Competitive retro-cycloaddition in [60]- and [70]fullerene homodimers (1a,1c) as well as [60]/[70]heterodimer (1b), linked through 2-pyrazolinopyrrolidino bridges, has been studied by means of HPLC, mass spectrometry, and theoretical calculations at the density functional theory (DFT) level by using the two-layered ONIOM approach. The results of these investigations indicate that the retro-cycl...

Esterification of oxidized carbon nanotubes (CNTs) can open a new route for the separation of zigzag and armchair nanotubes. We studied theoretically (by using hybrid DFT within the ONIOM embedding protocol) the reactions of monocarboxy-substituted oxidized tips of zigzag and armchair single-walled CNTs (SWCNTs) with methanol. According to the calculated values of activation energy, Gibbs free-...

We have designed and theoretically studied three different pairs of green fluorescent protein chromophores and their different homologue-based diradicals coupled with imino nitroxides. To begin with, the geometries of all these diradicals have been optimized at high spin (HS) state in the gas phase, in a water medium and in a blood plasma medium. The process of calculations is straightforward a...

The geometries of various tautomers and isomers of 2-methylamino-2-imidazoline, 2-methylamino-2oxazoline, 2-methylamino-2-thiazoline, 2-phenylamino-2-imidazoline, 2-phenylamino-2-oxazoline, and 2-phenylamino-2-thiazoline have been studied using the Becke3LYP/6–31+G(d,p) DFT, ONIOM(Becke3LYP/6–31+G(d,p):HF/3–21G∗) and ONIOM(Becke3LYP/6–31+G(d,p):AM1) methods. The optimized geometries indicate th...

Fourier transform infrared difference spectroscopy (FTIR DS) is widely used to study the structural details of electron transfer cofactors in photosynthetic protein complexes. In photosynthetic proteins quinones play an important role, functioning as a cofactor in light-driven electron transfer. In photosystem I (PS I) phylloquinone (PhQ) functions as an intermediary in electron transfer. To in...

Cob[N]alamin, Cbl, is a macrocyclic complex (~ 200 atoms/molecule) composed of a cobalt atom of variable oxidation state (i.e., Co, Co, or Co) located at the center of an almostflat deprotonated corrin ring [1, 2]. This macromolecule is well-known for its relevance in different metabolic processes occurring at the cellular level. However, recent experimental evidence has demonstrated that, beyo...

The purpose of this paper is 2-fold. First, we present several extensions to the ONIOM(QM:MM) scheme. In its original formulation, the electrostatic interaction between the regions is included at the classical level. Here we present the extension to electronic embedding. We show how the behavior of ONIOM with electronic embedding can be more stable than QM/MM with electronic embedding. We also ...

We developed and implemented the ONIOM-molecular dynamics (MD) method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion. In this method, the direct MD is performed by calculating the ONIOM energy and gradients of the system on the fly. We describe the first application of this ONOM-MD method t...