This review paper introduces the theoretical fundamentals of chemical reaction kinetics and thermodynamics, the history of their application in organic geochemistry, and future trends in the study of biomarker isomerization. Reaction kinetics were firstly applied and developed in organic geochemistry in 1970's as an organic maturity indicator tool for predicting the stage of oil and gas generation from kerogen. Between ca. 1975 and 1990 (the first period), empirical reaction kinetics was actively applied in organic geochemistry using nomographs and calculators. From ca. 1990 to 2005 (the second period), with widespread access to PCs, organic geochemists began to utilize computers extensively to easily process large datasets and to develop simulators for basin and petroleum system modeling based on the reaction kinetics for oil/gas generation and vitrinite reflectance. After ca. 2005 (the third period), datasets of apparent activation energy (E_a) and frequency factor (A) were comprehensively reviewed and summarized, in order to understand their practical implications. Simulations of molecular dynamics were also often performed in the third period, based on chemical thermodynamics theory.

Sampei and Suzuki (2005) showed that the kinetic parameters E_a and A obtained from laboratory heating experiments cannot be applied to reconstructing the evolution path of sterane-hopane epimerization in natural sedimentary basins. The E_a derived from heating experiments is about two times greater than that from natural sedimentary basins. Moreover, the A parameters derived in the laboratory and those from nature are quite different with the A values derived from heating experiments being several orders of magnitude greater than those from sedimentary basins. These differences are probably attributable to the low values of apparent activation entropy (S_a) found in natural sedimentary basins. The implications of the low S_a of biomarker isomerization in nature must be clarified in future, in order to improve the precision of organic maturity and paleo-temperature indicators. The equilibrium constant equation K_c=exp(-ΔG_r/RT) will draw more attention in estimating the isomer composition in equilibrium at a given temperature. Chemical thermodynamics theory suggests that the difference of Gibbs reaction energy (G_r) among isomers must be within ±10 kJ to estimate a practical Kc value using a dataset obtained from standard GC-MS analysis. The Kc of isomerization for particular organic molecules will become an important temperature-pressure indicator especially for low grade pelitic schists in regional metamorphism.

We report a mass spectra database of underivatized short-chain peptides by using ion-pair liquid chromatography with electrospray ionization-mass spectrometry (LC/ESI-MS). The ion-pairing chromatographic separation by a porous graphitic carbon stationary column with nonafluoropentanoic acid solution and acetonitrile solvent gradient revealed a positive correlation between the retention time and the degree of molecular hydrophobicity. The addition of a proton donor of 0.1% formic acid for the inverse gradient program induces an efficient stabilized ionization on the ESI positive mode. We compiled the summary of retention time and those of some typical mass fragmentation patterns on underivatized short-chain peptides and related-molecule groups. The present method will be applied to other multi-dimensional chromatographies for further detailed description of short-chain peptide chemistry.