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BioEqCalc 
A Package for Performing Equilibrium Calculations on Biochemical Reactions

David L. Akers and Robert N. Goldberg
Biotechnology Division
National Institute of Standards and Technology
Gaithersburg, Maryland 20899, USA
dla@cs.brown.edu; robert.goldberg@nist.gov.

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 (H[Graphics:Images/index_gr_1.gif]O), values of apparent equilibrium constants [Graphics:Images/index_gr_2.gif], standard transformed Gibbs free energies [Graphics:Images/index_gr_3.gif] and standard transformed enthalpies of reaction [Graphics:Images/index_gr_4.gif], calorimetric enthalpies of reaction [Graphics:Images/index_gr_5.gif], and changes in the binding [Graphics:Images/index_gr_6.gif] of ligands such as [Graphics:Images/index_gr_7.gif] and [Graphics:Images/index_gr_8.gif]. 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.

Introduction

A Simple Chemical Equilibrium Calculation: Phosphoric Acid

Speciation of Adenosine [Graphics:Images/index_gr_132.gif]-triphosphate

Hydrolysis of Adenosine [Graphics:Images/index_gr_224.gif]-triphosphate

Graphics

Additional Capabilities of BioEqCalc

Conclusion and Future Extensions of BioEqCalc

Global Variables

Glossary

Acknowledgment

References

Additional Material

About the Authors

Copyright and Disclaimer


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