Direct Chemical Dynamics Simulations Research Articles

Collision Induced Dissociation of Deprotonated Isoxazole and 3-Methyl Isoxazole via Direct Chemical Dynamics Simulations.

Isoxazoles are an important class of organic compounds widely employed in synthesis and drug design. Fragmentation chemistry of the parent isoxazole molecule and its substituents has been the subject of several experimental and theoretical investigations. Collision induced dissociation (CID) of isoxazole and its substituents has been studied experimentally under negative ion conditions. Based on the observed reaction products, dissociation patterns were proposed. In the present work, we studied the dissociation chemistry of deprotonated isoxazole and 3-methyl isoxazole using electronic structure theory calculations and direct chemical dynamics simulations. Various deprotonated isomers of these molecules were activated by collision with an Ar atom, and the ensuing fractionation patterns were studied using on-the-fly classical trajectory simulations at the density functional B3LYP/6-31+G* level of electronic structure theory. A variety of reaction products and pathways were observed, and it was found that a nonstatistical shattering mechanism dominates the CID dynamics of these molecules. Simulation results are compared with experiments, and detailed atomic level dissociation mechanisms are presented.

Direct chemical dynamics simulations of CN- + CH3I bimolecular nucleophilic substitution reaction.

Bimolecular nucleophilic substitution reactions have been studied for more than a century. Experimental and theoretical investigations of these reactions are extensively going on due to their wide applicability and the discovery of new features of these reactions. The CN- + CH3I nucleophilic substitution reaction can result in two isomeric products (NCCH3/CNCH3 + I-) because the incoming nucleophile has two reactive centers. Velocity map imaging experiments of this reaction have been reported and dominant direct rebound dynamics and high internal energy excitation of the reaction products were found in the experiments. However, it was not possible to directly obtain the isomer branching ratios from the experimental data and statistical ratios were predicted based on a numerical simulation. In the present work, direct chemical dynamics simulations of this reaction were performed using density functional theory and semi-empirical potential energy surfaces. Reactivity was low at all collision energies and direct rebound dynamics was observed in a major fraction of trajectories in agreement with experiments. However, the branching ratios computed from the trajectories were different from the previously reported estimates. Product energy distributions and scattering angles were computed and detailed atomic level reaction mechanisms are presented.

Theoretical Investigation of Dissociation versus Intramolecular Rearrangements in Aminohydroxymethylene.

Aminohydroxymethylene (H2N-C̈-OH) is the simplest aminooxycarbene which is a heteroatom stabilized carbene. This highly reactive molecule was prepared in an Ar matrix in a recent experimental work. Unimolecular reactivity of this astrochemically important molecule was investigated and only fragmentations were identified contrary to the observations of both fragmentations and intramolecular rearrangements in other hydroxycarbenes. These rearrangement reactions form the corresponding imine and carbonyl compounds. In the present work, direct chemical dynamics simulations of unimolecular chemistry of aminohydroxymethylene were performed in the gas phase to study atomic level dissociation mechanisms. Classical trajectories were generated on-the-fly using potentials and gradients computed at the density functional B3LYP/6-31+G* level of electronic structure theory. Simulation results showed that intramolecular rearrangements accompany fragmentations during the unimolecular decay process of aminohydroxymethylene. However, the average lifetime of the intermediate isomers were found to be only few picoseconds which might not have been long enough for detection in the experiments.

Direct dynamics in a proton transfer reaction of isomer product competition. Insight into the suppressed formation of the isoformyl cation.

