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International audience; In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion’s vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple “soft” collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.

Direct dynamics simulations, using B3LYP/6-311++G(2d,2p) theory, were used to study the unimolecular and intramolecular dynamics of vibrationally excited CH

Abnormalities in zinc metabolism have been linked to many diseases, including different kinds of cancers and neurological diseases. The present study investigates the fragmentation pathways of a zinc chaperon using a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analog methanobactin peptide-5, amb5). DFT/M05-2X and B3LYP geometry optimizations of [amb5-3H+Zn(II)]- predicted three lowest energy conformers with different chelating motifs. Direct dynamics simulations, using the PM7 semiempirical electronic structure method, were performed for these conformers, labeled a, b, and c, to obtain their fragmentation pathways at different temperatures in the range 1600-2250 K. The simulation results were compared with negative ion mode mass spectrometry experiments. For conformer a, the number of primary dissociation pathways are 11, 14, 24, 70, and 71 at 1600, 1750, 1875, 2000, and 2250 K, respectively. However, there are only 6, 10, 13, 14, and 19 pathways corresponding to these temperatures that have a probability of 2% or more. For conformer b, there are 67 pathways at 2000 K and 71 pathways at 2250 K. For conformer c, 17 pathways were observed at 2000 K. For conformer a, for two of the most common pathways involving C-C bond dissociation, Arrhenius parameters were calculated. The frequency factors and activation energies are smaller than those for C-C homolytic dissociation in alkanes due to increased stability of the product ions as a result of hydrogen bonding. The activation energies agree with the PM7 barriers for the C-C dissociations. Comparison of the simulation and experimental fragmentation ion yields shows the simulations predict double or triple cleavages of the backbone with Zn(II) retaining its binding sites, whereas the experiment exhibits single cleavages of the backbone accompanied by cleavage of two of the Zn(II) binding sites, resulting in b- and y-type ions.

Low-energy collision-induced dissociation (CID) of deprotonated l-cysteine S-sulfate, [cysS-SO 3 ] - , delivered in the gas phase by electrospray ionization, has been found to provide a means to form deprotonated l-cysteine sulfenic acid, which is a fleeting intermediate in biological media. The reaction mechanism underlying this process is the focus of the present contribution. At the same time, other novel species are formed, which were not observed in previous experiments. To understand fragmentation pathways of [cysS-SO 3 ] - , reactive chemical dynamics simulations coupled with a novel algorithm for automatic determination of intermediates and transition states were performed. This approach has allowed the identification of the mechanisms involved and explained the experimental fragmentation pathways. Chemical dynamics simulations have shown that a roaming-like mechanism can be at the origin of l-cysteine sulfenic acid.

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.

We compare algorithms to sample initial positions and momenta of a molecular system for classical trajectory simulations. We aim at reproducing the phase space quantum distribution for a vibrational eigenstate, as in Wigner theory. Moreover, we address the issue of controlling the total energy and the energy partition among the vibrational modes. In fact, Wigner's energy distributions are very broad, quite at variance with quantum eigenenergies. Many molecular processes depend sharply on the available energy, so a better energy definition is important. Two approaches are introduced and tested: the first consists in constraining the total energy of each trajectory to equal the quantum eigenenergy. The second approach modifies the phase space distribution so as to reduce the deviation of the single mode energies from the correct quantum values. A combination of the two approaches is also presented.

Anti-E2, syn-E2, inv-, and ret-SN2 reaction channels for the gas-phase reaction of F– + CH3CH2I were characterized with a variety of electronic structure calculations. Geometrical analysis confirmed synchronous E2-type transition states for the elimination of the current reaction, instead of nonconcerted processes through E1cb-like and E1-like mechanisms. Importantly, the controversy concerning the reactant complex for anti-E2 and inv-SN2 paths has been clarified in the present work. A positive barrier of +19.2 kcal/mol for ret-SN2 shows the least feasibility to occur at room temperature. Negative activation energies (−16.9, −16.0, and −4.9 kcal/mol, respectively) for inv-SN2, anti-E2, and syn-E2 indicate that inv-SN2 and anti-E2 mechanisms significantly prevail over the eclipsed elimination. Varying the leaving group for a series of reactions F– + CH3CH2Y (Y = F, Cl, Br, and I) leads to monotonically decreasing barriers, which relates to the gradually looser TS structures following the order F > Cl > Br ...

