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Publication Citation: BioEqCalc: A Package for Performing Equilibrium Calculations on Biochemical Reactions

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Author(s): D Akers; Robert N. Goldberg;
Title: BioEqCalc: A Package for Performing Equilibrium Calculations on Biochemical Reactions
Published: April 01, 2001
Abstract: A Mathematica package BioEqCalc.m has been developed for treating complex equilibria in aqueous solutions. The package is geared towards the treatment of biochemical systems and as such yields information on the molalities and mole fractions of the species in the solution, the activity coefficients of the species and the activity of the solvent (H2O), values of apparent equilibrium constants K', standard transformed Gibbs free energies {Δ}r )rG' and standard transformed enthalpies of reaction {Δ}rH' , calorimetric enthalpies of reaction {Δ}rH(cal), and changes in the binding {Δ}rN(X) of ligands such as X = H+ and Mg+2. Constraints such as constant pH, pX, and ionic strength I can be introduced into the calculations. The effects of ionic strength are accounted for in the computation. The chemical equilibrium problem is defined by input of the data in a convenient chemical format. Two- and three-dimensional plots of the apparent equilibrium constant as a function of temperature, pX, and ionic strength can be produced.
Citation: Mathematica Journal
Volume: 8
Issue: No. 1
Pages: pp. 86 - 113
Keywords: activity coefficients;biochemical reactions;chemical thermodynamics;computer programs;enthalpy of reaction;equilibirum calculations;equilibrium constants
Research Areas: Thermodynamics, Bioscience & Health, Chemistry