A Computational Study of Microhydrated N-Acetyl-Phenylalaninylamide (NAPA): Kinetics and Thermodynamics  

作　　者：Mohammad Alauddin Mohammad Masud Parvez Mohammad Abdul Matin Mohammad Alauddin;Mohammad Masud Parvez;Mohammad Abdul Matin(Department of Theoretical and Computational Chemistry, University of Dhaka, Dhaka, Bangladesh;Department of Chemistry, University of Barishal, Barishal, Bangladesh;Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh)

机构地区：[1]Department of Theoretical and Computational Chemistry, University of Dhaka, Dhaka, Bangladesh [2]Department of Chemistry, University of Barishal, Barishal, Bangladesh [3]Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh

出　　处：《Computational Molecular Bioscience》2023年第4期63-74,共12页计算分子生物学(英文)

摘　　要：The formations of [NAPA-A(H₂O)_n (n = 1, 2, 3, 4)] complexes have been studied employing DFT/wB97XD/cc-pVTZ computational level to understand the kinetics and thermodynamics for the hydration reactions of N-acetyl-phenylalaninylamide (NAPA). Thermodynamic parameters such as reaction energy (E), enthalpy (H), Gibb’s free energy (G), specific heat capacity (C_v), entropy (S), and change of these parameters (ΔE_r, ΔH_r, ΔGr, ΔC_r, and ΔS_r) were studied using the explicit solvent model. The predicted values of H, G, C, and S increase with the sequential addition of water in NAPA-A due to the increase in the total number of vibrational modes. On the other hand, the value of ΔE_r, ΔH_r, and ΔG_r increases (more negative to less negative) gradually for n = 1, 2, 3, and 4 that indicates an increase of hydration in NAPA-A makes exothermic to endothermic reactions. The barrier heights for the transition states (TS) of [NAPA-A(H₂O)_n (n = 1, 2, 3, 4)] complexes are predicted to lie at 4.41, 4.05, 3.72 and 2.26 kcal/mol respectively below the reactants. According to the calculations, the formations of [NAPA-A(H₂O)₁] and [NAPA-A(H₂O)₂] complexes are barrierless reactions because both water molecules are strongly bonded via two hydrogen bonds in the backbone of NAPA-A. On the contrary, the reactions of [NAPA-A(H₂O)₃] and [NAPA-A(H₂O)₄] complexation are endothermic and the barrier heights are predicted to stay at 6.30 and 10.54 kcal/mol respectively above the reactants. The free energy of activation (Δ^‡G⁰) for the reaction of [NAPA-A(H₂O)₁], [NAPA-A(H₂O)₂], [NAPA-A(H₂O)₃], and [NAPA-A(H₂O)₄] complexation are 4.43, 4.28, 3.83 and 5.11 kcal/mol respectively which are very low. As well as the rates of rThe formations of [NAPA-A(H₂O)_n (n = 1, 2, 3, 4)] complexes have been studied employing DFT/wB97XD/cc-pVTZ computational level to understand the kinetics and thermodynamics for the hydration reactions of N-acetyl-phenylalaninylamide (NAPA). Thermodynamic parameters such as reaction energy (E), enthalpy (H), Gibb’s free energy (G), specific heat capacity (C_v), entropy (S), and change of these parameters (ΔE_r, ΔH_r, ΔGr, ΔC_r, and ΔS_r) were studied using the explicit solvent model. The predicted values of H, G, C, and S increase with the sequential addition of water in NAPA-A due to the increase in the total number of vibrational modes. On the other hand, the value of ΔE_r, ΔH_r, and ΔG_r increases (more negative to less negative) gradually for n = 1, 2, 3, and 4 that indicates an increase of hydration in NAPA-A makes exothermic to endothermic reactions. The barrier heights for the transition states (TS) of [NAPA-A(H₂O)_n (n = 1, 2, 3, 4)] complexes are predicted to lie at 4.41, 4.05, 3.72 and 2.26 kcal/mol respectively below the reactants. According to the calculations, the formations of [NAPA-A(H₂O)₁] and [NAPA-A(H₂O)₂] complexes are barrierless reactions because both water molecules are strongly bonded via two hydrogen bonds in the backbone of NAPA-A. On the contrary, the reactions of [NAPA-A(H₂O)₃] and [NAPA-A(H₂O)₄] complexation are endothermic and the barrier heights are predicted to stay at 6.30 and 10.54 kcal/mol respectively above the reactants. The free energy of activation (Δ^‡G⁰) for the reaction of [NAPA-A(H₂O)₁], [NAPA-A(H₂O)₂], [NAPA-A(H₂O)₃], and [NAPA-A(H₂O)₄] complexation are 4.43, 4.28, 3.83 and 5.11 kcal/mol respectively which are very low. As well as the rates of r

关 键 词：Microhydration DFT Transition States KINETICS THERMODYNAMICS 

分 类 号：O62[理学—有机化学]