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

Area of Science:

• Computational enzymology
• Quantum chemistry
• Enzyme design

Background:

• Kemp elimination is a fundamental 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 investigate the sensitivity of these quantities to computational parameters, particularly Hartree-Fock exchange in density functional theory (DFT).
• To reassess the reliability of computational methods in predicting enzyme performance and reaction mechanisms.

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 was performed.
• Analysis of activation barriers and transition-state geometries was conducted.

Main Results:

• Barrier heights and transition-state geometries exhibit high sensitivity to the fraction of Hartree-Fock exchange, attributed to charge-delocalization error in DFT.
• Calculated activation barriers for the catalytic step range from 1 to 14 kcal/mol, with minimal basis-set effects.
• The reaction's mechanistic description (synchronous, concerted, or stepwise) depends on the computational level of theory used.

Conclusions:

• Apparent agreement between computational predictions and experimental rate constants can be misleading due to parameter sensitivity and experimental condition complexities.
• Computational strategies must account for DFT's charge-delocalization error and the level of theory's influence on mechanism.
• Agreement with experiment should not be the sole criterion for assessing the quality of computational simulations in enzyme design.