Bio-Thermo Database v1.00

Please cite the following reference in publications making use of this resource: X. Li, R. K. Dash, R. K. Pradhan, F. Qi, M. Thompson, K. C. Vinnakota, F. W, F. Yang, and D. A. Beard. A Database of Thermodynamic Quantities for the Reactions of Glycolysis and the Tricarboxylic Acid Cycle. The Journal of Physical Chemistry, J. Chem. Phys. B. (in review), 2010.

This web base bio-thermodynamic database can be used to obtain formation properties and dissociation constants (provided as pK's) for reference species associated with biochemical reactants at specified temperature and ionic strength; and to obtain reaction properties (including free energies and enthalpies) for associated reactions.

REACTANT PROPERTIES

Choose a reactant from the list below. The constants, pK and ΔrH0Kd at T=298.15 K and I=0 m
of this reactant's reference species will be shown in the yellow fields of “Constants”.

Input to your experimental conditions, click "Calculate New Constants", and estimated values of pK and ΔrH0Kd will be shown in the green fields.
Temp. (K)
 
I (M)
 

Contants:

Abbreviation
Name
Name ΔfG0
(standard Gibbs free energy of reaction, T = 298.15K,
I = 0M)
Zia
(charge number of species i )
nH a
(number of protons in reference species)
 
 
pK_H1
(first ion dissociation constant of Hydrogan)
ΔrHKd_H1
(first ion dissociation enthalpy of Hydrogen )
pk_H2
(second ion dissociation constant of Hydrogan)
ΔrHKd_H2
(second ion dissociation enthalpy of Hydrogen )
pK_Mg1
(first ion dissociation constant of Magnesium)
ΔrHKd_Mg1
(first ion dissociation enthalpy of Magnesium)
New pK1: New ΔrHKd_H1:
New pK2: New ΔrHKd_H2: New pK_Mg1: New ΔrHKd_Mg1:
pK_HMg
(dissociation constant of Hydrogen and Magnesium)
ΔrHKd_HMg
(dissociation enthalpy of Hydrogen and Magnesium)
pK_Mg2
(second ion dissociation constant of Magnesium)
ΔrHKd_Mg2
(second ion dissociation enthalpy of Magnesium)
pK_K1
(first ion dissociation constant of Potassium)
ΔrHKd_K1
(first ion dissociation enthalpy of Potassium)
New pK_HMg: New ΔrHKd_HMg:
New pK_Mg: New ΔrHKd_Mg2: New pK_K1: New ΔrHKd_K1:
pK_Na1
(first ion dissociation constant of Sodium)
ΔrHKd_Na1
(first ion dissociation enthalpy of Sodium)
pK_HNa
(dissociation constant of Hydrogenand Sodium)
ΔrHKd_HNa
(dissociation enthalpy of Hydrogen and Sodium)
pK_Ca1
(first ion dissociation constant of Calcium)
ΔrHKd_Ca1
(first ion dissociation enthalpy of Calcium)
New pK_Na1: New ΔrHKd_Na1:
New pK_HNa: New ΔrHKd_HNa: New pK_Ca1: New ΔrHKd_Ca1:
pK_HCa
(dissociation constant of Hydrogen and Calcium)
ΔrHKd_HCa
(second ion dissociation enthalpy of Calcium)
pK_Ca2
(Second ion dissociation constant of Calcium)
ΔrHKd_Ca2
(second ion dissociation enthalpy of Calcium)
Standard Temperature Standard Ionic Concentration
New pK_HCa: New ΔrHKd_HCa: New pK_Ca2: New ΔrHKd_Ca2: Experimental Temperatrue Experimental Ion Concentration

REACTION PROPERTIES

Choose reaction from the list below, the reaction's abbreviated name, real name, EC number, reaction form, standard equilibrium constant at (T = 298.15 K, I = 0 M), and standard Gibbs free energy at (T = 298.15 K, I = 0 M) will be shown at the boxes below.


Abbreviated Name
EC Number
Reaction Enthaipy
Reaction Name

Refrence Reaction form
Biochmical reation Form
Reactant's Charge
Reactant Stoic. Coeffi.
DfG for all reactants
   

Change to your experimental condition and click button "Calculation Apparent Equilibrium Constant & Standard transformed Gibbs free energy", the new constant will be shown at the boxes below.

Environment:(change to your experimental conditions)

Temp. (K)
I (M) pH  
 
       
Free Magnesium
concentration (M)
Free Potassium
concentration (M)
Free Sodium
concentration (M)
Free Calcium
concentration (M)

 

Reference Equilibrium Constant :
(Mass Raction radio T = 298.15 K, I = 0 M)

Equilibrium Constant :
(Mass Raction for Biochemical Reactions)

Reference Gibbs free energy: (kJ/mol)
(Mass Raction radio T = 298.15 K, I = 0 M)

Transformed Gibbs free energy: (kJ/mol)
(Mass Raction for Biochemical Reactions)

 

Under Construction

DISSOCIATION CONSTANT CORRECTION

This function tool uses to compute the ionic strength and temperature correction of the dissociation constant (provided as Kd) of a ligand-cation dissociation reaction (reactions with two products and one reactant).

Enthalpy (ΔH) at reported ionic strength

Ionic strength at which Enthalpy ΔH was reported

Ionic strength at which pK was reported

Temperature at which pK was reported

charge on the products

charge on the reactants

Dissociation constant (pK) at reported ionic strength and temperature

     (Kd is )

Ionic strength at which pK need to be calculated

Temperature at which pK need to be calculated

New pK   , Kd