Modified Rate Law for Bimolecular Reactions: Applicable to Surface as well as Non-surface Reactions

The rate equations in kinematics are expressed through basic laws under surface reaction as well as non-surface reaction. Rate law is center theme of non-surface reaction whereas Langmuir adsorption isotherms are basis of surface reaction rate expressions. A modified rate equation for bimolecular reaction is presented which considers both catalyst surface affairs as well as fraction of successful collision of different reactant for cracking and forming bonds. The modified rate law for bimolecular reaction for surface as well as non-surface reaction is stated as “Rate of a reaction is directly proportional to concentration as well as catalyst surface affair of each reactant” as r = k ΩA[A] ΩB[B] where catalyst surface affair of ith species is defined as Ωi = Ki/(1+Ki[i] + Kj[j] + …). Here, Ki is the equilibrium constant of “i” species for adsorption-desorption processes over catalyst. i, j,… indicates the different adsorbed chemical species at uniform catalyst sites and the same [i], [j], … indicates the concentration of different adsorbed chemical species at uniform catalyst sites.

Fast and automated identification of reactions with low barriers using meta-MD simulations

We test our meta-molecular dynamics (MD) based approach for finding low-barrier (<30 kcal/mol) reactions (SciPost Chem. 2021, 1, 003) on uni- and bimolecular reactions extracted from the barrier dataset developed by Grambow et al. (Scientific Data 2020, 7, 137). For unimolecular reactions the meta-MD simulations identify 25 of the 26 products found by Grambow et al., while the subsequent semiempirical screening eliminates an additional four reactions due to at an overestimation of the reaction energies or estimated barrier heights relative to DFT. In addition, our approach identifies an additional 36 reactions not found by Grambow et al., 10 of which are <30 kcal/mol. For bimolecular reactions the meta-MD simulations identify 19 of the 20 reactions found by Grambow et al., while the subsequent semiempirical screening eliminates an additional reaction. In addition, we find 34 new low-barrier reactions. For bimolecular reactions we found that it is necessary to ”encourage” the reactants to go to previously undiscovered products, by including products found by other MD simulations when computing the biasing potential as well as decreasing the size of the molecular cavity in which the MD occurs, until a reaction is observed. We also show that our methodology can find the correct products for two reactions that are more representative of those encountered in synthetic organic chemistry. The meta-MD hyperparameters used in this study thus appears to be generally applicable to finding low-barrier reactions.

Technical note: Entrainment-limited kinetics of bimolecular reactions in clouds

The method of entrainment-limited kinetics enables atmospheric chemistry models that do not resolve clouds to simulate heterogeneous (surface and multiphase) cloud chemistry more accurately and efficiently than previous numerical methods. The method, which was previously described for reactions with first-order kinetics in clouds, incorporates cloud entrainment into the kinetic rate coefficient. This technical note shows how bimolecular reactions with second-order kinetics in clouds can also be treated with entrainment-limited kinetics, enabling efficient simulations of a wider range of cloud chemistry reactions. Accuracy is demonstrated using oxidation of SO2 to S(VI) – a key step in formation of acid rain – as an example. Over a large range of reaction rates, cloud fractions, and initial reactant concentrations, the numerical errors in the entrainment-limited bimolecular reaction rates are typically << 1 % and always < 4 %, which is far smaller than the errors found in several commonly used methods of simulating cloud chemistry with fractional cloud cover.

Roles of bicarbonate ion in the deterministic Z-scheme and the stochastic murburn model for the light reaction of oxygenic photosynthesis

Bicarbonate ion has been proposed as a potential source for electrons/O-atom in the light reaction of oxygenic photosynthesis, both in the pre-Zscheme era and in recent times. In the light of murburn concept being mooted as a viable explanation for photophosphorylation, we present substantial theoretical analysis which supports the proposal that: (i) Bicarbonate ion can serve as a viable source of electrons to electron-discharged photosystems or other positively-charged intermediates (formed after photo-activation) in thylakoids. This is because electron abstraction from bicarbonate anion [(a). HCO3- → CO2 + *OH + e-; ° ≈ 491 kJ/mol] is more viable with respect to the classical alternative/available option like the neutral water molecule [(b). H2O → H+ + *OH + e-; ° ≈ 527 kJ/mol]. (ii) The hydroxyl radical directly produced in reaction (a) in conjunction with other diffusible reactive oxygen species (DROS) sponsor murburn phosphorylation cycles and/or dismutations/cross-reactions. Spontaneous involvement/formation of molecular oxygen in several such discretized bimolecular reactions is also a kinetically viable process. Therefore, the incorporation of an O-atom from bicarbonate into the oxygen gas evolved in the light reaction is a tenable outcome of the stochastic/statistical murburn model. We provide the pertinent equations and abrogate the bioenergetic calculations.

Oxidation or dehydrogenation of alpha-hydroxy acids in bioenergetic metabolism: A murburn perspective

Glycolate, lactate, malate, hydroxyglutarate and isocitrate are key alpha-hydroxyacyl metabolic intermediates found in the tissues/cells/organelles of diverse life forms. They are respectively oxidized to glyoxylate, pyruvate, oxaloacetate, ketoglutarate and oxalosuccinate in cell bioenergetic metabolism. These molecules form key junction points for divergent pathways of two to six carbon-backboned molecules (of various classes of biomolecules like carbohydrates, amino acids, etc.). The oxido-reduction of the alpha-hydroxyacyl species is traditionally believed to be carried out by reversible (de)hydrogenases, employing nicotinamide cofactors. Herein, I propose that while the reductive pathway can be mediated in a facile manner by the (de)hydrogenases, the oxidative reaction could more efficiently be coupled with murzyme activities, which employ diffusible reactive (oxygen) species (DRS/DROS/ROS). Such a murburn strategy would enable the system to tide over the highly unfavorable energy barriers of the sequential dehydrogenase reaction (~450 kJ/mol, or more!), to give kinetically viable bimolecular reactions catering to cellular needs. Further, such a scheme does not necessitate any ‘intelligent governance’ or ‘smart decision-making’ of/by the pertinent redox enzymes.