Application of the electron density force to chemical reactivity

Exploring the Reactivity of Donor-Acceptor Systems through a Combined Conceptual and Constrained DFT Approach

In the context of the conceptual density functional theory (cDFT) and based on the computational efficiency of the constrained DFT (CDFT), we demonstrate that chemical reactivity can be governed by the difference between the local interacting chemical potentials of the reactants (referred as Edual), in agreement with Sanderson's equalization principle. In a proof-of-concept study, we investigated illustrative examples involving typical non-covalent donor-acceptor systems and reactive systems are provided. For the selected systems, our approach reveals significant mimicking between Edual and the DFT-computed intermolecular interaction energy profiles. We further evaluate the influence of the Coulomb and exchange-correlation contributions in Edual. These latter results suggest that numerous potential energy surfaces of clusters can be explored using a Sanderson-like model only based on classical interactions between molecular orbitals domains. To conclude, this study achieved a deeper understanding of the principles of cDFT and assessed, in a wider context, its efficiency in predicting the chemical reactivity.

Linear chains of hydrogen molecules under pressure: An extreme-pressure continuum model study

New analytical gradients of the electronic energy of a confined molecular system within the extreme-pressure continuum model are presented and applied to the study of the equilibrium geometries of linear chains of hydrogen molecules nH₂ under pressures. The decrease in inter- and intramolecular H-H distances with the increase in the pressure has been studied up to 80 GPa. We have also shown that the compression of the bond-lengths can be interpreted in terms of the effect of the confining potential of the electron density of the molecular systems.

Use of Computational Biochemistry for Elucidating Molecular Mechanisms of Nitric Oxide Synthase

Nitric oxide (NO) is an essential signaling molecule in the regulation of multiple cellular processes. It is endogenously synthesized by NO synthase (NOS) as the product of L-arginine oxidation to L-citrulline, requiring NADPH, molecular oxygen, and a pterin cofactor. Two NOS isoforms are constitutively present in cells, nNOS and eNOS, and a third is inducible (iNOS). Despite their biological relevance, the details of their complex structural features and reactivity mechanisms are still unclear. In this review, we summarized the contribution of computational biochemistry to research on NOS molecular mechanisms. We described in detail its use in studying aspects of structure, dynamics and reactivity. We also focus on the numerous outstanding questions in the field that could benefit from more extensive computational investigations.

Comment on “Revisiting the definition of local hardness and hardness kernel” by C. A. Polanco-Ramirez, M. Franco-Pérez, J. Carmona-Espíndola, J. L. Gázquez and P. W. Ayers, Phys. Chem. Chem. Phys., 2017, 19, 12355

In this comment we show that the derivation proposed Polanco-Ramirez et al. appears naturally in the Taylor expansion of the energy, showing that their whole construction is not artificially built.

Deamination features of 5-hydroxymethylcytosine, a radical and enzymatic DNA oxidation product

The 5-methylcytosine derivative 5-hydroxymethylcytosine (5hmCyt), which is generated via enzymatic oxidation, is sometimes referred to as the sixth nucleobase due to its widespread presence in the DNA of brain and embryonic stem cells. In this study, we used density functional based methods and reactivity indices from conceptual DFT to explore the mechanism and key features of the hydrolytic deamination of 5hmCyt. The data obtained are used to compare and contrast this deamination reaction with those of other cytosine derivatives. The deamination process for 5hmCyt is similar to the corresponding processes for other unsaturated derivatives in that the amino form is the reactive one and water addition is the rate-limiting step. However, several differences due to the rotameric asymmetry of the current system are also noted.

Revisiting electroaccepting and electrodonating powers: proposals for local electrophilicity and local nucleophilicity descriptors

It is shown that the electrophilicity index is also a rational choice for measuring nucleophilicity.

Dual descriptor and molecular electrostatic potential: complementary tools for the study of the coordination chemistry of ambiphilic ligands

The possibility to retrieve the coordinating properties of ligands by a combined dual descriptor and molecular electrostatic potential analysis is shown, yielding a potentially predictive tool of their ambiphilicity and selectivity.