Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Summary

A protocol that uses enhanced QM/MM method to investigate the isotopic effect on the double proton transfer process in porphycene is presented here.

Abstract

The single deuterium substitution in porphycene leads to an asymmetric molecular geometry, which may affect the double proton transfer process in the porphycene molecule. In this study, we applied an enhanced QM/MM method called SITS-QM/MM to investigate hydrogen/deuterium (H/D) isotope effects on the double proton transfer in porphycene. Distance changes in SITS-QM/MM molecular dynamics simulations suggested that the deuterium substituted porphycene adopted the stepwise double proton transfer mechanism. The structural analysis and the free energy shifts of double proton transfer process indicated that the asymmetric isotopic substitution subtly compressed the covalent hydrogen bonds and may alter the original transition state location.

Introduction

The proton transfer process in porphycenes holds potential applications in developing molecular switches, transistors and information storage devices^1,2. In particular, tautomerization in porphycenes through double proton transfer process has attracted wide interest in the fields of spectroscopy and photophysics². The inner hydrogen atoms of porphycene can migrate from one trans isomer to the other equivalent trans isomer through double proton transfer process as shown in Figure 1. Two mechanisms have been proposed for the double proto....

Protocol

1. Building model

1. Build porphycene structure: Open GaussView software by double-click the mouse. Then click Element Fragment button in the menu of the GaussView to choose the needed elements. Construct porphycene. Then click File button to save as the pdb file.
2. Solvate the model: Solvate porphycene in a cubic TIP3P²¹ water box with an edge length of 38 Å by issuing the command in the linux operating system: genbox_d -cp prp-vac.pdb -cs spc216.gro -o solv.pdb -maxsol 1484 -box 3.8.

Results

The single deuterium substitution effect on double proton transfer process in porphycene was examined in the current protocol (Figure 1). The potential energy of QM sub-system and the water during pre-equilibrium and optimization step were checked to make sure the energy has been broadened to a wider energy range (Figure 2). The representative distance and angle changes (Figure 3 and Figure 4), and the .......

Discussion

The structure of porphycene was shown in Figure 1. The electrostatic embedding QM/MM hybrid potential with SITS method was used to describe the chemical reactions in water^23,24. The proton transfer occurs within porphycene³ and thus porphycene is set as QM region and the reminding water is set as MM region. Herein we adopted DFTB/MIO as our QM method to treat the porphycene by balancing the efficiency and accu.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
operating system	CentOS Linux release 6.0
QM4D software	http://www.qm4d.info/		in-house program
Computer desktop	HP