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In previous research, direct dynamics simulations have been used to provide atomistic information for the Cl− + CH3I, F− + CH3I, and OH− + CH3I SN2 and proton transfer (PT) reactions. An important component of these simulations is comparison with molecular beam, ion imaging experiments. From the simulations, comparisons may be made with the product translational energy distributions determined from the experiments and the simulations give quite good agreement with these distributions. Though the experiments provide the in-plane angular distribution for a reaction’s product translational energy distribution, the number of direct dynamics trajectories for a simulation is not sufficient to compare with this angular distribution. In the work presented here, the average percentage product translational energy partitioning for forward scattered events with scattering angle θ = 0–90° and for backward scattered events with θ = 90–180° are compared for the experiments and simulations. Overall good agreement is found, with a maximum difference as high as 5–10%. Additional atomistic details, regarding the dynamics of these reactions, are provided by scatter plots of their product relative translational energy versus the scattering angle θ.

Direct dynamics simulations were performed to investigate unimolecular dynamics of the F − ⋯HCH 2 I pre-reaction complex for the F − + CH 3 I S N 2 reaction. The simulations were performed for a total energy commensurate with the 0.32 eV collision energy considered in previous experiments and simulations of this reaction. Two excitation patterns of the complex were considered for the simulations: one with the excitation energy primarily in vibration and the other with the energy primarily in rotation. For the latter equal amounts of energy were added about the three external rotation axes of the complex, giving rise to J and K rotation quantum numbers of 357 and 66 for the initial excitation. For the vibrational excitation the unimolecular dynamics agrees with RRKM theory and dissociation of the complex to the F − + CH 3 I reactants is negligible, since the barrier for this reaction is 20.2 kcal/mol in contrast to the 2.4 kcal/mol barrier for accessing the S N 2 transition state (TS). The unimolecular dynamics are much different for the rotational excitation simulation. They are non-RRKM and the instantaneous unimolecular rate constant for F − ⋯HCH 2 I decomposition increases with time. Apparently, this arises from K -mixing and vibration/rotation energy redistribution. At the end of the 10 ps simulation, the instantaneous simulation rate constant for accessing the S N 2 transition state is an order of magnitude smaller than the harmonic RRKM rate constant with the K quantum number treated as an active degree of freedom, indicating that K -mixing and vibration/rotation energy redistribution are not complete on this time scale. For rotational excitation, dissociation to the F − + CH 3 I reactants is the dominant unimolecular pathway, instead of forming the S N 2 products. This is a result of a much higher rotational barrier at the S N 2 TS than for the TS leading to F − + CH 3 I.

The rate constant for OH − (H 2 O) 2 + CH 3 I reaction was determined by selected ion flow tube (SIFT) experiments for temperatures in the range of 298–398 K. It is found to be an order of magnitude smaller than the collision capture rate constant, a result substantially different than found previously for the OH − + CH 3 I and OH − (H 2 O) + CH 3 I reactions. The rate constants for these reactions are only ∼25% and ∼two times smaller, respectively, than their collision capture rate constants. Only two product ions are observed experimentally, i.e. I − and I − (H 2 O), and their respective percentage yields are 90:10 and 83:17 at 298 and 348 K. The kinetics for the OH − (H 2 O) 2 + CH 3 I reaction were also studied by direct dynamics simulations using the DFT/B97-1/ECP/d electronic structure theory, the same theory used in previous direct dynamics simulations of the OH − + CH 3 I and OH − (H 2 O) + CH 3 I reactions. Simulations for OH − (H 2 O) 2 + CH 3 I at 387 K give respective percentage yields of 91:9 for I − and I − (H 2 O), in good agreement with the experimental results. For both the experiments and simulations, the microsolvated ion I − (H 2 O) 2 is not formed and the formation of I − dominates I − (H 2 O). For the OH − + CH 3 I and OH − (H 2 O) + CH 3 I reactions the experimental and direct dynamics simulation rate constants agree. However, this is not the case for OH − (H 2 O) 2 + CH 3 I, for which the simulation rate constant is 8–9 times larger than the experimental value. Comparisons of the experimental, simulation, and collision capture rate constants for the OH − (H 2 O) 2 + CH 3 I reaction indicate the height of the submerged S N 2 barrier for the reaction is an important feature of its potential energy surface. The actual barrier is expected to be higher than the value given by the DFT/B97-1 calculations. In future work it will be important to perform higher level electronic structure calculations and establish an accurate value for this barrier. Preliminary calculations reported here indicate the barrier height is sensitive to the electronic structure method.

