BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.

This review contains selected values of thermodynamic quantities for the aqueous ionization reactions of 64 buffers, many of which are used in biological research. Since the aim is to be able to predict values of the ionization constant at temperatures not too far from ambient, the thermodynamic quantities which are tabulated are the pK, standard molar Gibbs energy ⌬ r G ‫ؠ‬ , standard molar enthalpy ⌬ r H°, and standard molar heat capacity change ⌬ r C p ‫ؠ‬ for each of the ionization reactions at the temperature T ϭ298.15 K and the pressure pϭ0.1 MPa. The standard state is the hypothetical ideal solution of unit molality. The chemical name͑s͒ and CAS registry number, structure, empirical formula, and molecular weight are given for each buffer considered herein. The selection of the values of the thermodynamic quantities for each buffer is discussed. © 2002 by the U.S. Secretary of Commerce on behalf of the United States. All rights reserved.Of primary interest to this review is the ͑thermodynamic͒ equilibrium constant K a,m ϭa͕H ϩ ͑aq͖͒•a͕A Ϫ ͑aq͖͒/a͕HA͑aq͖͒ ͑1͒ for the ionization reaction HA͑aq͒ϭH ϩ ͑aq͒ϩA Ϫ ͑aq). ͑2͒The above equilibrium constant has been defined in terms of activity and has been denoted as such by affixing a subscript a to the equilibrium constant. It is also necessary to specify the standard state. In this review the principal standard state used for the solute is the hypothetical ideal solution at the standard molality (m°ϭ1 mol kg Ϫ1 ). The standard state for the solvent is the pure solvent. This choice of a molality standard state has been indicated by attaching a subscript m to the equilibrium constant. Eq. ͑1͒ can also be written in terms of the molalities and activity coefficients ͑molality ba-sis͒ ␥ m of the solute species:The standard molality m°has been used in Eq. ͑3͒ to keep the equilibrium constant dimensionless. An alternative way of writing Eq. ͑3͒ iswhere K m ϭm͕H ϩ ͑aq͖͒•m͕A Ϫ ͑aq͖͒/͓m͕HA͑aq͖͒•m°], ͑5͒andHere K m is the equilibrium constant ͑molality basis͒ that pertains to an actual real solution as distinct from the equilibrium constant ͑activity basis͒ that relates to a hypothetical standard state that is approached by real solutions as the sum of the molalities of all solute species approaches zero. One can also formulate equilibrium constants in terms of concentrations c:andHere, c°is the standard concentration ͑1 mol dm Ϫ3 ͒ and ␥ c is the activity coefficient on a concentration basis. The density of the pure solvent is needed to calculate values of K a,m from K a,c and vice versa:On a logarithmic scale the difference between K a,c and K a,m in water at Tϭ298.15 K is very small (pK a,c ϭpK a,m 236 236 GOLDBERG, KISHORE, AND LENNEN

The criterion for chemical equilibrium at specified temperature, pressure, pH, concentration of free magnesium ion, and ionic strength is the transformed Gibbs energy, which can be calculated from the Gibbs energy. The apparent equilibrium constant (written in terms of the total concentrations of reactants like adenosine 5'-triphosphate, rather than in terms of species) yields the standard transformed Gibbs energy of reaction, and the effect of temperature on the apparent equilibrium constant at specified pressure, pH, concentration of free magnesium ion, and ionic strength yields the standard transformed enthalpy of reaction. From the apparent equilibrium constants and standard transformed enthalpies of reaction that have been measured in the adenosine 5'-triphosphate series and the dissociation constants of the weak acids and magnesium complexes involved, it is possible to calculate standard Gibbs energies of formation and standard enthalpies of formation of the species involved at zero ionic strength. This requires the convention that the standard Gibbs energy of formation and standard enthalpy of formation for adenosine in dilute aqueous solutions be set equal to zero. On the basis of this convention, standard transformed Gibbs energies of formation and standard transformed enthalpies of formation of adenosine 5'-trisphosphate, adenosine 5'-diphosphate, adenosine 5'-monophosphate, and adenosine at 298.15 K, 1 bar, pH = 7, a concentration of free magnesium ions of 10(-3) M, and an ionic strength of 0.25 M have been calculated.

