A test set of 21 radical addition and 28 hydrogen abstraction reactions has been studied at the W1, G4, G3X, G3X(MP2), and G3X(MP2)-RAD levels of theory with a view to establishing whether the recently introduced G4 theory offers improved performance over the G3 methods. All methods tested approximated the benchmark W1 values to within a mean absolute deviation (MAD) of 4 kJ mol(-1) or less, al...

The catalytic performances of titanium species in TS-1 zeolite for the hydroxylamine formation have been investigated using the density functional theory with the ONIOM scheme. The reaction process for making hydroxylamine is divided into two steps: (i) the H2O2 decomposition over the Ti species to produce the peroxo titanium species and (ii) the NH3 oxidation over the generated oxidizing speci...

The mechanism of Michael addition of malononitrile to chalcones catalyzed by Cinchona alkaloid aluminium(III) complex has been investigated by DFT and ONIOM methods. Calculations indicate that the reaction proceeds through a dual activation mechanism, in which Al(III) acts as a Lewis acid to activate the electrophile α,β-unsaturated carbonyl substrate while the tertiary amine in the Cinchona al...

In 2008, a successful computational design procedure was reported that yielded active enzyme catalysts for the Kemp elimination. Here, we studied these proteins together with a set of previously unpublished inactive designs to determine the sources of activity or lack thereof, and to predict which of the designed structures are most likely to be catalytic. Methods that range from quantum mechan...

We introduce embedded mean-field theory (EMFT), an approach that flexibly allows for the embedding of one mean-field theory in another without the need to specify or fix the number of particles in each subsystem. EMFT is simple, is well-defined without recourse to parameters, and inherits the simple gradient theory of the parent mean-field theories. In this paper, we report extensive benchmarki...

Objective(s): The novel 7-hydroxycoumarinyl gallates derivatives are detected in many pharmaceutical compounds like anticancer and antimicrobial agents. Whereas carbon nanotubes (CNTs) have been discussed for nanomedicine applications and in particular as drug delivery systems. The capability of armchair (5, 5) SWCNT -based drug delivery system in the therapy of anticancer has been investigated...

Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate l...

Introduction: TGF-β Receptor Type 1 (TGF-β1), also known as activin kinase type 5 (ALK-5), is a biological target related to some types of cancer, such as breast cancer. Inhibition of this target is a strategy that has been studied as a way to treat cancer. In this way, the objective of this work is to use computational chemistry to evaluate the main interactions that occur between the main res...

Nanotubes are a class of host cavities increasingly used to encapsulate unstable molecules, yet none have been exploited to host reactive sulfur species, such as thiozone (S(3)). In this paper, density functional theory and (ONIOM) calculations were used to compute single-walled carbon nanotube (SWNT)-thiozone combinations for the inclusion of S(3) into the hollow nanotube space and to rational...

We present ONIOM calculations using B3LYP/d95(d,p) as the high level and AM1 as the medium level on parallel β-sheets containing four strands of Ac-AAAAAA-NH2 capped with either Ac-AAPAAA-NH2 or Ac-AAAPAA-NH2. Because Pro can form H-bonds from only one side of the peptide linkage (that containing the C═O H-bond acceptor), only one of the two Pro-containing strands can favorably add to the sheet...