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Master Equation Studies of the Unimolecular Decay of Thermalized Methacrolein Oxide: The Impact of Atmospheric Conditions.

ABSTRACT: Master equation simulations of the unimolecular reaction dynamics of the Criegee intermediate methacrolein oxide (MACR oxide) have been performed under a variety of temperature and pressure conditions. These simulations provide insight into how the unimolecular kinetics vary across temperatures spanning the range 288-320 K. This work has incorporated a new potential energy surface and includes the anti-to-syn and cis-to-trans conformational dynamics of MACR oxide, as well as the unimolecular reactions to form dioxirane and dioxole species. The competition between the unimolecular reactivity of MACR oxide and previously documented bimolecular reactivity of MACR oxide with water vapor is explored, focusing on how this competition is affected by changes in atmospheric conditions. The impact on the role of MACR oxide as an atmospheric oxidant of SO₂ is noted.

SUBMITTER: Lee HK

PROVIDER: S-EPMC10226126 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

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Master Equation Studies of the Unimolecular Decay of Thermalized Methacrolein Oxide: The Impact of Atmospheric Conditions.

Lee Hyun Kyung HK Chantanapongvanij Pitchaya P Schmidt Rory R RR Stephenson Thomas A TA

The journal of physical chemistry. A 20230510 20

Master equation simulations of the unimolecular reaction dynamics of the Criegee intermediate methacrolein oxide (MACR oxide) have been performed under a variety of temperature and pressure conditions. These simulations provide insight into how the unimolecular kinetics vary across temperatures spanning the range 288-320 K. This work has incorporated a new potential energy surface and includes the anti-to-syn and cis-to-trans conformational dynamics of MACR oxide, as well as the unimolecular rea ...[more]

PMID: 37163697

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Project description:BackgroundThe concentration gradient of Bicoid protein which determines the developmental pathways in early Drosophila embryo is the best characterized morphogen gradient at the molecular level. Because different developmental fates can be elicited by different concentrations of Bicoid, it is important to probe the limits of this specification by analyzing intrinsic fluctuations of the Bicoid gradient arising from small molecular number. Stochastic simulations can be applied to further the understanding of the dynamics of Bicoid morphogen gradient formation at the molecular number level, and determine the source of the nucleus-to-nucleus expression variation (noise) observed in the Bicoid gradient.ResultsWe compared quantitative observations of Bicoid levels in immunostained Drosophila embryos with a spatially extended Master Equation model which represents diffusion, decay, and anterior synthesis. We show that the intrinsic noise of an autonomous reaction-diffusion gradient is Poisson distributed. We demonstrate how experimental noise can be identified in the logarithm domain from single embryo analysis, and then separated from intrinsic noise in the normalized variance domain of an ensemble statistical analysis. We show how measurement sensitivity affects our observations, and how small amounts of rescaling noise can perturb the noise strength (Fano factor) observed. We demonstrate that the biological noise level in data can serve as a physical constraint for restricting the model's parameter space, and for predicting the Bicoid molecular number and variation range. An estimate based on a low variance ensemble of embryos suggests that the steady-state Bicoid molecular number in a nucleus should be larger than 300 in the middle of the embryo, and hence the gradient should extend to the posterior end of the embryo, beyond the previously assumed background limit. We exhibit the predicted molecular number gradient together with measurement effects, and make a comparison between conditions of higher and lower variance respectively.ConclusionQuantitative comparison of Master Equation simulations with immunostained data enabled us to determine narrow ranges for key biophysical parameters, which for this system can be independently validated. Intrinsic noise is clearly detectable as well, although the staining process introduces certain limits in resolution.

Dataset Information

Master Equation Studies of the Unimolecular Decay of Thermalized Methacrolein Oxide: The Impact of Atmospheric Conditions.

Publications

Master Equation Studies of the Unimolecular Decay of Thermalized Methacrolein Oxide: The Impact of Atmospheric Conditions.

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