Density functional theory methods have been used to investigate the hepatitis delta virus (HDV) ribozyme and its catalyzed phosphodiester cleavage. In particular, the effects of the environment's polarity and/or specific hydrogen-bond interactions on the proton affinity of the active site cytosine's N3 ring center have been considered. In addition, the basicities of possible hydrated Mg2+ ion species were also examined. The mechanism previously proposed for the HDV ribozyme in which the active site cytosine (C75) is protonated and thus acts as an acid while the Mg2+ species acts as the complementary base was then investigated. The possible role of tautomerization of C75 is also discussed.

LpxC is a key enzyme in the biochemical synthesis of Lipid A, an important outer cell-membrane component found in a number of pathogenic bacteria. Using DFT, we have investigated the binding of the substrate within its active site as well as the deacetylation mechanism it catalyzes. The substrate is found to preferentially coordinate to the active site Zn2+ via its carbonyl oxygen between a Zn2+-bound H2O and an adjacent threonine (Thr191). Furthermore, upon substrate binding a nearby Glu78 residue is found to readily deprotonate the remaining Zn2+-bound H2O. Unlike several related metallopeptidases, the mechanism of LpxC is found to proceed via four steps; (i) initial hydroxylation of the substrates' carbonyl carbon to give a gem-diolate intermediate, (ii) protonation of the amide nitrogen by the histidine His265-H+, (iii) a barrier-less change in the active site-intermediate hydrogen-bond network and finally, (iv) C-N bond cleavage. Notably, the rate-determining step of the mechanism of LpxC is found to be the initial hydroxylation while the final C-N bond cleavage occurs with an overall barrier of 23.6 kJ mol-1. Furthermore, LpxC uses a general acid/base pair mechanism as indicated by the fact that both His265-H+ and Glu78 are accordingly involved.

Density functional theory methods have been employed to systematically investigate the overall mechanism of the second half-reaction of nitric oxide synthases. The initial heme-bound hydrogen peroxide intermediate previously identified is found to first undergo a simple rotation about its O-O peroxide bond. Then, via a "ping-pong" peroxidase-like mechanism the -O(in)H- proton is transferred back onto the substrate's -NO oxygen then subsequently onto the outer oxygen of the resulting Fe(heme)-OOH species. As a result, O(out) is released as H2O with concomitant formation of a compound I-type (Fe(heme)-O) species. Formation of the final citrulline and NO products can then be achieved in one step via a tetrahedral transition structure resulting from direct attack of the Fe(heme)-O moiety at the substrate's guanidinium carbon center. The possible role of alternative mechanisms involving a protonated compound II-type species or an initial transfer of only the -NH- hydrogen of the =NHOH+ group of N(omega)-hydroxy-L-arginine is also discussed.

The hybrid density functional theory method B3LYP in combination with three systematically larger active site models has been used to investigate the substrate binding and catalytic mechanism by which Neisseria gonorrhoeae methionine sulfoxide reductase B (MsrB) reduces methionine-R-sulfoxide (Met-R-SO) to methionine. The first step in the overall mechanism is nucleophilic attack of an active site thiolate at the sulfur of Met-R-SO to form an enzyme-substrate sulfurane. This occurs with concomitant proton transfer from an active site histidine (His480) residue to the substrates oxygen center. The barrier for this step, calculated using our largest most complete active site model, is 17.2 kJ mol(-1). A subsequent conformational rearrangement and intramolecular -OH transfer to form an enzyme-derived sulfenic acid ((Cys495)S-OH) is not enzymatically feasible. Instead, transfer of a second proton from a second histidyl active site residue (His477) to the sulfurane's oxygen center to give water and a sulfonium cation intermediate is found to be greatly preferred, occurring with a quite low barrier of just 1.2 kJ mol(-1). Formation of the final product complex in which an intraprotein disulfide bond is formed with generation of methionine preferably occurs in one step via nucleophilic attack of the sulfur of a second enzyme thiolate ((Cys440)S(-)) at the S(Cys495) center of the sulfonium intermediate with a barrier of 23.8 kJ mol(-1). An alternate pathway for formation of the products via a sulfenic acid intermediate involves enzymatically feasible, but higher energy barriers. The role and impact of hydrogen bonding and active site residues on the properties and stability of substrate and mechanism intermediates and the affects of mutating His477 are also examined and discussed.

The interaction of the nitric oxide ions NO+ and NO- with benzene (C6H6) and the aromatic R-groups of the amino acids phenylalanine (Phe), tyrosine (Tyr), histidine (His), and tryptophan (Trp) have been examined using the DFT method B3LYP and the conventional electron correlation method MP2. In particular, the structures and complexation energies of the resulting half-sandwich Ar...NO+/- and sandwich [Ar...NO...Ar]+/- complexes have been considered. For the Ar...NO+ complexes, the presence of an electron rich heteroatom within or attached to the ring is found to not preclude the cation...pi bound complex from being the most stable. Furthermore, unlike the anionic complexes, the pi...cation...pi ([Ar...NO...Ar]+) complexes do not correspond to a "doubling" of the parent half-sandwich.