Zwitterionic group 14 complexes of the alkali metals of formula [E(SiMe2OCH2CH2OMe)3M], where E = C, Si or Ge and M = Li, Na or K, have been prepared, structurally characterized and their electronic nature was investigated by computational methods., Zwitterionic group 14 complexes of the alkali metals of formula [C(SiMe2OCH2CH2OMe)3M], (M-1), [Si(SiMe2OCH2CH2OMe)3M], (M-2), [Ge(SiMe2OCH2CH2OMe)3M], (M-3), where M = Li, Na or K, have been prepared, structurally characterized and their electronic nature was investigated by computational methods. Zwitterions M-2 and M-3 were synthesized via reactions of [Si(SiMe2OCH2CH2OMe)4] (2) and [Ge(SiMe2OCH2CH2OMe)4] (3) with MOBut (M = Li, Na or K), resp., in almost quantitative yields, while M-1 were prepared from deprotonation of [HC(SiMe2OCH2CH2OMe)3] (1) with LiBut, NaCH2Ph and KCH2Ph, resp. X-ray crystallographic studies and DFT calculations in the gas-phase, including calculations of the NPA charges confirm the zwitterionic nature of these compounds, with the alkali metal cations being rigidly locked and charge separated from the anion by the internal OCH2CH2OMe donor groups. Natural bond orbital (NBO) analysis and the second order perturbation theory analysis of the NBOs reveal significant hyperconjugative interactions in M-1–M-3, primarily between the lone pair and the antibonding Si–O orbitals, the extent of which decreases in the order M-1 > M-2 > M-3. The experimental basicities and the calculated gas-phase basicities of M-1–M-3 reveal the zwitterionic alkali metal methanides M-1 to be significantly stronger bases than the analogous silanides M-2 and germanium M-3.

Direct dynamics simulations were performed to study the SN2 double inversion mechanism SN2-DI, with retention of configuration, for the F− + CH3I reaction. Previous simulations identified a transition state (TS) structure, i.e. TS0, for the SN2-DI mechanism, including a reaction path. However, intrinsic reaction coordinate (IRC) calculations from TS0 show it is a proton transfer (PT) TS connected to the F−⋯HCH2I SN2 pre-reaction complex and the FH⋯CH2I− proton transfer post-reaction complex. Inclusion of TS0 in the SN2-DI mechanism would thus involve non-IRC atomistic dynamics. Indeed, trajectories initiated at TS0, with random ensembles of energies as assumed by RRKM theory, preferentially form the SN2-DI products and ∼70% follow the proposed SN2-DI pathway from TS0 to the products. In addition, the Sudden Vector Projection (SVP) method was used to identify which CH3I vibrational mode excitations promote access to TS0 and the SN2-DI mechanism. Results of F− + CH3I simulations, with SVP specified mode excitations, are disappointing. With the CH3 deformations of CH3I excited, the SN2 single inversion mechanism is the dominant pathway. If the CH stretch modes are also excited, proton transfer dominates the reaction. SN2-DI occurs, but with a very small probability of ∼1%. The reasons behind these results are discussed.

Atomic nitrogen is formed in the high-temperature shock layer of hypersonic vehicles and contributes to the ablation of their thermal protection systems (TPSs). To gain atomic-level understanding of the ablation of carbon-based TPS, collisions of hyperthermal atomic nitrogen on representative carbon surfaces have recently be investigated using molecular beams. In this work, we report direct dynamics simulations of atomic-nitrogen [N(4S)] collisions with pristine, defected, and oxidized graphene. Apart from non-reactive scattering of nitrogen atoms, various forms of nitridation of graphene were observed in our simulations. Furthermore, a number of gaseous molecules, including the experimentally observed CN molecule, have been found to desorb as a result of N-atom bombardment. These results provide a foundation for understanding the molecular beam experiment and for modeling the ablation of carbon-based TPSs and for future improvement of their properties.

In a previous direct dynamics simulation of the Cl- + CH3I → ClCH3 + I- SN2 reaction, predominantly indirect and direct reaction was found at collision energies Erel of 0.20 and 0.39 eV, respectively. For the work presented here, these simulations were extended by studying the reaction dynamics from Erel of 0.15 to 0.40 eV in 0.05 eV intervals. A transition from a predominantly indirect to direct reaction is found for Erel of 0.27-0.28 eV, a finding consistent with experiment. The simulation results corroborate the understanding that in experiments indirect reaction is characterized by small product translational energies and isotropic scattering, while direct reaction has higher translational energies and anisotropic scattering. The traditional statistical theoretical model for the Cl- + CH3I SN2 reaction assumes the Cl--CH3I pre-reaction complex (A) is formed, followed by barrier crossing, and then formation of the ClCH3-I- post-reaction complex (B). This mechanism is seen in the dynamics, but the complete atomistic dynamics are much more complex. Atomistic SN2 mechanisms contain A and B, but other dynamical events consisting of barrier recrossing (br) and the roundabout (Ra), in which the CH3-moiety rotates around the heavy I-atom, are also observed. The two most important mechanisms are only formation of A and Ra + A. The simulation results are compared with simulations and experiments for Cl- + CH3Cl, Cl- + CH3Br, F- + CH3I, and OH- + CH3I.

The role of vibrational excitation of reactants in driving reactions involving polyatomic species has been often studied by means of classical or quasi-classical trajectory simulations. We propose a different approach based on investigation of vibrational features of the Cl

In a recent direct dynamics simulations of the collision induced dissociation (CID) of the doubly protonated tripeptide threonine-isoleucine-lysine and threonine-leucine-lysine ions, TIK(H+)2 and TLK(H+)2, a shattering fragmentation mechanism was found, in which the ion fragmented upon impact with N2 (Z. Homayoon et al., Phys. Chem. Chem. Phys., 2018, 20, 3614). In using models to interpret experiments of biological ion CID, it is important to know the collision energy threshold for the shattering mechanism. In the work presented here, direct dynamics simulations were performed to study shattering fragmentation versus the collision energy (Erel) for N2 + TIK(H+)2. From the probability of shattering fragmentation and the minimum energy transfer for fragmentation versus Erel, a threshold of ∼55 kcal mol-1 was identified for N2 + TIK(H+)2 shattering fragmentation. This threshold is substantially higher than the lowest activation energy of 14.7 kcal mol-1, found from direct dynamics simulations, for the thermal dissociation of TIK(H+)2.

