Water-assisted proton transfer in ferredoxin I

Reaction Mechanisms and Kinetics of Nanozymes: Insights from Theory and Computation

"Nanozymes" usually refers to inorganic nanomaterials with enzyme-like catalytic activities. The research into nanozymes is one of the hot topics on the horizon of interdisciplinary science involving materials, chemistry, and biology. Although great progress has been made in the design, synthesis, characterization, and application of nanozymes, the study of the underlying microscopic mechanisms and kinetics is still not straightforward. Density functional theory (DFT) calculations compute the potential energy surfaces along the reaction coordinates for chemical reactions, which can give atomistic-level insights into the micro-mechanisms and kinetics for nanozymes. Therefore, DFT calculations have been playing an increasingly important role in exploring the mechanisms and kinetics for nanozymes in the past years. The calculations either predict the microscopic details for the catalytic processes to complement the experiments or further develop theoretical models to depict the physicochemical rules. In this review, the corresponding research progress is summarized. Particularly, the review focuses on the computational studies that closely interplay with the experiments. The relevant experimental results without DFT calculations will be also briefly discussed to offer a historic overview of how the computations promote the understanding of the microscopic mechanisms and kinetics of nanozymes.

Vibrational Spectroscopy and Proton Transfer Dynamics in Protonated Oxalate

The dynamics and infrared spectroscopic signatures of proton transfer in protonated oxalate (p-Oxa) are studied using classical and quantum dynamics. The intermolecular interactions are described by a force field suitable to follow proton transfer. This allows to carry out multiple extended classical molecular dynamics (MD) and ring polymer MD simulations from which the infrared spectrum is determined. Simulations at 600 K sample the quantum mechanical ground state probability distribution and best reproduce the experimentally observed maximum absorption wavelength and part of the line shape. Comparison with the experimentally measured spectrum provides an estimate for the barrier height for proton transfer which can not be determined directly from experiment. A barrier of 4.2 kcal/mol is found to best reproduce the position and width of the infrared absorption of the transferring proton in p-Oxa and also leads to an infrared (IR) spectrum in good agreement with experiment for the deuterated species d-Oxa. A novel means to capture the two resonance forms of oxalate depending on the localization of the excess proton on either CO moiety is found to yield improved results for the spectroscopy in the framework region between 1000 and 2000 cm^-1.

Spectroscopy and dynamics of double proton transfer in formic acid dimer

We present the isolated gas phase infrared spectra of formic acid dimer, (HCOOH)2, and its deuterated counterpart formic-d acid, (DCOOH)2, at room temperature. The formic acid dimer spectrum was obtained by spectral subtraction of a spectrum of formic acid vapor recorded at low pressure from that recorded at a higher pressure. The spectra of formic acid vapor contain features from both formic acid monomer and formic acid dimer, but at low and high pressures of formic acid, the equilibrium is pushed towards the monomer and dimer, respectively. A similar approach was used for the formic-d acid dimer. Building on the previous development of the Molecular Mechanics with Proton Transfer (MMPT) force field for simulating proton transfer reactions, molecular dynamics (MD) simulations were carried out to interpret the experimental spectra in the OH-stretching region. Within the framework of MMPT, a combination of symmetric single and double minimum potential energy surfaces (PESs) provides a good description of the double proton transfer PES. In a next step, potential morphing together with electronic structure calculations at the B3LYP and MP2 level of theory was used to align the computed and experimentally observed spectral features in the OH-stretching region. From this analysis, a barrier for double proton transfer between 5 and 7 kcal mol(-1) was derived, which compares with a CCSD(T)/aug-cc-pVTZ calculated barrier of 7.9 kcal mol(-1). Such a combination of experimental and computational techniques for estimating barriers for proton transfer in gas phase systems is generic and holds promise for further improved PESs and energetics of these important systems. Additional MD simulations at the semi-empirical DFTB level of theory agree quite well for the center band position but underestimate the width of the OH-stretching band.

Reaction Pathway and Free Energy Barrier for Urea Elimination in Aqueous Solution

To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25.3 kcal/mol. The free energy barrier of 25.3 kcal/mol predicted for the dominant reaction pathway of urea elimination in aqueous solution is in good agreement with available experimental kinetic data.

A sugar isomerization reaction established on various (βα)₈-barrel scaffolds is based on substrate-assisted catalysis

In the course of tryptophan biosynthesis, the isomerization of phosphoribosylanthranilate (PRA) is catalyzed by the (βα)₈-barrel enzyme TrpF. The reaction occurs via a general acid-base mechanism with an aspartate and a cysteine residue acting as acid and base, respectively. PRA isomerase activity could be established on two (βα)₈-barrel enzymes involved in histidine biosynthesis, namely HisA and HisF, and on a HisAF chimera, by introducing two aspartate-to-valine substitutions. We have analyzed the reaction mechanism underlying this engineered activity by measuring its pH dependence, solving the crystal structure of a HisF variant with bound product analogue, and applying molecular dynamics simulations and mixed quantum and molecular mechanics calculations. The results suggest that PRA is anchored by the C-terminal phosphate-binding sites of HisA, HisF and HisAF. As a consequence, a conserved aspartate residue, which is equivalent to Cys7 from TrpF, is properly positioned to act as catalytic base. However, no obvious catalytic acid corresponding to Asp126 from TrpF could be identified in the three proteins. Instead, this role appears to be carried out by the carboxylate group of the anthranilate moiety of PRA. Thus, the engineered PRA isomerization activity is based on a reaction mechanism including substrate-assisted catalysis and thus differs substantially from the naturally evolved reaction mechanism used by TrpF.