Predicting the Decomposition Mechanism of the Serine α-Amino Acid in the Gas Phase and Condensed Media
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PROVIDER: S-EPMC10882666 | biostudies-literature | 2024 Feb
REPOSITORIES: biostudies-literature
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Project description:Chelation complexes of the histidine-containing tripeptides HisAlaAla, AlaHisAla, and AlaAlaHis with Ni(II) and Cu(II) having a -1 net charge are characterized in the gas phase by infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory calculations. We address the question of whether the gas-phase complexes carry over characteristics from the corresponding condensed-phase species. We focus particularly on three aspects of their structure: (i) square-planar chelation by the deprotonated amide nitrogens around the metal ion (low-spin for the Ni case), (ii) metal-ion coordination of the imidazole side chain nitrogen, and (iii) the exceptional preference for metal-ion chelation by peptides with His in the third position from the N-terminus, as in the amino terminal Cu and Ni (ATCUN) motif. We find that square-planar binding around the metal ion, involving bonds to both deprotonated backbone nitrogens, one of the carboxylate oxygens and the N-terminal nitrogen, is the dominant binding motif for all three isomers. In contrast to the condensed-phase behavior, the dominant mode of binding for all three isomers does not involve the imidazole side chain, which is instead placed outside the coordination zone. Only for the AlaAlaHis isomer, the imidazole-bound structure is also detected as a minority population, as identified from a distinctive short-wavelength IR absorption. The observation that this conformation exists only for AlaAlaHis correlates with condensed-phase behavior at neutral-to-basic pH, in the sense that the isomer with His in the third position is exceptionally disposed to metal ion chelation by four nitrogen atoms (4N) when compared with the other isomers. These results also emphasize the divergence between the conformational stabilities in the gas phase and in solution or crystalline environments: in the gas phase, direct metal binding of the imidazole is overall less favorable than the alternative of a remote imidazole that can act as an intramolecular H-bond donor enhancing the gas-phase stability.
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Project description:Organic hydroperoxides (ROOHs) play key roles in the atmosphere as a reactive intermediate species. Due to the low volatility and high hydrophilicity, ROOHs are expected to reside in atmospheric condensed phases such as aerosols, fogs, and cloud droplets. The decomposition mechanisms of ROOHs in the liquid phase are, however, still poorly understood. Here we report a temperature-dependent kinetics and theoretical calculation study of the aqueous-phase decompositions of C12 or C13 α-alkoxyalkyl-hydroperoxides (α-AHs) derived from ozonolysis of α-terpineol in the presence of 1-propanol, 2-propanol, and ethanol. We found that the temporal profiles of α-AH signals, detected as chloride-adducts by negative ion electrospray mass spectrometry, showed single-exponential decay, and the derived first-order rate coefficient k for α-AH decomposition increased as temperature increased, e.g., k(288 K) = (5.3 ± 0.2) × 10-4 s-1, k(298 K) = (1.2 ± 0.3) × 10-3 s-1, k(308 K) = (2.1 ± 1.4) × 10-3 s-1 for C13 α-AHs derived from the reaction of α-terpineol Criegee intermediates with 1-propanol in the solution at pH 4.5. Arrhenius plot analysis yielded an activation energy (E a) of 12.3 ± 0.6 kcal mol-1. E a of 18.7 ± 0.3 and 13.8 ± 0.9 kcal mol-1 were also obtained for the decomposition of α-AHs (at pH 4.5) derived from the reaction of α-terpineol Criegee intermediates with 2-propanol and with ethanol, respectively. Based on the theoretical kinetic and thermodynamic calculations, we propose that a proton-catalyzed mechanism plays a central role in the decomposition of these α-AHs in acidic aqueous organic media, while water molecules may also participate in the decomposition pathways and affect the kinetics. The decomposition of α-AHs could act as a source of H2O2 and multifunctionalized species in atmospheric condensed phases.
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Project description:We report on the characterization by mass spectrometry (MS) of a rapid, reagentless and site-specific cleavage at the N-terminus of the amino acid cysteine (C) in peptides and proteins induced by the thermal decomposition at 220-250 °C for 10 s in solid samples. This thermally induced cleavage at C occurs under the same conditions and simultaneously to our previously reported thermally induced site-specific cleavage at the C-terminus of aspartic acid (D) (Zhang, S.; Basile, F. J. Proteome Res. 2007, 6, (5), 1700-1704). The C cleavage proceeds through cleavage of the nitrogen and α-carbon bond (N-terminus) of cysteine and produces modifications at the cleavage site with an amidation (-1 Da) of the N-terminal thermal decomposition product and a -32 Da mass change of the C-terminal thermal decomposition product, the latter yielding either an alanine or β-alanine residue at the N-terminus site. These modifications were confirmed by off-line thermal decomposition electrospray ionization (ESI)-MS, tandem MS (MS/MS) analyses and accurate mass measurements of standard peptides. Molecular oxygen was found to be required for the thermal decomposition and cleavage at C as it induced an initial cysteine thiol side chain oxidation to sulfinic acid. Similar to the thermally induced D cleavage, missed cleavages at C were also observed. The combined thermally induced digestion process at D and C, termed thermal decomposition/digestion (TDD), was observed on several model proteins tested under ambient conditions and the site-specificity of the method confirmed by MS/MS.
