Exploring Organic Chemistry with DFT: Radical, Organo-metallic, and Bio-organic Applications

Abstract

In this review we report the results of DFT investigations which have been carried out in different fields of organic and organometallic chemistry, including radical reactivity, structure and reactivity of organometallic compounds, and biochemical/biophysical properties of long chain unsaturated systems. Many of the most popular non-local corrected functionals (e.g. B3LYP, BHLYP, BLYP, BP86) have been benchmarked both versus experimental and high level ab initio (e.g. MP2, MP4, CAS-SCF/CAS-PT2) data, resulting in an impressive agreement. The DFT approach appears to be a powerful tool, which can be used as a valid alternative to more traditional correlated methods, to achieve mechanistic information of chemical/ physical interest in the modelling of organic and biochemical systems.In particular, in the examples selected in this review, we discuss the results obtained for the addition reaction of alkyl radicals to double bonds and for the hydrogen/ chlorine abstraction reaction by alkyl and silyl radicals from various organic substrates. Moreover, binding interactions (i.e. geometries and energies) in organometallic compounds are shown to be satisfactorily reproduced via DFT and examples of nickel-catalyzed [2 2] cycloaddition reaction and homogeneous Ziegler-Natta catalysis are investigated. Finally, a DFT modelling for the singletoxygen quenching ability and radical trapping activity of carotenes is presented. The simulated data provide a rationale for the protective action of carotenes observed in biological tissues and elucidates the physical and chemical mechanisms involved in the reactivity of carotenes versus oxygen and radicals.

Effect of metal Ions (Ni2+, Cu2+ and Zn2+) and water coordination on the structure of L-phenylalanine, L-tyrosine, L-tryptophan and their zwitterionic forms

“…Zn 2+ is a d 10 ion, so its complex is a closed-shell system with a singlet ground state. Previous investigations have shown [ 37 – 39 ] that the density functional theory method yields results, which compare favorably with the corresponding results obtained using the high level ab initio coupled-cluster method. Hence, DFT can sometimes be an economic alternative to ab initio methods for studying larger systems.…”

Rate constants and transition‐state geometry of reactions of alkyl, alkoxyl, and peroxyl radicals with thiols

“…Transition‐state geometry for these reactions was calculated by the hybrid density functional method B3LYP. This approach is a reliable tool of theoretical investigation of radical reactions 29,30. All calculations were carried out using the Gaussian‐98 program 31.…”

Density functional theory modeling of chromate adsorption onto ferrihydrite nanoparticles

“…Most vibrational modes are modeled reasonably accurately with the DFT methods applied here as demonstrated by comparisons of modeled and observed frequencies on aqueous species [ 10 ]. However, modeling some modes is problematic, notably those involving metal–oxygen double bonds where electron correlation is significantly more important [ 53 ]. These stronger bonds are likely to have higher frequencies compared to single bonds, so this limitation of the applied DFT techniques is likely a source of error here.…”