In Density Functional Theory (DFT) direct dynamics simulations with Unrestricted Hartree Fock (UHF) theory, triplet instability often emerges when numerically integrating a classical trajectory. A broken symmetry initial guess for the wave function is often used to obtain the unrestricted DFT potential energy surface (PES), but this is found to be often insufficient for direct dynamics simulations. An algorithm is described for obtaining smooth transitions between the open-shell and the closed-shell regions of the unrestricted PES, and thus stable trajectories, for direct dynamics simulations of dioxetane and its •OCH2 -CH2 O• singlet diradical. © 2018 Wiley Periodicals, Inc.

Competiting SN2 substitution and E2 elimination reactions are of central importance in preparative organic synthesis. Here, we unravel how individual solvent molecules may affect underlying SN2/E2 atomistic dynamics, which remains largely unclear with respective to their effects on reactivity. Results are presented for a prototype microsolvated case of fluoride anion reacting with ethyl bromide. Reaction dynamics simulations reproduce experimental findings at near thermal energies and show that the E2 mechanism dominates over SN2 for solvent-free reaction. This is energetically quite unexpected and results from dynamical effects. Adding one solvating methanol molecule introduces strikingly distinct dynamical behaviors that largely promote the SN2 reaction, a feature which attributes to a differential solute–solvent interaction at the central barrier that more strongly stabilizes the transition state for substitution. Upon further solvation, this enhanced stabilization of the SN2 mechanism becomes more pro...

Monte Carlo sampling calculations were performed to determine the anharmonic sum of states, N

Ozonolysis produces chemically activated carbonyl oxides (Criegee intermediates, CIs) that are either stabilized or decompose directly. This branching has an important impact on atmospheric chemistry. Prior theoretical studies have employed statistical models for energy partitioning to the CI arising from dissociation of the initially formed primary ozonide (POZ). Here, we used direct dynamics simulations to explore this partitioning for decomposition of c-C

In a previous UB3LYP/6-31G* direct dynamics simulation, non-Rice-Ramsperger-Kassel-Marcus (RRKM) unimolecular dynamics was found for vibrationally excited 1,2-dioxetane (DO); [R. Sun et al., J. Chem. Phys. 137, 044305 (2012)]. In the work reported here, these dynamics are studied in more detail using the same direct dynamics method. Vibrational modes of DO were divided into 4 groups, based on their characteristic motions, and each group excited with the same energy. To compare with the dynamics of these groups, an additional group of trajectories comprising a microcanonical ensemble was also simulated. The results of these simulations are consistent with the previous study. The dissociation probability, N(t)/N(0), for these excitation groups were all different. Groups A, B, and C, without initial excitation in the O-O stretch reaction coordinate, had a time lag to of 0.25-1.0 ps for the first dissociation to occur. Somewhat surprisingly, the C-H stretch Group A and out-of-plane motion Group C excitations had exponential dissociation probabilities after to, with a rate constant ∼2 times smaller than the anharmonic RRKM value. Groups B and D, with excitation of the H-C-H bend and wag, and ring bend and stretch modes, respectively, had bi-exponential dissociation probabilities. For Group D, with excitation localized in the reaction coordinate, the initial rate constant is ∼7 times larger than the anharmonic RRKM value, substantial apparent non-RRKM dynamics. N(t)/N(0) for the random excitation trajectories was non-exponential, indicating intrinsic non-RRKM dynamics. For the trajectory integration time of 13.5 ps, 9% of these trajectories did not dissociate in comparison to the RRKM prediction of 0.3%. Classical power spectra for these trajectories indicate they have regular intramolecular dynamics. The N(t)/N(0) for the excitation groups are well described by a two-state coupled phase space model. From the intercept of N(t)/N(0) with random excitation, the anharmonic correction to the RRKM rate constant is approximately a factor of 1.5.

The reaction of

Classical chemical dynamics simulation results are presented for the thermal desorption kinetics and energetics of protonated dialanine ions (ala2-H+) physisorbed on/in a perfluorinated self-assembled monolayer (F-SAM) surface. Previously developed analytic potentials were used for the F-SAM and the ala2-H+/F-SAM intermolecular interaction, and the AMBER valence force field was used for ala2-H+. The activation energy, Ea = 13.2 kcal/mol, determined from the simulations is consistent with previous simulations of the ala2-H+/F-SAM binding energy. The A-factor, 7.8 × 1011 s–1, is about an order of magnitude lower than those representative of small molecule desorption from metal and semiconductor surfaces. This finding is consistent with the decreased entropies of ala2-H+ and the F-SAM upon desorption. Using the Arrhenius parameters for ala2-H+ desorption from the F-SAM, the lifetime of ala2-H+ adsorbed on the F-SAM at 300 K is 5 × 10–3 s. Larger peptide ions are expected to have longer adsorption lifetimes.