A recent guided ion beam study of the HCl + HCl+ reaction has revealed two different products [Phys. Chem. Chem. Phys. 2015, 17 (25), 16454–16461]. The first is the proton transfer product, H2Cl+ + Cl, where the cross section of the reactions associated with this product, as predicted, monotonically decreases as the collision energy between the product increases. The second is the product HCl+ + HCl, where the cross section of the reaction shows a local maximum at the collision energy of 0.5 eV. The nature of this unusual behavior of the cross section is not clear. In this manuscript, state of the art ab initio molecular dynamics (AIMD) simulation is performed to study this bimolecular collision of HCl+ + HCl. The potential energy of profile of this system is first characterized with high-level ab initio methods, and then a computationally efficient method is selected for AIMD simulation. The cross sections from AIMD agree well with those from the experiments for both products. The AIMD trajectories reveal the complexity of this seemingly-simple reaction – a total of five different pathways that result in the aforementioned two products. The simulation also sheds light on the mystery of the local maximum of the cross section regarding the HCl+ + HCl product.

For some gas-phase X − + CH 3 Y → XCH 3 + Y − S N 2 nucleophilic substitution reactions a pre-reaction complex is formed in which the attacking anion binds to a H-atom to form X − ⋯HCH 2 Y. In this work properties of this complex are investigated, for the OH − + CH 3 I and F − + CH 3 I reactions, to determine whether the HO − ⋯HCH 2 I and F − ⋯HCH 2 I complexes should be considered hydrogen-bonded complexes. Properties considered for these complexes are their structures, vibrational frequencies, well depths, and partial atomic charges. Also considered is the role of the HO − ⋯HCH 2 I complex in proton transfer for both the proton transfer and S N 2 reaction pathways. The results of these analyses indicate that these X − ⋯HCH 2 Y complexes are hydrogen bonding complexes.

The potential energy surface (PES) of the F − + CH 3 I → FCH 3 + I − S N 2 nucleophilic substitution reaction has been studied previously using MP2 and DFT levels of theory ( J. Phys. Chem. A 2010, 114 , 9635–9643). This work indicated that DFT gives a better representation of the PES which has only an hydrogen-bonded entrance channel reaction path, with a hydrogen-bonded transition state [F··HCH 2 ··I] − connecting the hydrogen-bonded pre-reaction complex F − ⋯HCH 2 I and C 3v post-reaction complex FCH 3 ⋯I − . For the work presented here, CCSD(T) with three different basis set and two effective core potentials (i.e. PP/d, PP/t and ECP/d) was employed to investigate stationary point properties for this reaction. Besides the hydrogen-bonded entrance channel stationary points, CCSD(T) also predicts a traditional C 3v transition state [F··CH 3 ··I] − connecting a C 3v pre-reaction complex F − ⋯CH 3 I with the C 3v post-reaction complex FCH 3 ⋯I − . Though CCSD(T) gives a CH 3 F⋯I − binding energy and CH 3 F and CH 3 I geometries in almost exact agreement with experiment, it gives a heat of reaction ∼20 kJ/mol less exothermic than experiment. The MP2 PES for this reaction, determined in the previous study, is very similar to the CCSD(T), but obtained with a much smaller computational cost. Direct dynamics simulations for the F − + CH 3 I → FCH 3 + I − reaction are feasible with MP2.

International audience; In the present work we have investigated the gas phase reactivity of protonated urea after collision with the diatomic inert gas N2, by studying the energy transfer and fragmentation induced by collisions. We first developed an analytical pair potential to describe the interaction between the projectile and the ion, and then performed QM/MM direct chemical dynamics simulations of the collision between the projectile and protonated urea in its two most stable isomers. In particular, the effect of the diatomic projectile, and the role of its initial rotational state, were compared with the fragmentation and energy transfer obtained previously (J. Phys. Chem. A 2009, 113, 13853) for the monoatomic projectile Ar. The diatomic projectile was found to be less efficient in energy transfer compared to the monoatomic projectile. In addition, rotational activation of UreaH+ is dependent on the initial rotational quantum number of N2. Finally, we investigated the UreaH+ gas phase reactivity as a function of its rovibrational activation by means of chemical dynamics simulations where the initial structure for the simulations is the transition state (TS) that the system can reach after collisional activation of the most stable isomer. The simulation time-length is not able to directly access this TS from the most stable isomer since its lifetime is notably longer, of about two order of magnitude in time.

