We develop a theoretical approach to point defects in zeolites as catalytically active framework sites, advance structural models for the most important defects and, by calculating the energy minimum configurations, study the main stages of the defect transformation in synthesis, postsynthetic treatment, and aging processes. Calculations have been focused on common hydrogen containing defects in zeolites including bridging hydroxyl and complexed silanol groups. The Bronsted acid site [AlH](Si), the vicinal disilanols and hydroxyl nests (or hydrogarnet defect) have been investigated using a periodic density functional theory approach employing numeric atomic orbital basis sets, as implemented in the Dmol(3) code. We propose a new mechanism for the modification of zeolite frameworks based on the silanol inversion. We identified a novel, low energy path (with reaction energy ca. 21 kcal/mol) to an elusive trigonal aluminum species, which does not involve dehydroxylation processes. The inversion in the vicinal disilanol structure reported previously has been confirmed to lead to a lower energy configuration with two loosely bound single silanol groups, which we suggest cannot be associated with H-1 NMR shifts of hydrogen bonded silanols. The inversion of the hydroxyl nest is shown to preserve a close trisilanol ring structure with extensive hydrogen bonding while opening this defect to an interaction with guest molecules in the pores of zeolites. On the basis of a low energy of ca. 0.5 kcal/mol calculated for the inversion of the hydroxyl nest, we propose that in zeolite materials T-site (silicon or aluminum) vacancies are realized in two major conformations: a traditional nest structure and a pair consisting of a trisilanol ring and a single silanol group.