Dissociation chemistry of the diproline anion [Pro

A zero-point energy (ZPE) constraint model is proposed for classical trajectory simulations of unimolecular decomposition and applied to CH4* → H + CH3 decomposition. With this model trajectories are not allowed to dissociate unless they have ZPE in the CH3 product. If not, they are returned to the CH4* region of phase space and, if necessary, given additional opportunities to dissociate with ZPE. The lifetime for dissociation of an individual trajectory is the time it takes to dissociate with ZPE in CH3, including multiple possible returns to CH4*. With this ZPE constraint the dissociation of CH4* is exponential in time as expected for intrinsic RRKM dynamics and the resulting rate constant is in good agreement with the harmonic quantum value of RRKM theory. In contrast, a model that discards trajectories without ZPE in the reaction products gives a CH4* → H + CH3 rate constant that agrees with the classical and not quantum RRKM value. The rate constant for the purely classical simulation indicates that anharmonicity may be important and the rate constant from the ZPE constrained classical trajectory simulation may not represent the complete anharmonicity of the RRKM quantum dynamics. The ZPE constraint model proposed here is compared with previous models for restricting ZPE flow in intramolecular dynamics, and connecting product and reactant/product quantum energy levels in chemical dynamics simulations.

Experimental and simulation studies of the OH – (H2O) + CH3I reaction give temperature dependent rate constants which are in excellent agreement. Though there are statistical uncertainties, there is an apparent small decrease in the rate constant as the temperature is increased from − 60 to 125 ℃, and for this temperature range the rate constant is ∼ 1.6 times smaller than that for the unsolvated reactants OH – + CH3I. Previous work [J. Phys. Chem. A 117 (2013) 14019] for the unsolvated reaction found that the S N 2 and proton transfer pathways, forming CH3OH + I – and CH2I – + H2O, have nearly equal probabilities. However, for the microsolvated OH – (H2O) + CH3I reaction the S N 2 pathways dominate. An important contributor to this effect is the stronger binding of H2O to the OH – reactant than to the proton transfer product CH2I – , increasing the barrier for the proton transfer pathway. The effect of microsolvation on the rate constant for the OH – (H2O)0,1 + CH3I reactions agrees with previous experimental studies for X – (H2O)0,1 + CH3Y reactions. The simulations show that there are important non-statistical attributes to the entrance- and exit-channel dynamics for the OH – (H2O) + CH3I reaction.

Classical chemical dynamics simulations were performed to study the intramolecular and unimolecular dissociation dynamics of the benzene dimer, Bz2 → 2 Bz. The dissociation of microcanonical ensembles of Bz2 vibrational states, at energies E corresponding to temperatures T of 700-1500 K, were simulated. For the large Bz2 energies and large number of Bz2 vibrational degrees of freedom, s, the classical microcanonical (RRKM) and canonical (TST) rate constant expressions become identical. The dissociation rate constant for each T is determined from the initial rate dN(t)/dt of Bz2 dissociation, and the k(T) are well-represented by the Arrhenius eq k(T) = A exp(-E(a)/RT). The E(a) of 2.02 kcal/mol agrees well with the Bz2 dissociation energy of 2.32 kcal/mol, and the A-factor of 2.43 × 10(12) s(-1) is of the expected order-of-magnitude. The form of N(t) is nonexponential, resulting from weak coupling between the Bz2 intramolecular and intermolecular modes. With this weak coupling, large Bz2 vibrational excitation, and low Bz2 dissociation energy, most of the trajectories dissociate directly. Simulations, with only the Bz2 intramolecular modes excited at 1000 K, were also performed to study intramolecular vibrational energy redistribution (IVR) between the intramolecular and intermolecular modes. Because of restricted IVR, the initial dissociation is quite slow, but N(t) ultimately becomes exponential, suggesting an IVR time of 20.7 ps.

Relaxation of vibrationally excited C6F6* in a thermalized bath of N2 molecules is studied by condensed-phase chemical dynamics simulations. The average energy of C6F6 as a function of time, ⟨E(t)⟩, was determined using two different models for the N2–C6F6 intermolecular potential, and both gave statistically the same result. A simulation with a N2 bath density of 20 kg/m3 was performed to check the convergence and validate the results obtained previously with a higher bath density of 40 kg/m3. The initial ensemble of C6F6 is nearly monoenergetically excited, but the ensemble acquires as energy distribution P(E) as it is collisionally relaxed. An evaluation of P(E) and the root-mean-square deviation ⟨ΔE2⟩1/2 of P(E), versus time, shows that P(E) first broadens and then narrows. Simulations with the C6F6 vibrational excitation energy of 85.8 kcal/mol, studied experimentally, show that the width of P(E) does not affect the average collisional deactivation rate. The role of the intramolecular vibrational fre...

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.