A QM + MM direct dynamics simulation, using MP2/6-31G* theory as a model for the intramolecular potential of protonated glycine (gly-H+), is used to study gly-H+ + diamond {1 1 1} SID. The simulations are performed for collisions normal (θi = 0°) and oblique (θi = 45°) to the surface and at a collision energy of 70 eV (1614 kcal/mol). The gly-H+ energy-transfer dynamics, observed in this study, are in accord with previous studies in which AMBER and AM1 were used for the ion's intramolecular potential [S.O. Meroueh, Y. Wang, W.L. Hase, J. Phys. Chem. A 106 (2002) 9983]. A particularly important finding is that a significant fraction of the gly-H+ ions fragment by a shattering mechanism as they collide with the surface. This result supports earlier studies in which shattering fragmentation was also observed for both gly-H+ and gly2-H+, in QM + MM direct dynamics simulations in which the AM1 semiempirical QM model was used for the ion's intramolecular potential, instead of the MP2/6-31G* model. Using MP2/6-31G* the predominant shattering fragmentation channels, in decreasing order of importance, are NH3 + CH2COOH+, NH3 + CO + CH2OH+, H2 + NH2CHCOOH+, and NH2CH2+ + C(OH)2 for θi = 0°, and NH3 + CH2COOH+, NH2CH2+ + C(OH)2, NH2CH2+ + HCOOH, and NH + C(OH)2CH3+ for θi = 45°. SID at θi = 45° was studied previously with AM1 and the percentage of gly-H+ trajectories which shatter with MP2/6-31G* is the same as found for AM1.

Classical trajectory simulations are performed to study energy transfer in collisions of protonated diglycine, (gly) 2 H + , and dialanine, (ala) 2 H + , ions with the diamond {1 1 1} surface, for a collision energy E i in the range of 5–110 eV and incident angles of 0 and 45° with respect to the surface normal. The distribution of energy transfer to vibrational/rotational degrees of freedom, Δ E int , and to the surface, Δ E surf , and of energy remaining in peptide ion translation, E f , are very similar for (gly) 2 H + and (ala) 2 H + . The average percent energy transferred to Δ E surf and E f increases and decreases, respectively, with increase in E i . Average energy transfer to Δ E int is less dependent on E i , but does decrease with increase in E i . The AMBER and AM1 models for the (gly) 2 H + intramolecular potential give statistically identical energy transfer distributions in (gly) 2 H + + diamond {1 1 1} collisions. A comparison of the current study with previous trajectory simulations of glyH + , (gly) 3 H + , and (gly) 5 H + collisions with diamond {1 1 1} shows that the energy transfer efficiencies to Δ E int , Δ E surf , and E f are similar for (gly) n H + , n =1–5. The energy transfer distributions for (gly) 2 H + + diamond {1 1 1} collisions depend on the collision angle and do not scale in accord with the normal component of the collision energy E i n for collisions with θ i of 0 and 45°.

Classical trajectory simulations were carried out to study details of the energy transfer mechanism for activation of polyglycine (gly) n and polyalanine (ala) n peptide ions via collisions with Ar atoms. The Amber valence force field was used to represent the peptide intramolecular potential and the argon–peptide interaction was modeled using parameters previously determined from high level ab initio calculations. Energy transfer was studied versus collision impact parameter b , the collision energy, and peptide temperature and structure. Energy transfer to rotation becomes important for extended peptides at large b , but with averaging over impact parameter is smaller than transfer to vibration. Specific pathways for vibrational energy transfer were distinguished by determining the efficiency of energy transfer with various combinations of low and high frequency modes constrained. With all stretching and bending modes constrained the efficiency of energy transfer is more than 80% of that without constraints, which illustrates the efficient excitation of the torsional modes. Varying the peptide structure has a significant effect on the energy transfer efficiency, with larger energy transfer for the folded structures. The efficiency of energy transfer increases with increase in collisional energy.