SAAD DAHLAB University, Blida 1

Faculty of Natural and Life Sciences

From Quantum Chemistry to Drug Design: A Kinetic–Thermodynamic Study

1 Department of process engineering, Faculty of Science and technology, University of Saida, BP 138, Saida. Algeria.

2 Department of Chemistry, Faculty of Science and technology, University of Saida, BP 138, Saida. Algeria.

* E-mail: [Link]@[Link]

Computational Method
All quantum chemical calculations were carried out using the Gaussian 09 software suite. The geometry optimizations and electronic structure
calculations were performed using Density Functional Theory (DFT) with the M05-2X hybrid functional and the 6-31+G(d) basis set. This level of
theory has been shown to provide an accurate balance for calculating thermodynamic and kinetic parameters in free radical scavenging reactions.

Solvent effects were incorporated using the SMD (Solvation Model based on Density) continuum solvation model. To simulate biologically relevant
environments, calculations were conducted in two solvents: pentyl ethanoate (to model a lipid medium) and water (to model an aqueous medium).

Vibrational frequency analyses were performed at the same level of theory to characterize all stationary points. Local minima were confirmed by
the absence of imaginary frequencies, while transition states were identified by a single imaginary frequency corresponding to the intended
reaction coordinate. The connection between transition states and correct minima was verified via Intrinsic Reaction Coordinate (IRC)
calculations.

Standard thermodynamic corrections were applied to calculate enthalpies and Gibbs free energies at 298.15 K and 1 atm. The kinetic analysis was
conducted using conventional Transition State Theory (TST), allowing the calculation of individual and overall rate constants (*k*) for the radical
scavenging processes. The assessment of overall antioxidant activity followed the validated QMORSA (Quantum Mechanics-based test for Overall
Radical Scavenging Activity) protocol.

PKa Study
The acid-base equilibria of the bromophenol analogs were investigated. The pKa values for the first deprotonation were estimated using a fitted
parameter (FP) method, which correlates experimental pKa data with computed Gibbs free energy differences in solution between the acidic and
conjugate base forms. The molar fractions of the neutral and anionic species at physiological pH (7.4) were subsequently derived from these
calculated pKa values.

This computational pKa analysis provides a critical foundation for the kinetic modeling. It confirms that for most tested bromophenol analogs
(except compound 2), the anionic species plays a non-negligible to major role in their antioxidant activity in aqueous environments at physiological
pH. This directly explains the observed dominance of the SPLET mechanism in water, as the anionic form is a key reactant in this pathway. The
data also allow for the precise calculation of pH-dependent overall rate constants by weighting the contribution of each acid-base species.

Figure 2 illustrates the optimized transition state geometries for the most favorable Hydrogen Atom Transfer (HAT) pathway at the
reactive site 2a in an aqueous environment. The structures reveal the characteristic elongation of the O–H bond in the bromophenol and
the approaching O–O bond of the CH₃OO• radical. A comparison of the imaginary frequencies (IF) among the compounds provides
insight into the stiffness of the transition state and correlates with their calculated kinetic efficiency, visually supporting the finding that
reactivity is enhanced in polar solvents.

Table 3 presents the decisive kinetic data, quantifying the radical scavenging speed of the compounds. It conclusively
shows that the designed Compound 5 is the most potent, with a rate constant 4,159 times greater than ascorbic acid in
lipid media. The table also highlights the dramatic solvent effect, where reactivity increases substantially in water, and
confirms the anionic form as the primary active species in aqueous solution.

The details of the branching ratios, revealing the contribution of each reaction pathway to the overall activity. It
demonstrates a clear mechanistic shift: the HAT mechanism dominates (100%) in lipid media, while in water, the SPLET
mechanism, facilitated by the anionic species, becomes the major pathway (e.g., ~72% for Compound 4). This table
directly links the speciation (pKa) to the operative chemical mechanism.

Table 3 focuses on the enhanced kinetics of the designed Compound 5 in direct comparison to ascorbic acid. It
consolidates the key result that Compound 5 is the superior antioxidant across both solvents. The data underscores the
success of the rational design strategy, showing exceptionally high rate constants and confirming the SPLET mechanism
as dominant for this compound in aqueous environments.