schrodinger.application.jaguar.kinetics module

schrodinger.application.jaguar.kinetics.tst_rate_constant(dG: float, temp: float) → float

The tst rate constant in s^-1 * (mol/L)^-1 assumes dG is evaluated at a std concentration of 1 mol/liter. There is a factor of 1/C0^(n-1) which is numerically unimportant but sets the units.

Parameters

  • dG – Gibbs energy of activation in kcal/mol

  • temp – temperature in Kelvin

Returns

the rate constant

schrodinger.application.jaguar.kinetics.equilibrium_constant(dG: float, temp: float) → float

Compute the equilibrium constant

Parameters

  • dG – Gibbs free energy of reaction in kcal/mol

  • temp – temperature in Kelvin

Returns

the equilibrium constant

schrodinger.application.jaguar.kinetics.half_life(kf: float, Keq: float) → float

Compute the half life for the reaction. This is the time it takes for the reactant concentration to reach 0.5*([A]0 + [A]eq), one half of the way between initial and equilibrium concentrations. Assumes first order kinetics and other species at unit concentration for higher order kinetics (pseudo first order).

Parameters

  • kf – the forward rate constant

  • Keq – the equilibrium constant

Returns

the half life in units of 1/kf

schrodinger.application.jaguar.kinetics.depletion_at_t12(Keq: float) → float

fraction depletion of reactant at time t1/2

Parameters

Keq – the equilibrium constant

Returns

fraction of the reactant thats been depleted at the half life. This is 0.5 for an irreversible reaction

schrodinger.application.jaguar.kinetics.kinetics_table(Gr: Dict[float, schrodinger.application.jaguar.utils.FreeEnergy], Gts: Dict[float, schrodinger.application.jaguar.utils.FreeEnergy], Gp: Dict[float, schrodinger.application.jaguar.utils.FreeEnergy], rxn_number: int, nreactants: int, nproducts: int, debug: bool = False) → str

Produce a table which lists some rate and thermodynamic data at a variety of temperatures for a single elementary step. The reaction which is assumed to obey first order kinetics

Parameters

  • Gr – relates temperature to utils.FreeEnergy tuple for reactant

  • Gts – relates temperature to utils.FreeEnergy tuple for TS

  • Gp – relates temperature to utils.FreeEnergy tuple for product

  • rxn_number – Number of reaction for this Gibbs data, this is added to a title in the figure.

  • nreactants – number of reactant molecules

  • nproducts – number of product molecules

Returns

the kinetics table as a string