Gas phase unimolecular fragmentation of the two model doubly protonated tripeptides threonine-isoleucine-lysine (TIK) and threonine-leucine-lysine (TLK) is studied using chemical dynamics simulations. Attention is focused on different aspects of collision induced dissociation (CID): fragmentation pathways, energy transfer, theoretical mass spectra, fragmentation mechanisms, and the possibility of distinguishing isoleucine (I) and leucine (L). Furthermore, discussion is given regarding the differences between single collision CID activation, which results from a localized impact between the ions and a colliding molecule N

International audience; In the present work, we investigated the reaction dynamics that will possibly lead to the formation of protonated glycine by an ion–molecule collision. In particular, two analogous reactions were studied: NH3OH+ + CH3COOH and NH2OH2+ + CH3COOH that were suggested by previous experiments to be able to form protonated glycine loosing a neutral water molecule. Chemical dynamics simulations show that both reactants can form a molecule with the mass of the protonated glycine but with different structures, if some translational energy is given to the system. The reaction mechanisms for the most relevant product isomers are discussed as well as the role of collision energy in determining reaction products. Finally, in comparing collision dynamics at room and at very low initial internal temperature of the reactants, the same behavior was obtained for forming the protonated glycine isomers products. This supports the use of standard gas phase ion-chemistry setups to study collision-induced reactivity as a model for astrophysical cold conditions, when some relative translation energy is given to the system.

International audience; In a recent direct dynamics simulations of the collision induced dissociation (CID) of the doubly protonated tripeptide threonine–isoleucine–lysine and threonine–leucine–lysine ions, TIK(H+)2 and TLK(H+)2, a shattering fragmentation mechanism was found, in which the ion fragmented upon impact with N2 (Z. Homayoon et al., Phys. Chem. Chem. Phys., 2018, 20, 3614). In using models to interpret experiments of biological ion CID, it is important to know the collision energy threshold for the shattering mechanism. In the work presented here, direct dynamics simulations were performed to study shattering fragmentation versus the collision energy (Erel) for N2 + TIK(H+)2. From the probability of shattering fragmentation and the minimum energy transfer for fragmentation versus Erel, a threshold of ∼55 kcal mol−1 was identified for N2 + TIK(H+)2 shattering fragmentation. This threshold is substantially higher than the lowest activation energy of 14.7 kcal mol−1, found from direct dynamics simulations, for the thermal dissociation of TIK(H+)2.

Previous chemical dynamics simulations (Phys. Chem. Chem. Phys., 2014, 16, 23769-23778) were analyzed to delineate atomistic details for collision of N-protonated dialanine (ala2-H(+)) with a C8 perfluorinated self-assembled monolayer (F-SAM) surface. Initial collision energies Ei of 5-70 eV and incident angles θi of 0° and 45°, with the surface normal, were considered. Four trajectory types were identified: (1) direct scattering; (2) temporary sticking/physisorption on top of the surface; (3) temporary penetration of the surface with additional physisorption on the surface; and (4) trapping on/in the surface, by physisorption or surface penetration, when the trajectory is terminated. Direct scattering increases from 12 to 100% as Ei is increased from 5 to 70 eV. For the direct scattering at 70 eV, at least one ala2-H(+) heavy atom penetrated the surface for all of the trajectories. For ∼33% of the trajectories all eleven of the ala2-H(+) heavy atoms penetrated the F-SAM at the time of deepest penetration. The importance of trapping decreased with increase in Ei, decreasing from 84 to 0% with Ei increase from 5 to 70 eV at θi = 0°. Somewhat surprisingly, the collisional energy transfers to the F-SAM surface and ala2-H(+) are overall insensitive to the trajectory type. The energy transfer to ala2-H(+) is primarily to vibration, with the transfer to rotation ∼10% or less. Adsorption and then trapping of ala2-H(+) is primarily a multi-step process, and the following five trapping mechanisms were identified: (i) physisorption-penetration-physisorption (phys-pen-phys); (ii) penetration-physisorption-penetration (pen-phys-pen); (iii) penetration-physisorption (pen-phys); (iv) physisorption-penetration (phys-pen); and (v) only physisorption (phys). For Ei = 5 eV, the pen-phys-pen, pen-phys, phys-pen, and phys trapping mechanisms have similar probabilities. For 13.5 eV, the phys-pen mechanism, important at 5 eV, is unimportant. The radius of gyration of ala2-H(+) was calculated once it is trapped on/in the F-SAM surface and trapping decreases the ion's compactness, in part by breaking hydrogen bonds. The ala2-H(+) + F-SAM simulations are compared with the penetration and trapping dynamics found in previous simulations of projectile + organic surface collisions.

Born-Oppenheimer direct dynamics simulations were performed to study atomistic details of the F + CH

Intermolecular energy transfer for the vibrationally excited propylbenzene cation (C9H12+) in a helium bath was studied with chemical dynamics simulations. The bond energy bond order relationship and electronic structure calculations were used to develop an intramolecular potential for C9H12+. Spin component scaled MP2/6-311++G** calculations were used to develop an intermolecular potential for He + C9H12+. The He + He intermolecular potential was determined from a previous explicitly correlated Gaussian electronic structure calculation. For the simulations, C9H12+ was prepared with a 100.1 kcal/mol excitation energy to compare with experiment. The average energy transfer from C9H12+, ⟨ΔEc⟩, decreased as C9H12+ was vibrationally relaxed and for the initial excitation energy ⟨ΔEc⟩ = 0.64 kcal/mol. This result agrees well with the experimental ⟨ΔEc⟩ value of 0.51 ± 0.26 kcal/mol for collisions of He with the ethylbenzene cation. The ⟨ΔEc⟩ value found for He + C9H12+ collisions is compared with reported values of ⟨ΔEc⟩ for He colliding with other molecules.

