A Relation between Different Scales of Electrophilicity: Are the Scales Consistent Along a Chemical Reaction?

Revisiting nucleophilicity: an index for chemical reactivity from a CDFT approach

CONTEXT

Understanding and predicting the nucleophilic reactivity are paramount in elucidating organic chemical reactions and designing new synthetic pathways. In this study, we propose a nucleophilicity index within the framework of Conceptual Density Functional Theory (CDFT). Through rigorous theoretical formulations, we introduce an original quantum reactivity descriptor that captures the nucleophilic propensity of molecules based on their electronic structure and chemical environment. Subsequently, this proposed index is applied to a series of nucleophiles (pyrrolidines derivatives), spanning a diverse range of chemical functionalities. Our computational assessments reveal insightful correlations between the predicted nucleophilicity index and experimental observations of nucleophilic behavior. Thereby, they offer a promising avenue for advancing the understanding of organic reactivity and guiding synthetic efforts.

METHODS

Experimentally, Mayr's experimental parameters accounting for nucleophilicity were selected for the pyrrolidines. This study used DFT calculations at the B3LYP/Aug-cc-pVTZ level of theory using the Gaussian 16 program. Geometry optimization was thus performed, and the methodology employed for the computation of quantum reactivity descriptor is presented. Solvent effect was also taken into account using IEFPCM, and empirical dispersion correction (GD3) was employed.

Molecular Mechanisms of Drug Action: X-ray Crystallography at the Basis of Structure-based and Ligand-based Drug Design

Biological systems are recognized for their complexity and diversity and yet we sometimes manage to cure disease via the administration of small chemical drug molecules. At first, active ingredients were found accidentally and at that time there did not seem a need to understand the molecular mechanism of drug functioning. However, the urge to develop new drugs, the discovery of multipurpose characteristics of some drugs, and the necessity to remove unwanted secondary drug effects, incited the pharmaceutical sector to rationalize drug design. This did not deliver success in the years directly following its conception, but it drove the evolution of biochemical and biophysical techniques to enable the characterization of molecular mechanisms of drug action. Functional and structural data generated by biochemists and structural biologists became a valuable input for computational biologists, chemists and bioinformaticians who could extrapolate in silico, based on variations in the structural aspects of the drug molecules and their target. This opened up new avenues with much improved predictive power because of a clearer perception of the role and impact of structural elements in the intrinsic affinity and specificity of the drug for its target. In this chapter, we review how crystal structures can initiate structure-based drug design in general.

Analysis of Reaction Processes On the Basis of the Evolution of Dynamic Orbital Forces: Examples of Cycloadditions, SN 2 Substitution, Nucleophilic Addition, and Hydrogen Transposition

The derivative of the energy of a canonical molecular orbital (MO) [or dynamical orbital forces (DOFs)] with respect to a bond length provides a reliable index of the bonding/antibonding character of this MO on this bond. The DOFs of selected MOs as a function of the reaction coordinate were computed for a panel of model reaction mechanisms: [2+4] (Diels-Alder) cycloaddition, [2+2] cycloaddition, second-order nucleophilic substitution (S_N 2), nucleophilic addition to a carbonyl group, and [1,2] hydrogen transposition. The results highlight the nature of the reorganization of the main MOs and the stage of the reaction coordinate (RC) at which it occurs. For instance, in the Diels-Alder reaction, one can identify a part of the reaction that is dominated by repulsive four-electron interactions and another part dominated by attractive two-electron interactions. Also, the shape of the DOF as a function of the reaction coordinate reveals the existence of avoided MO crossings and their location on the RC. Even for spontaneous reactions with monotonic variation in the potential energy, extrema of the MO energy and sudden electron rearrangements can be put into evidence. This study provides quantitative support to classical MO analyses of reactivity such as correlation diagrams and frontier approximation.

Atomic Resolution for the Energy Derivatives on the Reaction Path

Definite algorithms for calculation of the atomic contributions to the reaction force Fξ and the reaction force constant kξ (the first and the second derivatives of the energy over the reaction path step) are presented. The electronic part in the atomic and group contributions has been separated, and this opened the way to identification of the reactive molecule fragments on the consecutive stages of the reaction path. Properties have been studied for the two canonical test reactions: CO + HF → HCOF and HONS → ONSH.