Density Functional Theory Charge Delocalization Error Determines Computed Activation Barriers in Enzymatic Kemp...

Area of Science:

• Computational chemistry
• Enzyme design
• Biocatalysis

Background:

• Kemp elimination is a key reaction in computational enzyme design, with engineered enzymes showing high activity.
• The reaction's apparent simplicity (exergonic, single-step, base-catalyzed) has made it a focus for computational studies.
• Recent findings necessitate a re-evaluation of computational strategies for studying Kemp eliminases.

Purpose of the Study:

• To systematically analyze the barrier height and transition-state geometry of Kemp elimination catalyzed by HG3.17.
• To assess the sensitivity of these quantities to computational parameters, particularly the fraction of Hartree-Fock exchange in density functional theory (DFT).
• To re-evaluate the reliability of computational methods in predicting enzyme performance.

Main Methods:

• Static Quantum Mechanics/Molecular Mechanics (QM/MM) calculations were employed.
• Systematic variation of the fraction of Hartree-Fock exchange in the density functional.
• Analysis of activation barriers and transition-state geometries.

Main Results:

• Barrier heights and transition-state geometries are highly sensitive to the fraction of Hartree-Fock exchange, attributed to charge-delocalization error in DFT.
• Calculated activation barriers for the catalytic step range from 1-14 kcal/mol, with minimal basis-set effects.
• The reaction mechanism (synchronous, concerted, or stepwise) appears dependent on the computational level of theory.

Conclusions:

• Apparent agreement between computational predictions and experimental rate constants may be misleading.
• Numerical parameters in simulations, such as the fraction of Hartree-Fock exchange, significantly influence results.
• Caution is advised against using agreement with experiment as the sole criterion for assessing simulation quality in enzyme design.