy, are shown to be highly correlated with each other and are linearly correlated with known experimental pKa values of the halogenated phenols. The linear correlations have been used to predict the pKa values of all fluorophenols and bromophenols in the series. The predicted pKa values are shown to be consistent from different molecular properties and are in good agreement with available experimental values. This study suggests that calculated molecular properties of hydrogen-bonded complexes allow the effective and systematic prediction of pKa values for a large range of organic acids using the established linear correlations

Theoretical Study of Hydrogen-Bonded Complexes of Chlorophenols with Water or Ammonia: Correlations and Predictions of p<i>K</i>_a Values

A simple practical method for predicting the acidity constants (as pKa values) of chlorophenols is proposed based on density functional theory calculations of a series of hydrogen-bonded complexes of phenol and 19 different congeners of chlorophenol, with a single probe molecule, either water or ammonia. Relevant structural parameters and molecular properties of these complexes, primarily involving the acidic hydroxyl group, are examined and plotted against the known pKa values of 14 chlorophenols and phenol. Strong linear correlations are found for these compounds. Such correlations are used to determine the pKa values of five chlorophenols whose experimental acidities have large uncertainties. Similar predicted pKa values are obtained by using different structural parameters and molecular properties for the complexes with either probe molecule. The study may be extended to determine the acidity of other compounds with a single acidic functional group

Theoretical Study of Molecular Structures and Properties of the Complete Series of Chlorophenols

Density functional theory and ab initio molecular orbital calculations have been carried out to investigate the molecular structures and properties of all 19 chlorophenol congeners. The results have been delineanated systematically in terms of the position and the total number of chlorine substitutions. Intramolecular hydrogen bonding in ortho chlorophenols and the induction by the electron-withdrawing chlorine are identified as strongly affecting the stability, structure, and properties of these compounds. Ortho chlorophenols are found to be more stable than other isomers as a result of intramolecular hydrogen bonding. Correlations between the known acidities of chlorophenols and the molecular structures are presented. Ortho chlorophenols are more acidic than other isomers because of the large inductive effect of chlorine on the hydroxyl group in close proximity. For the same reason, the acidity of a chlorophenol increases with the number of chlorine substitutions. Major trends and variations in molecular structure and properties, including O−H and C−O bond lengths, O−H stretching and torsional frequencies, average C−C bond lengths, and C−Cl bond lengths, are discussed in light of the intramolecular hydrogen bonding and the induction of chlorine

Molecular Structures and Properties of the Complete Series of Bromophenols: Density Functional Theory Calculations

The complete series of 19 bromophenols have been studied by density functional theory (DFT) calculations at the B3LYP/6-311G++(d,p) level. The molecular structures and properties of bromophenols are strongly influenced by intramolecular hydrogen bonding of ortho-bromine, steric and inductive effects of substituted bromine, and other intramolecular electrostatic interactions. Systematic trends in several structural parameters and molecular properties of bromophenols have been found with the increasing number of bromine substitutions, including increase in O−H bond length, decrease in C−O bond length, red shift in O−H stretching frequency, and blue shift in O−H torsional frequency. Correlations among several key molecular parameters as well as those with available aqueous pKa values are examined. Comparisons with chlorophenols have indicated that the inductive effect of substituted bromine appears larger and bromophenols are slightly stronger acids than chlorophenols

Spatial Differences in an Integral Membrane Proteome Detected in Laser Capture Microdissected Samples

The combination of laser capture microdissection and mass spectrometry represents a powerful technology for studying spatially resolved proteomes. Moreover, the compositions of integral membrane proteomes have rarely been studied in a spatially resolved manner. In this study, ocular lens tissue was carefully dissected by laser capture microdissection and conditions for membrane protein enrichment, trypsin digestion, and mass spectrometry analysis were optimized. Proteomic analysis allowed the identification of 170 proteins, 136 of which were identified with more than one peptide match. Spatial differences in protein expression were observed between cortical and nuclear samples. In addition, the spatial distribution of post-translational modifications to lens membrane proteins, such as the lens major intrinsic protein AQP0, were investigated and regional differences were measured for AQP0 C-terminal phosphorylation and truncation