Direct dynamics simulations were performed to study the S

In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces ‘on the fly’ has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

Influences of solvent molecules on S

For the traditional model of gas-phase X(-) + CH3Y SN2 reactions, C3v ion-dipole pre- and postreaction complexes X(-)---CH3Y and XCH3---Y(-), separated by a central barrier, are formed. Statistical intramolecular dynamics are assumed for these complexes, so that their unimolecular rate constants are given by RRKM theory. Both previous simulations and experiments have shown that the dynamics of these complexes are not statistical and of interest is how these nonstatistical dynamics affect the SN2 rate constant. This work also found there was a transition from an indirect, nonstatistical, complex forming mechanism, to a direct mechanism, as either the vibrational and/or relative translational energy of the reactants was increased. The current Account reviews recent collaborative studies involving molecular beam ion-imaging experiments and direct (on-the-fly) dynamics simulations of the SN2 reactions for which Cl(-), F(-), and OH(-) react with CH3I. Also considered are reactions of the microsolvated anions OH(-)(H2O) and OH(-)(H2O)2 with CH3I. These studies have provided a detailed understanding of the atomistic mechanisms for these SN2 reactions. Overall, the atomistic dynamics for the Cl(-) + CH3I SN2 reaction follows those found in previous studies. The reaction is indirect, complex forming at low reactant collision energies, and then there is a transition to direct reaction between 0.2 and 0.4 eV. The direct reaction may occur by rebound mechanism, in which the ClCH3 product rebounds backward from the I(-) product or a stripping mechanism in which Cl(-) strips CH3 from the I atom and scatters in the forward direction. A similar indirect to direct mechanistic transition was observed in previous work for the Cl(-) + CH3Cl and Cl(-) + CH3Br SN2 reactions. At the high collision energy of 1.9 eV, a new indirect mechanism, called the roundabout, was discovered. For the F(-) + CH3I reaction, there is not a transition from indirect to direct reaction as Erel is increased. The indirect mechanism, with prereaction complex formation, is important at all the Erel investigated, contributing up ∼60% of the reaction. The remaining direct reaction occurs by the rebound and stripping mechanisms. Though the potential energy curve for the OH(-) + CH3I reaction is similar to that for F(-) + CH3I, the two reactions have different dynamics. They are akin, in that for both there is not a transition from an indirect to direct reaction. However, for F(-) + CH3I indirect reaction dominates at all Erel, but it is less important for OH(-) + CH3I and becomes negligible as Erel is increased. Stripping is a minor channel for F(-) + CH3I, but accounts for more than 60% of the OH(-) + CH3I reaction at high Erel. Adding one or two H2O molecules to OH(-) alters the reaction dynamics from that for unsolvated OH(-). Adding one H2O molecule enhances indirect reaction at low Erel, and changes the reaction mechanism from primarily stripping to rebound at high Erel. With two H2O molecules the dynamics is indirect and isotropic at all collision energies.

Direct dynamics simulations, using B3LYP/6-311++G(2d,2p) theory, were used to study the unimolecular and intramolecular dynamics of vibrationally excited CH3NC. Microcanonical ensembles of CH3NC, excited with 150, 120, and 100 kcal/mol of vibrational energy, isomerized to CH3CN nonexponentially, indicative of intrinsic non-Rice-Ramsperger-Kassel-Marcus (RRKM) dynamics. The distribution of surviving CH3NC molecules vs time, i.e., N(t)/N(0), was described by two separate functions, valid above and below a time limit, a single exponential for the former and a biexponential for the latter. The dynamics for the short-time component are consistent with a separable phase space model. The importance of this component decreases with vibrational energy and may be unimportant for energies relevant to experimental studies of CH3NC isomerization. Classical power spectra calculated for vibrationally excited CH3NC, at the experimental average energy of isomerizing molecules, show that the intramolecular dynamics of CH3NC are not chaotic and the C-N≡C and CH3 units are weakly coupled. The biexponential N(t)/N(0) at 100 kcal/mol is used as a model to study CH3NC → CH3CN isomerization with biexponential dynamics. The Hinshelwood-Lindemann rate constant kuni(ω,E) found from the biexponential N(t)/N(0) agrees with the Hinshelwood-Lindemann-RRKM kuni(ω,E) at the high and low pressure limits, but is lower at intermediate pressures. As found from previous work [S. Malpathak and W. L. Hase, J. Phys. Chem. A 123, 1923 (2019)], the two kuni(ω,E) curves may be brought into agreement by scaling ω in the Hinshelwood-Lindemann-RRKM kuni(ω,E) by a collisional energy transfer efficiency factor βc. The interplay between the value of βc, for the actual intermolecular energy transfer, and the ways the treatment of the rotational quantum number K and nonexponential unimolecular dynamics affect βc suggests that the ability to fit an experimental kuni(ω,T) with Hinshelwood-Lindemann-RRKM theory does not identify a unimolecular reactant as an intrinsic RRKM molecule.

