Page 57 - Thermodynamics of Biochemical Reactions

3.8 Chemical Thermodynamic Tables Including Biochemical Species 51

the command <<BasicBiochemData2* and a notebook (BasicBiochemData2.nb)
that contains explanations and examples in addition to the data.
Goldberg and Akers (2001) have also published a Mathematica package for
calculations on biochemical reactions.
BasicBiochemData2 contains a table of data on 131 reactants that is
reproduced in Table 3.2 in the appendix of this chapter. It is hard to overemphas-
ize the usefulness of this table or the importance of extending it. It can be used to
calculate equilibrium constants for chemical reactions between species in the table
at desired ionic strengths in the range 0 to 0.35 M. This table can also be used to
calculate acid dissociation constants at desired ionic strengths, as shown in Table
1.3. When A,H" is known for all of the species in a chemical reaction, Table 3.2
can be used to calculate A,H". This makes it possible to calculate equilibrium
constants at temperatures other than 298.15 K. Only a few C;,,, values are known
for these species, and so equilibrium constants cannot be calculated very far from
room temperature. Since A,S" = (A,H' - A,G")/?; reaction entropies can also be
calculated, and this is of special interest when reactant species and product species
differ significantly in the disorder they introduce. For example, reactions that
produce gases are generally go further to the right than reactions that do not
because A,S" is large and positive.
Some comments are needed about the names of species used in making
calculations. Since Table 3.2 and later tables are produced using Mathematica, it
is necessary to use short one-dimensional names that begin with lowercase letters
and do not directly indicate ionic charges. The stereochemical labels are put at
the end of the name, if necessary, so that they do not interfere with alphabetizing
the list. Gaseous species are labeled with "g" at the end of the name, and the
corresponding dissolved species are labeled "aq." The species of C0,tot are
CO:-, HC03-, CO,(aq), and H,CO, (see Section 8.7). When values are given
for gaseous and dissolved forms, the corresponding Henry law constants can be
calculated. The distribution of CO, between gaseous and dissolved forms is of
special interest because we will see later (Chapter 8) that the Henry law constant
is also a function of pH. In Table 3.2 the chemical names of the reactants are given
first, and then the name used in Mathematica.
Proteins that are reactants in biochemical reactions are also be included in
BasicBiochemData2; examples included are cytochrome c, ferrodoxin, and
thioredoxin. Later in Chapter 7 it is shown that the effect of pH on a biochemical
reaction involving a protein can be calculated if the pKs of groups in the reactive
site of the protein can be determined.
It is important to understand that the number of digits used in a ther-
modynamic table of this type does not indicate the accuracy of the measured
values because the information in the table is in the differences between values.
An error of 0.01 kJ mol-I in the standard transformed Gibbs energy of formation
of a species leads to about a 1% error in the equilibrium constant of a chemical
reaction at 298.15K. This table can be extended a good deal in the future, as
indicated by the data on apparent equilibrium constants and transformed
enthalpies of reaction in the critical compilations of Goldberg and Tewari
(Goldberg et al., 1993; Goldberg and Tewari, 1994a, b, 1995a, b; Goldberg,
1999).
The procedure for calculating standard formation properties of species at zero
ionic strength from measurements of apparent equilibrium constants is discussed
in the next chapter. The future of the thermodynamics of species in aqueous
solutions depends largely on the use of enzyme-catalyzed reactions. The reason
that more complicated ions in aqueous solutions were not included in the NBS
Tables (1992) is that it is difficult to determine equilibrium constants in systems
where a number of reactions occur simultaneously. Since many enzymes catalyze
clean-cut reactions, they make it possible to determine apparent equilibrium
constants and heats of reaction between very complicated organic reactants that
could not have been studied classically.