Chemical Dynamics Simulations Studies On The Dissociation And Collision Mechanisms Of Peptides Containing Arginine

Peptides are important substances for the metabolic functions of living organisms.Arginine is an essential amino acid within the human body,hence it is a very important structure to study.An effective method for studying peptide ion structures is mass spectrometry,however,peptide ions that contain arginine are prone to cyclisation and rearrangement.The structure cannot be accurately determined by mass spectrometry due to deviations.This paper finds the dynamic mechanisms of peptide ions that contain arginine by studying the effects of the dissociation sites,collision processes and energy transfer efficiencies.This study provides important theoretical support towards how mass spectrometry can be used to identify peptide ion structures and surface modifications of arginine.Glycine-arginine(GR-H⁺)is the simplest form of dipeptide ion that contains arginine.Chemical dynamics simulations were used to study both the collision induced and thermal dissociation pathways of GR-H⁺using the initial collision energies of 13,15,20 and 25 e V and vibration temperatures of 2000,2500,3000 and3500 K with corresponding vibration energies of 17,21,25,and 29 e V,respectively.The Rice-Ramsperger-Kassel-Marcus(RRKM)theory was used to calculate the rate constants and the Arrhenius parameters of GR-H⁺thermal dissociation,with discussions on the affects of the different excitation modes on the dissociation mechanisms.GR-H⁺dissociation mainly consists of two types:side chain fracture and skeleton fracture.The sites of collision induced dissociation are more abundant than those of thermal decomposition.By comparing with experimental results,the reliability of the calculation results is confirmed,and the theoretical calculations provide a theoretical reference for analyzing the structural formula and dissociation pathways that cannot be determined experimentally.The collision mechanisms of arginine-free peptide ions(gly_n-H⁺n=3,5,and7)and perfluorinated hydrocarbon surfaces(F-SAM)were studied using chemical dynamics simulations.The influences can be discussed from collision energies,peptide ions size and surface properties on the reaction mechanisms,trapping properties and energy transfer efficiencies during collision.For collisions between gly₃-H⁺,gly₅-H⁺or gly₇-H⁺and F-SAM,the probability of the trapping mechanism decreases with an increase in collision energy,and the probability increases with an increase in peptide size.The limiting probability(P₀)of energy transfer to the surface is provided by fitting the P₀exp(–b/E_i)function.The corresponding P₀ values of gly₃-H⁺,gly₅-H⁺and gly₇-H⁺are 0.82,0.80 and 0.77 respectively,which indicates that there is a slight decrease in the average percentages for surface vibrations P(?E_surf)with an increase in the size of peptide ions.Surface properties are,therefore,an important factor in determining energy transfer efficiencies.The force field parameters were developed for Arg/F-SAM by fitting the high-level interaction potential between C⁺(NH₂)₃ and CF₄,based on Buckingham function.Chemical dynamics simulations were studied to explore the collision processes of arginine-containing peptide ions(GR-H⁺)and F-SAM.The influences can be discussed from collision energies,peptide ions size,surface properties and arginine on the reaction mechanisms and trapping properties during collision.Three trajectory types(direct scattering,temporary sticking,and trapping)were observed during the collisions between GR-H⁺and F-SAM.The probability of trapping trajectories notably decreases with an increase in E_i,when?_i is increased from 0°to 45°.GR-H⁺penetrated F-SAM at the 5th-6th midpoint,which is greater than the gly_n system due to the stronger interaction between the protonated guanidino group and F-SAM.The average percentage of energy transfer to the GR-H⁺internal degrees of freedom is only slightly dependent on the collision energy,incident angle,and size of the ions.However,surface properties were highlighted as an important factor in determining energy transfer efficiencies,as the F-SAM serve as a“hard wall”and therefore transfer increased internal energy to the peptide ions.