Large-scale trajectory simulations of different projectiles colliding with an organic surface, as well as a gas−surface model for energy transfer, are employed to investigate the effects of the mass, size, shape, and vibrational frequency(ies) of the projectile and of the projectile−surface interaction potential on the energy-transfer dynamics. The gas−surface model employed in this work relies on simple gas-phase scattering models. When energy transfer is analyzed in the limit of high incident energies, the following results are found in this study. The percent of energy transfer to vibration (and rotation) of light diatomic projectiles decreases as the projectile's mass increases, while this transfer is almost independent of the mass for heavier projectiles. Transfer to final translation of diatomic projectiles is a U-shaped function of the projectile's mass, as predicted by the hard cube model. For larger projectiles, the partitioning of the energy transferred to the internal degrees of freedom (dof) between vibration and rotation depends on the projectile's size. In other words, transfer to rotation is more important for the smaller projectiles, while transfer to vibration dominates for the bigger ones, which have more vibrational dof. For small projectiles (less than 10 atoms), transfer to vibration increases as a function of the projectile's size. However, for larger projectiles, the percent transfer to vibration is nearly constant, a result that can be attributed to a mass effect and also to the fact that only a reduced subset of "effective" vibrational dof is being activated in the collisions. For linear hydrocarbons colliding with the perfluorinated self-assembled monolayer (F- SAM), the number of "effective" modes was estimated to be around 18, which corresponds to a percent energy transfer to vibration of 20−22%. The percent transfer to vibration of the more compact cyclic molecules is a bit higher than that for their linear counterparts.

Chemical dynamics simulations are reported which provide atomistic details of collisions of protonated dialanine, ala2-H(+), with a perfluorinated octanethiolate self-assembled monolayer (F-SAM) surface. The simulations are performed at collision energies Ei of 5.0, 13.5, 22.5, 30.00, and 70 eV, and incident angles 0° (normal) and 45° (grazing). Excellent agreement with experiment (J. Am. Chem. Soc., 2000, 122, 9703-9714) is found for both the average fraction and distribution of the collision energy transferred to the ala2-H(+) internal degrees of freedom. The dominant pathway for this energy transfer is to ala2-H(+) vibration, but for Ei = 5.0 eV ∼20% of the energy transfer is to ala2-H(+) rotation. Energy transfer to ala2-H(+) rotation decreases with increase in Ei and becomes negligible at high Ei. Three types of collisions are observed in the simulations: i.e. those for which ala2-H(+) (1) directly scatters off the F-SAM surface; (2) sticks/physisorbs on/in the surface, but desorbs within the 10 ps numerical integration of the simulations; and (3) remains trapped (i.e. soft-landed) on/in the surface when the simulations are terminated. Penetration of the F-SAM by ala2-H(+) is important for the latter two types of events. The trapped trajectories are expected to have relatively long residence times on the surface, since a previous molecular dynamics simulation (J. Phys. Chem. B, 2014, 118, 5577-5588) shows that thermally accommodated ala2-H(+) ions have an binding energy with the F-SAM surface of at least ∼15 kcal mol(-1).

Direct dynamics simulations and selected ion flow tube (SIFT) experiments were performed to study the kinetics and dynamics of the OH(-) + CH3I reaction versus temperature. This work complements previous direct dynamics simulation and molecular beam ion imaging experiments of this reaction versus reaction collision energy (Xie et al. J. Phys. Chem. A 2013, 117, 7162). The simulations and experiments are in quite good agreement. Both identify the SN2, OH(-) + CH3I → CH3OH + I(-), and proton transfer, OH(-) + CH3I → CH2I(-) + H2O, reactions as having nearly equal importance. In the experiments, the SN2 pathway constitutes 0.64 ± 0.05, 0.56 ± 0.05, 0.51 ± 0.05, and 0.46 ± 0.05 of the total reaction at 210, 300, 400, and 500 K, respectively. For the simulations this fraction is 0.56 ± 0.06, 0.55 ± 0.04, and 0.50 ± 0.05 at 300, 400, and 500 K, respectively. The experimental total reaction rate constant is (2.3 ± 0.6) × 10(-9), (1.7 ± 0.4) × 10(-9), (1.9 ± 0.5) × 10(-9), and (1.8 ± 0.5) × 10(-9) cm(3) s(-1) at 210, 300, 400, and 500 K, respectively, which is approximately 25% smaller than the collision capture value. The simulation values for this rate constant are (1.7 ± 0.2) × 10(-9), (1.8 ± 0.1) × 10(-9), and (1.6 ± 0.1) × 10(-9) cm(3)s(-1) at 300, 400, and 500 K. From the simulations, direct rebound and stripping mechanisms as well as multiple indirect mechanisms are identified as the atomic-level reaction mechanisms for both the SN2 and proton-transfer pathways. For the SN2 reaction the direct and indirect mechanisms have nearly equal probabilities; the direct mechanisms are slightly more probable, and direct rebound is more important than direct stripping. For the proton-transfer pathway the indirect mechanisms are more important than the direct mechanisms, and stripping is significantly more important than rebound for the latter. Calculations were performed with the OH(-) quantum number J equal to 0, 3, and 6 to investigate the effect of OH(-) rotational excitation on the OH(-) + CH3I reaction dynamics. The overall reaction probability and the probabilities for the SN2 and proton-transfer pathways have little dependence on J. Possible effects on the atomistic mechanisms were investigated for the SN2 pathway and the probability of the direct rebound mechanism increased with J. However, the other atomistic mechanisms were not appreciably affected by J.

