2 research outputs found
Adsorption of Nitrogen-Containing Compounds on the (100) α‑Quartz Surface: Ab Initio Cluster Approach
A cluster
approach extended to the ONIOM methodology has been applied
using several density functionals and Møller–Plesset perturbation
theory (MP2) to simulate the adsorption of selected nitrogen-containing
compounds [NCCs, 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT),
2,4-dinitroanisole (DNAN), and 3-nitro-1,2,4-triazole-5-one (NTO)]
on the hydroxyated (100) surface of α-quartz. The structural
properties were calculated using the M06-2X functional and 6-31GÂ(d,p)
basis set. The M06-2X-D3, PBE-D3, and MP2 methods were used to calculate
the adsorption energies. Results have been compared with the data
from other studies of adsorption of compounds of similar nature on
silica. Effect of deformation of the silica surface and adsorbates
on the binding energy values was also studied. The atoms in molecules
(AIM) analysis was employed to characterize the adsorbate–adsorbent
binding and to calculate the bond energies. The silica surface shows
different sorption affinity toward the chemicals considered depending
on their electronic structure. All target NCCs are physisorbed on
the modeled silica surface. Adsorption occurs due to the formation
of multiple hydrogen bonds between the functional groups of NCCs and
surface silanol groups. Parallel orientation of NCCs interacting with
the silica surface was found to be favorable when compared with perpendicularly
oriented NCCs. NTO was found to be the most strongly adsorbed on the
silica surface among all of the considered compounds. Dispersion correction
was shown to play an important role in the DFT calculations of the
adsorption energies of silica–NCC systems
A new mechanism of post-transfer editing by aminoacyl-tRNA synthetases: catalysis of hydrolytic reaction by bacterial-type prolyl-tRNA synthetase
<p>Aminoacyl tRNA synthetases are enzymes that specifically attach amino acids to cognate tRNAs for use in the ribosomal stage of translation. For many aminoacyl tRNA synthetases, the required level of amino acid specificity is achieved either by specific hydrolysis of misactivated aminoacyl-adenylate intermediate (pre-transfer editing) or by hydrolysis of the mischarged aminoacyl-tRNA (post-transfer editing). To investigate the mechanism of post-transfer editing of alanine by prolyl-tRNA synthetase from the pathogenic bacteria <i>Enterococcus faecalis</i>, we used molecular modeling, molecular dynamic simulations, quantum mechanical (QM) calculations, site-directed mutagenesis of the enzyme, and tRNA modification. The results support a new tRNA-assisted mechanism of hydrolysis of misacylated Ala-tRNA<sup>Pro</sup>. The most important functional element of this catalytic mechanism is the 2′-OH group of the terminal adenosine 76 of Ala-tRNA<sup>Pro</sup>, which forms an intramolecular hydrogen bond with the carbonyl group of the alanine residue, strongly facilitating hydrolysis. Hydrolysis was shown by QM methods to proceed via a general acid-base catalysis mechanism involving two functionally distinct water molecules. The transition state of the reaction was identified. Amino acid residues of the editing active site participate in the coordination of substrate and both attacking and assisting water molecules, performing the proton transfer to the 3′-O atom of A76.</p