Caffeine, a ubiquitous natural product, is widely consumed by humans. The metabolic mechanisms of caffeine by flavin-containing monooxygenase (FMO) were systematically investigated in this study by quantum mechanics calculations. Four main metabolic pathways were characterized, including N-demethylations at N1-, N3-, and N7- sites (paths I–III) and C-8 oxidation (path IV). N-demethylation proceeds via the concerted homolytic cleavages of C–H and O–O bonds, while C-8 oxidation is an oxygen atom transfer mechanism. It shows that C-8 oxidation predominates over N-demethylations and trimethyluric acid is therefore the optimum metabolite of caffeine by FMO. Additionally, N3-demethylation is more favorable than N1 and N7-demethylations. This study can offer important clues for the bio-decaffeination techniques.

•The N-demethylation mechanisms of theobromine catalyzed by CYP1A2 were explored using the unrestricted B3LYP theory.•The rate-limiting N-methyl hydroxylation occurs in a HAT mechanism.•The carbinolamines generated are prone to decomposition through the contiguous heteroatom-assisted proton transfer.•The N-demethylation reaction proceeds through a SSM mechanism and HS is more favorable than LS.•3-N demethylation is kinetically more feasible than 7-N demethylation and 7-methylxanthine is the optimum metabolite of theobromine.Theobromine, a widely consumed pharmacological active substance, can cause undesirable muscle stiffness, nausea and anorexia in high doses ingestion. The main N-demethylation metabolic mechanism of theobromine catalyzed by P450 isoenzyme 1A2 (CYP1A2) has been explored in this work using the unrestricted hybrid density functional method UB3LYP in conjunction with the LACVP(Fe)/6-31G (H, C, N, O, S, Cl) basis set. Single-point calculations including empirical dispersion corrections were carried out at the higher 6-311++G** basis set. Two N-demethylation pathways were characterized, i.e., 3-N and 7-N demethylations, which involve the initial N-methyl hydroxylation to form carbinolamines and the subsequent carbinolamines decomposition to yield monomethylxanthines and formaldehydes. Our results have shown that the rate-limiting N-methyl hydroxylation occurs via a hydrogen atom transfer (HAT) mechanism, which proceeds in a spin-selective mechanism (SSM) in the gas phase. The carbinolamines generated are prone to decomposition via the contiguous heteroatom-assisted proton-transfer. Strikingly, 3-N demethylation is more favorable than 7-N demethylation due to its lower free energy barrier and 7-methylxanthine therefore is the optimum product reported for the demethylation of theobromine catalyzed by CYP1A2, which are in good agreement with the experimental observation. This work has first revealed the detail N-demethylation mechanisms of theobromine at the theoretical level. It can offer more significant information for the metabolism of purine alkaloid.

•The reductive repair mechanisms of dTg via electron transfer were explored at the theoretical level.•dT is the most feasible reductive product of dTg.•dT is also the feasible degradation product of 5-HOdT.•This work helps shed light on the interaction between low-energy electron and DNA base.The potential energy surface for the reductive repair of thymidine glycol (dTg) via electron transfer in aqueous solution has been mapped out in the present study employing a hybrid function of BH&HLYP in conjunction with the 6-311+G(d,p) basis set. Two types of repair mechanisms have been explored, including the reductive modification of the base portion and the excision of the base. The results indicate that thymidine (dT) is the most energetically feasible reductive product of dTg and also is the feasible degradation product of 5-hydroxy-5,6-dihydrothymidin-6-yl radical. The latter, however, has not been characterized in the previous experimental investigation. The insights explored in this paper help shed light on the interaction between low-energy electron and DNA base.