Titration calorimetry was used to measure equilibrium constants and standard molar enthalpies for the reactions of phenethylamine, ephedrines, and related substances with a-and /3-cyclodextrin. Changes in the chemical shifts A6 of both the ligand and cyclodextrin protons were measured with NMR. The thermodynamic results have been examined in terms of structural features of the ligand that affect these interactions such as the separation of the charge at an amino group and the aromatic ring, steric effects, the presence of additional functional groups (amino, hydroxy, methoxy, and methyl) attached to the aromatic ring, the presence and location of hydroxy group(s) on the ligand, changes in the chirality of the ligand, and the flexibility of the organic molecules attached to the aromatic ring. It was found that the values of thermodynamic quantities for these reactions in phosphate and acetate buffers were different. This difference is attributable to the presence of a hydrophobic alkyl group in the neutral acetic acid molecule and its interaction with the cyclodextrins. Also, there are significant differences in the thermodynamic quantities for the reactions of the chiral isomers of ephedrine and pseudoephedrine in their reactions with /3-cyclodextrin. A plot of the standard molar enthalpy vs the standard molar entropy for the reactions of these chiral isomers with a-and /3-cyclodextrin is linear; the relative order of the ephedrines and pseudoephedrines in the enthalpy-entropy plot is the same for the reactions of these substances with both a-and /3-cyclodextrin. NMR studies demonstrated that the magnitude of the upfield shifts of the cyclodextrin's H3 and H5 protons, A<5(H3) and A<5(H5), and their relative ratio, A<5(H5)/A<5(H3), can be used, respectively, as a measure of the complex stability and the depth of inclusion of the ligand into the cavity. The equilibrium constants determined by titration calorimetry correlate well with the changes in chemical shifts Ad determined by NMR.

http://xpdb.nist.gov/enzyme_thermodynamics/

Titration calorimetry was used to determine equilibrium constants and standard molar enthalpy, Gibbs energy, and entropy changes for the reactions of a series of acids, amines, and cyclic alcohols with α- and β-cyclodextrin. The results have been examined in terms of structural features in the ligands such as the number of alkyl groups, the charge number, the presence of a double bond, branching, and the presence of methyl and methoxy groups. The values of thermodynamic quantities, in particular the standard molar Gibbs energy, correlate well with the structural features in the ligands. These structural correlations can be used for the estimation of thermodynamic quantities for related reactions. Enthalpy−entropy compensation is evident when the individual classes of substances studied herein are considered, but does not hold when these various classes of ligands are considered collectively. The NMR results indicate that the mode of accommodation of the acids and amines in the α-cyclodextrin cavity is very similar, but that the 1-methyl groups in 1-methylhexylamine and in 1-methylheptylamine and the N-methyl group in N-methylhexylamine lie outside the α-cyclodextrin cavity. This latter finding is consistent with the calorimetric results. Many of the thermodynamic and NMR results can be qualitatively understood in terms of van der Waals forces and hydrophobic effects.

The main calorimetric principles used in isothermal microcalorimetry are briefly discussed. Different chemical calibration and test reactions are discussed, with a focus on reactions suitable for ambient conditions: reactions initiated by mixing of liquids (including titration microcalorimetry), dissolution of solid compounds and of slightly soluble gases, a photochemical process, and thermal power signals released over an extended period of time. Guidelines on the use of standardized chemical test and calibration reactions in isothermal microcalorimetry are presented. A standardized terminology in reporting characteristics of isothermal microcalorimeters is proposed.

This review contains recommended values of the thermodynamic and transport properties of the five and six membered ring carbohydrates and their phosphates in both the condensed and aqueous phases. Equilibrium data, enthalpies, heat capacities, and entropies have been collected from the literature. The accuracy of these data have been assessed, adjusted to 298.15 K and to a common standard state, and entered into a catalog of thermochemical reactions. The solution of this reaction catalog yields a set of recommended values for the formation properties of these substances. The volumetric data have also been critically evaluated. Recommended values are presented for standard state molar volumes and the temperature and pressure derivatives of the molar volume, i. e., the expansivity and the compressibility. The excess property data of aqueous solutions of these substances have been correlated to yield recommended values of the parameters of the virial expansion model used to represent the data. The transport data considered here includes both viscosity and diffusion data of aqueous solutions of the carbohydrates. The available phase diagram data and transition temperatures are summarized.