Proton transfer between HOCO+ and CO produces the formyl cation HCO+ and isoformyl cation HOC+ isomers initiating multiple astrochemical reaction networks. Here, the direct chemical dynamics simulations are performed to uncover the underlying atomistic dynamics of the above reaction. The simulations reproduce the measured product energy and scattering angle distributions and reveal that the reaction proceeds predominantly through a direct stripping mechanism which results in the prominent forward scattering observed in experiments. The reaction dynamics show propensity for the HCO+ product even at a collision energy larger than the threshold for HOC+ formation. This is a consequence of the larger opacity and impact parameter range for HCO+. In accordance with the revealed direct mechanistic feature, the reaction can be controlled by orienting the reactants into a reactive H-C orientation that also favors HCO+ formation. Considering the lack of equilibrated reactant complexes and the on the fly migration of the proton, the CO2-catalyzed isomerization is assumed to have insignificant impact on the isomer ratios. This work provides insights of dynamical effects besides energetics into the interesting finding of strongly suppressed formation of the metastable isoformyl cation for related proton transfer reactions in the measurements.

Chemical dynamics simulations of collision induced dissociation of deprotonated glycolaldehyde

First step of formose or Butlerov reaction involves C–C bond formation between two formaldehyde molecules resulting in glycolaldehyde. This reaction happens under basic conditions in solution. A tandem mass spectrometry investigation of dissociation of deprotonated glycolaldehyde in the gas phase, to study the formose reaction in a retro-synthetic point of view, has been reported. In the present work, we have carried out electronic structure theory calculations and quasi-classical direct chemical dynamics simulations to model the gas phase dissociation of the conjugate base of glycolaldehyde. The dynamics simulations were performed on-the-fly using the hybrid density functional B3LYP theory with the 6-31+G∗ basis set under collision induced dissociation (CID) conditions. Trajectories were launched with two different deprotonated forms of glycolaldehyde for a range of collision energies mimicking experiments. Reverse formose reaction was observed primarily from the slightly higher energy isomer via a non-statistical pathway. Intramolecular hydrogen transfer was ubiquitous in the trajectories. Simulation results were compared with experiments and detailed atomic level dissociation mechanisms are presented.

Unimolecular Dissociation of γ-Ketohydroperoxide via Direct Chemical Dynamics Simulations.

γ-Ketohydroperoxide [3-(hydroperoxy)propanal] is an important reagent in synthetic chemistry and, in particular, oxidation reactions. It is considered to be a precursor for secondary organic aerosol formation in the troposphere. Due to enhanced reactivity and limitations associated with analytical techniques, theoretical methods have been employed to study the unimolecular reactivity of hydroperoxides. A number of automated reaction discovery techniques have been used to study the reactivity of γ-ketohydroperoxide, and a large number of reactions have been reported in such studies. In the present work, we have investigated the unimolecular reaction dynamics of this molecule using electronic structure theory calculations and direct chemical dynamics simulations to assess the relevance of different reaction pathways. Classical trajectories were launched from the reactant well with fixed amounts of total energies and integrated on-the-fly using density functional B3LYP/6-31+G* model chemistry. Three dissociation channels among the previously reported reactions were identified as important. Korcek decomposition, which was proposed earlier as a source of carbonyl compounds from thermal decomposition of γ-ketohydroperoxide, was not observed in the present high-temperature simulations. However, trajectories showed the formation of carbonyl compounds such as aldehydes via other pathways. Results are compared with previous studies, and detailed atomic-level reaction mechanisms are presented.

Competing Molecular and Radical Pathways in the Dissociation of Halons via Direct Chemical Dynamics Simulations.

A great deal of attention has been given to the decomposition chemistry of halons (halomethanes) due to their role in stratospheric ozone depletion. Knowledge of certain aspects of dissociation of halons such as the competition between radical and molecular pathways and their mechanistic details is limited. Halon molecules can isomerize to an iso form containing a halogen-halogen bond and such iso-halon forms have been identified as intermediates in condensed phase chemistry. Recently, a quantum chemistry study of role of iso-halons in the gas phase decomposition of halomethanes has been reported. In the present work, we have investigated the ground state dissociation chemistry of select halon molecules - CF2Cl2, CF2Br2, CHBr3, and CH2BrCl using electronic structure theory calculations and direct chemical dynamics simulations. Classical trajectories were generated on-the-fly using density functional PBE0/6-31G* level of theory at a fixed total energy. Simulation results showed that molecular products, in general, were dominant for all the four molecules at the chosen energy. A variety of mechanisms such as direct dissociation via multicenter transition states, decomposition via isomerization, radical recombinations, and roaming pathways contributed to the formation of molecular products. Atomic level mechanisms are presented, and the role of iso-halons in the gas phase chemistry of halomethanes is clearly established.