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Project description:This study aimed to prepare titania (TiO₂) nanotube (TNT) arrays grown on un-activated carbon fibers (UCFs), with the application of different TiO₂ loadings based on the coating-hydrothermal process, and to evaluate their photocatalytic activity for the degradation of sub-ppm levels of aromatic pollutants (benzene, toluene, ethyl benzene, and o-xylene (BTEX)) using a plug-flow photocatalytic reactor. The characteristics of the prepared photocatalysts were determined by scanning electron microscopy (SEM), energy-dispersive X-ray (EDX), transmission electron microscopy (TEM), UV-visible absorption spectroscopy (UV-Vis) and X-ray diffraction (XRD) analyses. Spectral analysis showed that the prepared photocatalysts were closely associated with the characteristics of one-dimensional nanostructured TiO₂ nanotubes for TNTUCFs and spherical shapes for TiO₂-coated UCF (TUCF). The photocatalytic activities of BTEX obtained from TNTUCFs were higher than those obtained from a reference photocatalyst, TUCF). Specifically, the average degradation efficiencies of BTEX observed for TNTUCF-10 were 81%, 97%, 99%, and 99%, respectively, while those observed for TUCF were 14%, 42%, 52%, and 79%, respectively. Moreover, the photocatalytic activities obtained for TNTUCFs suggested that the degradation efficiencies of BTEX varied with changes in TiO₂ loadings, allowing for the optimization of TiO₂ loading. Another important finding was that input concentrations and air flow rates could be important parameters for the treatment of BTEX, which should be considered for the optimization of TNTUCFs application. Taken together, TNTUCFs can be applied to effectively degrade sub-ppm levels of gas-phase aromatic pollutants through the optimization of operational conditions.
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Project description:The gas phase pyrolysis of trichlorfon was investigated by the on-line gas chromatography - mass spectrometry (GC-MS) pyrolysis and theoretical calculations. Two reaction channels were proposed in the pyrolytic reaction, by analyzing the detected pyrolytic products in the total ion chromatography, including 2,2,2-trichloroacetaldehyde, dimethyl phosphite, and dichlorvos. Theoretical calculations showed that there is an intramolecular hydrogen bond between the hydroxyl group and the phosphate O atom in trichlorfon, through which the hydroxyl H atom can be easily transferred to phosphate O atom to trigger two pyrolytic channels. In path-a, migration of H atom results in direct decomposition of trichlorfon to give 2,2,2-trichloroacetaldehyde and dimethyl phosphite in one step. In path-b, migration of H atom in trichlorfon is combined with formation of the O-P bond to give an intermediate, followed by HCl elimination to afford dichlorvos. Path-a is kinetically more favorable than path-b, which is consistent with the GC-MS results.
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Project description:Electrolysis is a potential candidate for a quick method of wastewater cleansing. However, it is necessary to know what compounds might be formed from bioorganic matter. We want to know if there are toxic intermediates and if it is possible to influence the product formation by the variation in initial conditions. In the present study, we use Car-Parrinello molecular dynamics to simulate the fastest reaction steps under such circumstances. We investigate the behavior of amino acids and peptides under anodic conditions. Such highly reactive situations lead to chemical reactions within picoseconds, and we can model the reaction mechanisms in full detail. The role of the electric current is to discharge charged species and, hence, to produce radicals from ions. This leads to ultra-fast radical reactions in a bulk environment, which can also be seen as redox reactions as the oxidation states change. In the case of amino acids, the educts can be zwitterionic, so we also observe complex acid-base chemistry. Hence, we obtain the full spectrum of condensed-phase chemistry.
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Project description:Quantum mechanical tunnelling describes transmission of matter waves through a barrier with height larger than the energy of the wave1. Tunnelling becomes important when the de Broglie wavelength of the particle exceeds the barrier thickness; because wavelength increases with decreasing mass, lighter particles tunnel more efficiently than heavier ones. However, there exist examples in condensed-phase chemistry where increasing mass leads to increased tunnelling rates2. In contrast to the textbook approach, which considers transitions between continuum states, condensed-phase reactions involve transitions between bound states of reactants and products. Here this conceptual distinction is highlighted by experimental measurements of isotopologue-specific tunnelling rates for CO rotational isomerization at an NaCl surface3,4, showing nonmonotonic mass dependence. A quantum rate theory of isomerization is developed wherein transitions between sub-barrier reactant and product states occur through interaction with the environment. Tunnelling is fastest for specific pairs of states (gateways), the quantum mechanical details of which lead to enhanced cross-barrier coupling; the energies of these gateways arise nonsystematically, giving an erratic mass dependence. Gateways also accelerate ground-state isomerization, acting as leaky holes through the reaction barrier. This simple model provides a way to account for tunnelling in condensed-phase chemistry, and indicates that heavy-atom tunnelling may be more important than typically assumed.
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