Computational study on the adsorption and mechanisms of the hydrogenation of N-Cbz-protected glycine, alanine, valine, and phenylalanine on palladium, Pd (1 0 0), surface

Abstract

Materials Studio (MS) is powerful software (with various useful tools) that is designed for simulating and modeling of different molecules and materials in computational chemistry, cheminformatics, bioinformatics, and etc. Density functional theory (DFT), with periodic slab model, is one of the most applied theoretical approaches for understanding surface-adsorbate interaction strength and reactivity. In this study, DFT method have been used via Materials Studio software to study the adsorption (at T = 298.15 K, 308.15 K, and 318.15 K) and hydrogenation (at constant temperature T = 298.15 K) of four series of N-Cbz-protected amino acids (Cbz-aa’s include N-Cbz-L-phenylalanine, Cbz-pheala, N-Cbz-L-valine, Cbz-val, N-Cbz-L-alanine, Cbz-ala, and N-Cbz-L-glycine, Cbz-gly) on palladium, Pd (1 0 0), surface. During calculations of this study, a cell with periodic boundary conditions was constructed and each Cbz-aa was located and studied in this cell. For calculations of the hydrogenation of Cbz-aa’s on Pd (1 0 0) surface at constant temperature, Materials Studio QMERA (combined QM/MM methods) has been employed. For calculations of the adsorption of Cbz-aa’s on Pd (1 0 0) surface at different temperatures, the Materials Studio Sorption module has been applied. In the adsorption processes, average adsorption isosteric heat (Qst) and average total energy or overall system energies (Etotal) were extracted. In the hydrogenation processes, the energy of reaction (ΔH) and energy barrier (Eb) were obtained. In this study, three different mechanisms (mechanism 1: M1, mechanism 2: M2, and mechanism 3: M3) were suggested for the hydrogenation of each Cbz-aa on Pd (1 0 0) surface. We suggested these mechanisms based on the sites (atoms) that are probable for adding two hydrogen atoms (from H2) as well as the strength of bonds that should be broken for adding two hydrogen atoms (from H2). For these three mechanisms, the energy of reaction (ΔH), transition state, and energy barrier (Eb) were calculated. The obtained values of ΔH show that mechanism 3 (M3) provides the most facile mechanism to perform hydrogenation of Cbz-aa’s on Pd (1 0 0) surface. Further, the negative sign of ΔH for M3 shows that mechanism 3 is an exothermic reaction in the case of all our studied Cbz-aa’s. Hydrogenation and adsorption data show that Qst very slowly decreases and Etotal very slowly increases when temperature increases. Also, molecular weight and stereochemistry of Cbz-aa’s molecules are two important factors that affect the values of Qst, Etotal, Eb, and ΔH.