Exploratory Direct Dynamics Simulations of 3O2 Reaction with Graphene at High Temperatures

Direct chemical dynamics simulations at high temperatures of reaction between 3O2 and graphene containing varied number of defects were performed using the VENUS-MOPAC code. Graphene was modeled using (5a,6z)-periacene, a poly aromatic hydrocarbon with 5 and 6 benzene rings in the armchair and zigzag directions, respectively. Up to six defects were introduced by removing carbon atoms from the basal plane. Usage of the PM7/unrestricted Hartree–Fock (UHF) method, for the simulations, was validated by benchmarking singlet-triplet gaps of n-acenes and (5a,nz) periacenes with high-level theoretical calculations. PM7/UHF calculations showed that graphene with different number of vacancies has different ground electronic states. Dynamics simulations were performed for two 3O2 collision energies Ei of 0.4 and 0.7 eV, with the incident angle normal to the graphene plane at 1375 K. Collisions on graphene with one, two, three, and four vacancies (1C-, 2C-, 3C-, and 4C-vacant graphene) showed no reactive trajectories...

Theoretical study of perbenzoate anion decomposition pathways in the gas phase

Perbenzoic acid (a weak organic acid) and its conjugate base (perbenzoate anion, C6H5C(O)O2−) are important organic reagents used extensively in synthetic chemistry. A few studies are available in the literature on the structure and reactivity of the perbenzoate anion. Gas phase dissociation of the perbenzoate anion and its substituted analogues by collision induced dissociation mass spectrometry experiments revealed carbon dioxide (CO2) loss as the major dissociation pathway. CO2 loss was proposed to occur via intramolecular nucleophilic attack by the negatively charged oxygen atom at the ipso or ortho position of the benzene ring. In the present work, we investigated decomposition pathways of perbenzoate anion in the gas phase via classical direct chemical dynamics simulations to establish the atomic level reaction mechanisms. Classical trajectories were integrated on-the-fly using the density functional B3LYP/6-31+G* level of electronic structure theory. Removal of CO3, CO2 from the perbenzoate anion and isomerization to an oxydioxirane intermediate were the primary reaction pathways observed in the simulations. In a major fraction of the trajectories, elimination of CO2 happened via initial CO3 loss from the perbenzoate anion followed by removal of O atom from the unstable neutral CO3 molecule.

Dynamic exit-channel pathways of the microsolvated HOO-(H2O) + CH3Cl SN2 reaction: Reaction mechanisms at the atomic level from direct chemical dynamics simulations.

Microsolvated bimolecular nucleophilic substitution (SN2) reaction of monohydrated hydrogen peroxide anion [HOO-(H2O)] with methyl chloride (CH3Cl) has been investigated with direct chemical dynamics simulations at the M06-2X/6-31+G(d,p) level of theory. Dynamic exit-channel pathways and corresponding reaction mechanisms at the atomic level are revealed in detail. Accordingly, a product distribution of 0.85:0.15 is obtained for Cl-:Cl-(H2O), which is consistent with a previous experiment [D. L. Thomsen et al. J. Am. Chem. Soc. 135, 15508 (2013)]. Compared with the HOO- + CH3Cl SN2 reaction, indirect dynamic reaction mechanisms are enhanced by microsolvation for the HOO-(H2O) + CH3Cl SN2 reaction. On the basis of our simulations, further crossed molecular beam imaging experiments are highly suggested for the SN2 reactions of HOO- + CH3Cl and HOO-(H2O) + CH3Cl.

