Revealing Novel Mechanism Of S_N2 Reaction Using Ab Initio Molecular Dynamics

The bimolecular nucleophilic substitution reaction,also known as S_N2 reaction,is a very important class of reactions in organic and bio-chemistry.Where S represents"substitution",N represents"nucleophilic",and 2 represents the reaction rate depending on the concentration of the two reactant molecules.In the past studies on the dynamics of S_N2 reactions,researchers usually investigate the reaction mechanisms based on constructed potential energy surfaces.However,there are drawbacks in such studies based on constructued potential energy surfaces.First,the dynamics of the reaction can only simulate the existing reaction paths on the potential energy surface,including transition states,reactant complexes,and product complexes.Therefore,dynamics calcution can only simulate existing mechanism on the potential energy surface.In addition,the construction of potential energy surfaces is very difficult.Most potential energy surfaces are not full-dimensional potential energy surfaces.This means that some important reaction paths will be missed and the reaction mechanism of the reaction cannot be fully revealed.Besides,to date,the potential energy surface of the reaction system with more than 7 atoms have not be constructed yet.It is difficult to describe the polyatomic reaction system based on the potential energy surface method.In our study,we used a modified ab initio molecular dynamics method to study the mechanisms of the S_N2 reaction.The method we use does not require the construction of a potential energy surface in advance.Instead,it uses a method called“on the fly”to perform dynamic simulations.The principle of this simulation is:First,according to the Born Oppenheimer approximation,we first fix the entire reaction atomic nuclei,and then calculate the potential energy part of the system through the density functional theory.According to the obtained potential energy,we can calculate the force of the atomic nuclei,and then by using Newtonian mechanics,specifically the velocity Verlet algorithm,computes the movement of nuclei within a short period of time.The entire calculation process is then repeated until the reaction is over or the reaction no longer occurs.Such a calculation method does not need to construct the entire potential energy surface in advance,but calculates a potential energy for each movement step,so it is called"on the fly"method.Recent studies have improved our understanding of the mechanism and dynamics of bimolecular nucleophilic substitution?S_N2?reaction at carbon center.Take F?+CH₃Cl as an example.So far,researchers have found eight reaction mechanisms.The first is three direct reaction mechanisms.Includes rebound,stripping mechanisms,and front-side attack mechanisms.The rebound mechanism and the stripping mechanism are very similar.They all have a transition state of backside attack.However,the difference is that the kinetic energy distribution of the products is very different.In the rebound mechanism,the kinetic energy of the reaction system is mostly concentrated on the leaving group,but in the stripping mechanism,the opposite is true.Not only that,there is a difference in the probability of occurrence of the two impact parameters:When the impact parameter is small,the rebound mechanism contributes more to the reaction,and when the impact parameter is larger,the stripping mechanism accounts for a higher proportion of the total reaction mechanism.The front-side attack mechanism is different from the former.The front-side attack mechanism will directly break the chemical bond between the leaving group and the center atom,which requires a higher initial collision energy.In addition,there are five indirect reflection mechanisms,including ion complex mechanism,hydrogen bond mechanism,roundabout mechanism,front-side complex mechanism,and double-inversion mechanism.The ion complex mechanism means that the reactants will first form an ion complex and then the back side attack mechanism will end the reaction.The hydrogen bond mechanism means that the attacking group first hydrogen bonds with a hydrogen atom and then completes the reaction by Walden inversion.The roundabout mechanism refers to that the attacking group first rotates one or two circle around the substituent under the guidance of weak interactions,and then the back-side attack mechanism occurs.This reaction mechanism has been observed in experimental research.The front-side complex mechanism means that the F ion first forms a complex with the leaving group,and then it wraps around to the backside and complete the reaction by Walden inversion.The recently discovered double inversion mechanism is that the reaction system first undergoes a process of inducing inversion and then Walden inversion completes the entire reaction process,so the double inversion mechanism is called.Nonetheless,the S_N2 reaction at nitrogen center has received less attention and is less understood.Here in chapter 3,we report a new reaction mechanism for the S_N2 reaction at nitrogen center F?+NH₂Cl using ab initio molecular dynamics calculations.The new mechanism involves the rotation of NHCl with one proton of NH₂Cl abstracted by the nucleophile,followed by a classical,backside-attack process.A double inversion mechanism,first revealed recently for the S_N2 reaction at carbon center,is also observed for the title reaction at nitrogen center.In contrast to the F?+CH₃Cl with a proton-abstraction induced first inversion transition state,the F?+NH₂Cl is a hydrogen-bond induced inversion.The new reaction mechanism opens a reaction channel to avoid the proton-abstraction mechanism at low collision energy.The double inversion mechanism of the title reaction with a negative first-inversion transition is expected to have a larger contribution to the reaction rate than the F?+CH₃Cl with a positive first-inversion transition state.In the fourth chapter of this paper,we also reported a new mechanism in the F?+CH₃Cl reaction.This mechanism has the same transition state as the proton transfer mechanism but avoids the proton transfer reaction channel.It is a reaction mechanism in which protons surround and combine with the backside attack mechanism.It has never been found in previous studies.It is worth noting that there is a hydrogen transfer process in this new mechanism,involving both hydrogen bonds of C-H-F and Cl-H-F.At lower collision energies,this mechanism provides a new reaction channel for the proton transfer mechanism.This shows that the exploration of the S_N2 response mechanism is far from over.More in-depth exploration of the theoretical and experimental studies of the S_N2 reaction mechanism needs to be carried out to study a variety of S_N2 reactions including aqueous and slightly soluble reactions.Ab initio molecular dynamics methods also shows great research potential,and researchers can try to use this method to study reactions that contain more atoms.We think the new proposed mechanisms,the PAR&BAR and double-inversion mechanism,should occur for all the X?+NH2Y[X,Y=F,Cl,Br,I]SN2 reaction at N center,furthermore,they may be general mechanism for S_N2 reactions.Moreover,in this study,we only investigated the reaction mechanisms of the F?+NH₂Cl reaction.The reactivity of each mechanism has not been quantitatively determined at different energy range.Additional work needs to be done to probe the reaction mechanism,especially the new proposed PAR&BAR mechanism,both in gas phase and solution phase and to study the dynamical quantities of the S_N2 reaction at N center.