Ab initio Molecular Dynamics Simulation Study of Dissociation Electron Attachment to Lactic Acid and Isomer

Ying Zhang,Xiaoan Zhang,Zhongfeng Xu,Yongtao Zhao

doi:10.1038/s41598-019-56019-4

Abstract

Dissociation processes of lactic acid and its isomer formed by low-energy dissociation electron attachment (DEA) in the gas phase are investigated by using ab initio molecular dynamics (MD) simulations. The ab initio MD simulations using an atom-centered density matrix propagation (ADMP) method are carried out to investigate the DEA dissociation process of lactic acid and its isomer. The analysis of the simulated dissociation trajectories of lactic acid and its isomer indicates that the C-C, C-H, and C-O bonds are cleaved within femtoseconds of the simulation time scale in the DEA dissociation process, and the difference in dissociation trajectory depends on the size of the three basis sets. The simulation results enable us to gain insights into the DEA dissociation process of lactic acid and its isomer. In this work, we present a comparative study of the 6-31 + G(d,p), 6-311++G(2d,2p), and Aug-cc-pVDZ basis sets of the DEA dissociation simulation of lactic acid and its isomer. The comparative study results indicate that the 6-311++G(2d,2p) is an excellent basis set for the ADMP trajectory simulation of lactic acid and its isomer in the DEA dissociation process. The natural bond orbital (NBO) analysis is carried out to characterize variation in the charge population and charge transfer accompanied by the C-C, C-H, and C-O bond dissociation processes for lactic acid and its isomer in the ADMP trajectory simulation. ADMP simulation and NBO analysis of the dissociation trajectory is considered an important initial and decisive step in DEA dissociation dynamics for lactic acid and its isomer.

Highlights

To account for the underlying dynamics in radiation damage with biological systems, a large number of secondary particles, such as low-energy electrons, should be considered; the generation of these particles leads to irreversible damage to cellular, DNA nucleobases, organic acids, and amino acids[1,2,3,4,5,6]
The dissociation dynamics of lactic acid and its isomer in gas phase for the dissociation electron attachment (DEA) process is investigated by using ab initio molecular dynamics (MD) simulations combined atom-centered density matrix propagation (ADMP) method
The ADMP simulations coupled with the Becke3-parameter Lee-Yang-Parr (B3LYP) theory of the 6-31G + (d,p), 6-311++G(2d,2p), and Aug-cc-pDVZ basis sets are employed to optimize the ground state geometries and obtain dipole moments and harmonic vibrational frequencies of lactic acid and its isomer

Summary

Introduction

To account for the underlying dynamics in radiation damage with biological systems, a large number of secondary particles, such as low-energy electrons (less than 20 eV), should be considered; the generation of these particles leads to irreversible damage to cellular, DNA nucleobases, organic acids, and amino acids[1,2,3,4,5,6]. The intensive DEA research on biological systems (e.g., DNA, proteins, and amino acids) focuses on electron attachment mechanism and molecule dissociation dynamics[10,11,12,13,14,15,16]; limited studies report the lactic acid dissociation dynamics in the DEA process. Previous theoretical studies using Schwinger multichannel method, single-center expansion quantum scattering calculation method, eigenchannel R-matrix method, and R-matrix method on DEA dissociation dynamics calculations obtained excellent results[15,16,17,18,19] These studies concentrated on characterizing the dissociation dynamics of electron molecule resonance in physics[20], but they could not simulate the subsequent dissociation process.

Methods

Results

Conclusion