Chiral carbon centers are present in a wide array of biological molecules, and the loss or inversion of their stereochemistry leads to abnormal structure and function. One way that carbon centers reverse their stereochemistry is through racemization reactions by oxidative or reductive species. Protonated hypochlorous acid (ClOH2 +), formed spontaneously in vivo as a consequence of reactive oxidative species, can oxidize and abstract a hydride from its chiral carbon center, which produces a planar prochiral carbocation. This planar prochiral carbocation is susceptible to hydrogenation on either of its faces, allowing for inversion of its stereochemistry.
This study investigated the thermodynamics of the racemization of carbon stereocenter analogues methane, propane, and alanine, by hydride abstraction with ClOH2 + and hydrogenation from another stereocenter. Using ab initio calculations in Gaussian09 at the B3LYP/6-31G(d) level of theory, it was determined that the reaction is exergonic and characterized by a favourable energy of activation in vacuum. Racemization completed using an additional stereocenter as a hydride donor resulted in the exergonic formation of another prochiral carbon center in addition to the racemized stereocenter. This implied that biologically active chiral carbon centers may be spontaneously oxidized by ClOH2 + to form a reactive prochiral carbon, which may react with other monomers to form aberrant racemization products. This racemization of carbon stereocenters disrupts the structure and function of biological molecules, contributing to neurodegeneration, cardiovascular disease, and several age-related diseases.
A vast number of biological molecules, including nearly all amino acids and proteins, are stereospecific. Their specificity is crucial for normal functioning, and racemization may result in protein dysfunction that results in a host of human diseases [1]. The majority of amino acids in the human body are L-amino acids, with a small percentage of D-amino acids (D-AAs). While these D-AAs have selectively important physiological roles, their presence in high concentration can lead to disease in the central nervous system [2], vascular system [3], and musculoskeletal system [4]. Although degradative pathways for D-AAs do exist, they have not been extensively studied. If the rate of D-AA production is too high, these degradative processes may not be able to maintain normal levels of them [5]. Therefore, it is vitally important that the body maintain a low rate of D-AA formation.
In the past decade, it has become increasingly clear that natural oxidative processes important for biological functioning also contribute to an increase in D-AAs [6]. Generation of superoxide (O2 -) occurs as a by-product of many of these processes, which may be reduced to form a variety of reactive oxygen species (ROS) [7]. Superoxide spontaneously reacts with water to produce hydrogen peroxide (H2O2), which may be enzymatically converted to hypochlorous acid (HOCl) [8].
Cl– + H2O2 → HOCl + HO+
Cellular compartments specialized for degrading biomolecules, such as lysosomes and autophagosomes, have an acidic environment where the pH drops below 5.5 [9]. This allows localized and nearby chlorine species to be protonated and form protonated hypochlorous acid (ClOH2 +) [10]. Although it is known that there are enzymatic pathways for the synthesis of D-AAs, their spontaneous formation by oxidation and racemization of L-AAs by ROS such as ClOH2 + has not been studied [5]. It is known that HOCl may oxidize certain amino acid groups, but not the backbone of a peptide [11]. This study proposes that a more reactive form, ClOH2 +, may be potent enough to oxidize the alpha carbon of an amino acid, therefore catalyzing the formation of a prochiral carbocation intermediate and its racemization.
Computational chemistry approaches can be used to evaluate the viability of oxidative racemization of amino acids. Starting with simple carbon models such as methane and propane, then more complex protein residue structures such as alanine and alanine diamide, reactions involving ClOH2 + and the proton-alpha carbon moiety (H-Cα) of the models can be studied, and the thermodynamic values associated with hydride abstraction reactions can be determined. Furthermore, these approaches can be extended to evaluate a mechanism for the propagation of this racemization reaction involving a hydride transfer between two different alpha carbons.
Investigating a mechanism for the spontaneous ROS-mediated racemization of an amino acid model can illuminate a potential process through which D-AAs are generated in the cell. Although they are traditionally thought to arise from natural biosynthetic pathways, this study suggests that there may be a considerable amount of D-AAs derived from the racemization of L-amino acids by reaction with ROS. Further work on evaluating the viability of the propagation of this racemization by hydride transfer between the planar carbocation intermediate and other Cα to amplify the total amount of racemized alpha carbons in a chain-like reaction can prove useful as well. Analysis of the thermodynamics of these reactions will aid in evaluating the viability of ROS-promoted racemization.
Thermodynamic analysis of total (rovibrational + electrical) energy (ΔEtotal), enthalpy (ΔH), and Gibbs free energy (ΔG) of the reactants, transition states, intermediates, and products for the reactions in Figure 1 were determined through ab initio calculations using density function theory (DFT) at the B3LYP level of theory [12, 13] with a 6-31G(d) basis set [14] with an ultrafine grid integration. While the transition states of the reactions required the building of a unique Z-matrix to ensure appropriately- defined bond and angle parameters, the reactants and products were designed using GaussView 5 software [15] and the calculations were conducted using Gaussian09 software [16].
The reactants and products were optimized at a standard 297K in vacuo, which were then used to perform a frequency calculation in the same conditions to yield the thermodynamic values ΔE, ΔH, and ΔG. These values were then converted from Hartrees to kJ/mol, where 1 Hartree = 2625.5 kJ/mol in standard conditions. Using the optimized values of the bond lengths, bond angles, and dihedral angles from the calculations conducted on the reactants, the unique Z-matrices were designed to preserve these values as the initial points of the transition states and the intrinsic reaction coordinate (IRC) calculations. These were calculated with an initial force constant calculation, which was optimized to a transition state minimum.
The reactants and products were optimized at a standard 297K in vacuo, which were then used to perform a frequency calculation in the same conditions to yield the thermodynamic values ΔE, ΔH, and ΔG. These values were then converted from Hartrees to kJ/mol, where 1 Hartree = 2625.5 kJ/mol in standard conditions. Using the optimized values of the bond lengths, bond angles, and dihedral angles from the calculations conducted on the reactants, the unique Z-matrices were designed to preserve these values as the initial points of the transition states and the intrinsic reaction coordinate (IRC) calculations. These were calculated with an initial force constant calculation, which was optimized to a transition state minimum.
The calculations outlined in the previous section yielded values of ΔEtotal, ΔH, and ΔG for the reactants, transition states, intermediates, and products in (Figure 1). From these values, various vital thermodynamic values such as forward and reverse activation energy (ΔG‡f, ΔG‡r) and overall change in Gibbs free energy (ΔGreaction) were calculated. In interpreting the viability of the reactions from a thermodynamic standpoint, ΔG‡f and ΔGreaction are key indicators, and are shown in Figure 2 and Figure 3.
As a general measure of the relative stability of a given chemical species, the evolution of the Gibbs free energy as a function of the reaction coordinate plays a key role in understanding the oxidation reactions. These relationships are shown in Figure 4, Figure 5, and Figure 6.
We would like to acknowledge our appreciation to the Department of Chemistry and the Research Opportunity Program at the University of Toronto for the opportunity to conduct this study. We would like to thank Professor Csizmadia for his guidance, Natalie Galant for her overarching support of the entire group, and Anita Rágyanszki for her consistent support and assistance in times of great stress. We would also like to thank Nidaa Rasheed and Fiser Béla for their support, guidance, and technical assistance throughout the study, and every member of the Csizmadia group for fostering an environment that encouraged exploration and discovery across two continents.