Ab Initio Molecular Dynamics Simulation Study of Dissociative Electron Attachment to Dialanine Conformers

Abstract

Dissociative electron attachment (DEA) processes of six low-lying conformers (1-6) of dialanine in the gas phase are investigated by using ab initio molecular dynamics simulations. The incoming electron is captured and primarily occupies the virtual molecular orbital π*, which is followed by the different dissociation processes. The electron attachments to conformers 1 and 2 having the stronger N-H···N and O-H···O intramolecular hydrogen bonds do not lead to fragmentations, but two different backbone bonds are broken in the DEAs to conformers 3 (or 4) and 6, respectively. It is interesting that the hydrogen abstraction of -NH from the terminal methyl group -CH3 is found in the roaming dissociation of the temporary anion of conformer 3. The present simulations enable us to have more insights into the peptide backbone bond breaks in the DEA process and demonstrate a promising way toward understanding of the radiation damages of complicated biological system.

Unimolecular decomposition pathways of negatively charged nitriles by ab initio molecular dynamics

“…Moreover, in numerous studies hybrid functionals are used in combination with ab initio molecular dynamics (AIMD), 16 which has shown great promise in the interpretation of dissociation dynamics and decomposition pathways relevant to DEA. [17][18][19][20][21][22] Here we describe a first implementation of a negative-ion mode within the QCEIMS 23 approach. QCEIMS is a systematic, robust, and exhaustive way of simulating unimolecular decomposition pathways of now both molecular radical cations and anions in great detail.…”

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

“…The dipole moment µ in Table 1 displays that the values are larger than 2.8 D with the three different basis sets. According to previous research 21,31 , a large dipole moment indicates the formation of valence-bound anion and the existence of strong electrostatic dipole fields, benefitting the capture of low-energy electron in the DEA process. However, these dipole moments perform poorly in the dissociation trajectory simulation.…”

“…The ground state geometry of lactic acid and isomer are optimized by employing the Becke3-parameter Lee-Yang-Parr (B3LYP) functional of the density functional theory 30 coupled with the 6-31 + G(d,p), 6-311++G(2d,2p), and Aug-cc-pVDZ basis sets. This level of theory, which is highly efficient and has become one of the most preferred theoretical methods of geometry optimization and DEA dissociation process in complicated biomolecules systems, successfully predicts the experimentally observed dissociation process 21 . Vibrational frequency calculations are performed to verify that the optimized lactic acid and its isomer correspond to a local minimum at the B3LYP theory level.…”

“…Ab initio molecular dynamics (MD) simulations founded on quantum mechanics methods are available and provide insights into the dissociation dynamics of complicated biomolecules. This approach is well suited for the dissociation dynamics of biological systems, such as dialamine conformers 21 . The recent research of ab initio MD used an extended Lagrangian MD method, which includes atom-centered Gaussian basis functions and one-particle electronic density matrix propagation 22–25 .…”

On-the-fly dynamics simulations of transient anions

“…If the system of interest is a large molecule, one has to restrict the multidimensional potential energy surfaces to one 21 or two 17 vibrational coordinates. Molecular dynamics simulations are sometimes employed for the later stages of DEA, [22][23][24] but without accounting for the autodetachment probability of its initial stage, when the anion is still transient. Alternatively, potential energy curves computed along reaction coordinates can also help understanding DEA mechanisms.…”