In a previous study (J. Phys. Chem. C 2011, 115, 12403), cluster models for the TiO2 rutile(110) surface and MP2 calculations were used to develop an analytic potential energy function for dimethyl methylphosphonate (DMMP) interacting with this surface. In the work presented here, this analytic potential and MP2 cluster models are compared to DFT “slab” calculations for DMMP interacting with the TiO2(110) surface and with DFT cluster models for the TiO2(110) surface. The DFT slab calculations were performed with the PW91 and PBE functionals. The analytic potential gives DMMP/TiO2(110) potential energy curves in excellent agreement with those obtained from the slab calculations. The cluster models for the TiO2(110) surface, used for the MP2 calculations, were extended to DFT calculations with the B3LYP, PW91, and PBE functionals. These DFT calculations do not give DMMP/TiO2(110) interaction energies that agree with those from the DFT slab calculations. Analyses of the wave functions for these cluster model...

In a direct dynamics simulation, the technologies of chemical dynamics and electronic structure theory are coupled so that the potential energy, gradient, and Hessian required from the simulation are obtained directly from the electronic structure theory. These simulations are extensively used to (1) interpret experimental results and understand the atomic-level dynamics of chemical reactions; (2) illustrate the ability of classical simulations to correctly interpret and predict chemical dynamics when quantum effects are expected to be unimportant; (3) obtain the correct classical dynamics predicted by an electronic structure theory; (4) determine a deeper understanding of when statistical theories are valid for predicting the mechanisms and rates of chemical reactions; and (5) discover new reaction pathways and chemical dynamics. Direct dynamics simulation studies are described for bimolecular SN2 nucleophilic substitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments, and semiclassical vibrational spectra. Also included are discussions of quantum effects, the accuracy of classical chemical dynamics simulation, and the methodology of direct dynamics.

Anti-E2, syn-E2, inv-, and ret-S

Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

Simulation results are presented for Xe atoms colliding with the {0001} surface of hexagonal ice (Ih) with incident energies EI of 3.88, 4.56, 5.71, and 6.50 eV and incident angles θI of 0, 25, 45,...

International audience; Direct dynamics simulations, utilizing the RM1 semiempirical electronic structure theory, were performed to study the thermal dissociation of the doubly protonated tripeptide threonine–isoleucine–lysine ion, TIK(H+)2, for temperatures of 1250–2500 K, corresponding to classical energies of 1778–3556 kJ/mol. The number of different fragmentation pathways increases with increase in temperature. At 1250 K there are only three fragmentation pathways, with one contributing 85% of the fragmentation. In contrast, at 2500 K, there are 61 pathways, and not one dominates. The same ion is often formed via different pathways, and at 2500 K there are only 14 m/z values for the product ions. The backbone and side-chain fragmentations occur by concerted reactions, with simultaneous proton transfer and bond rupture, and also by homolytic bond ruptures without proton transfer. For each temperature the TIK(H+)2 fragmentation probability versus time is exponential, in accord with the Rice–Ramsperger–Kassel–Marcus and transition state theories. Rate constants versus temperature were determined for two proton transfer and two bond rupture pathways. From Arrhenius plots activation energies Ea and A-factors were determined for these pathways. They are 62–78 kJ/mol and (2–3) × 1012 s–1 for the proton transfer pathways and 153–168 kJ/mol and (2–4) × 1014 s–1 for the bond rupture pathways. For the bond rupture pathways, the product cation radicals undergo significant structural changes during the bond rupture as a result of hydrogen bonding, which lowers their entropies and also their Ea and A parameters relative to those for C–C bond rupture pathways in hydrocarbon molecules. The Ea values determined from the simulation Arrhenius plots are in very good agreement with the reaction barriers for the RM1 method used in the simulations. A preliminary simulation of TIK(H+)2 collision-induced dissociation (CID), at a collision energy of 13 eV (1255 kJ/mol), was also performed to compare with the thermal dissociation simulations. Though the energy transferred to TIK(H+)2 in the collisions is substantially less than the energy for the thermal excitations, there is substantial fragmentation as a result of the localized, nonrandom excitation by the collisions. CID results in different fragmentation pathways with a significant amount of short time nonstatistical fragmentation. Backbone fragmentation is less important, and side-chain fragmentation is more important for the CID simulations as compared to the thermal simulations. The thermal simulations provide information regarding the long-time statistical fragmentation.