Steric Effects of Solvent Molecules on SN2 Substitution Dynamics.

Influences of solvent molecules on SN2 reaction dynamics of microsolvated F-(H2O)n with CH3I, for n = 0-3, are uncovered by direct chemical dynamics simulations. The direct substitution mechanism, which is important without microsolvation, is quenched dramatically upon increasing hydration. The water molecules tend to force reactive encounters to proceed through the prereaction collision complex leading to indirect reaction. In contrast to F-(H2O), reaction with higher hydrated ions shows a strong propensity for ion desolvation in the entrance channel, diminishing steric hindrance for nucleophilic attack. Thus, nucleophilic substitution avoids the potential energy barrier with all of the solvent molecules intact and instead occurs through the less solvated barrier, which is energetically unexpected because the former barrier has a lower energy. The work presented here reveals a trade-off between reaction energetics and steric effects, with the latter found to be crucial in understanding how hydration influences microsolvated SN2 dynamics.

Microsolvated F(-)(H2O) + CH3I S(N)2 Reaction Dynamics. Insight into the Suppressed Formation of Solvated Products.

Microsolvation offers a bottom-up approach to investigate details of how solute-solvent interactions affect chemical reaction dynamics. The dynamics of the microsolvated S(N)2 reaction F(-)(H2O) + CH3I are uncovered in detail by using direct chemical dynamics simulations. Direct rebound and stripping and indirect atomic-level mechanisms are observed. The indirect events comprise ∼70% of the solvated reaction and occur predominantly via a hydrogen-bonded F(-)(H2O)···HCH2I prereaction complex. The reaction dynamics show propensity for the direct three-body dissociation channel F(-)(H2O) + CH3I → CH3F + I(-) + H2O after passing the reaction's dynamical bottleneck. The water molecule leaves the reactive system before traversing the postreaction region of the PES, where water transfer toward the product species occurs. This provides an insight into the very interesting finding of strongly suppressed formation of energetically favored solvated products for almost all SN2 reactions under microsolvation.

Dynamics of the F(-) + CH3I → HF + CH2I(-) Proton Transfer Reaction.

Direct chemical dynamics simulations, at collision energies Erel of 0.32 and 1.53 eV, were performed to obtain an atomistic understanding of the F(-) + CH3I reaction dynamics. There is only the F(-) + CH3I → CH3F + I(-) bimolecular nucleophilic substitution SN2 product channel at 0.32 eV. Increasing Erel to 1.53 eV opens the endothermic F(-) + CH3I → HF + CH2I(-) proton transfer reaction, which is less competitive than the SN2 reaction. The simulations reveal proton transfer occurs by two direct atomic-level mechanisms, rebound and stripping, and indirect mechanisms, involving formation of the F(-)···HCH2I complex and the roundabout. For the indirect trajectories all of the CH2I(-) is formed with zero-point energy (ZPE), while for the direct trajectories 50% form CH2I(-) without ZPE. Without a ZPE constraint for CH2I(-), the reaction cross sections for the rebound, stripping, and indirect mechanisms are 0.2 ± 0.1, 1.2 ± 0.4, and 0.7 ± 0.2 Å(2), respectively. Discarding trajectories that do not form CH2I(-) with ZPE reduces the rebound and stripping cross sections to 0.1 ± 0.1 and 0.7 ± 0.5 Å(2). The HF product is formed rotationally and vibrationally unexcited. The average value of J is 2.6 and with histogram binning n = 0. CH2I(-) is formed rotationally excited. The partitioning between CH2I(-) vibration and HF + CH2I(-) relative translation energy depends on the treatment of CH2I(-) ZPE. Without a CH2I(-) ZPE constraint the energy partitioning is primarily to relative translation with little CH2I(-) vibration. With a ZPE constraint, energy partitioning to CH2I(-) rotation, CH2I(-) vibration, and relative translation are statistically the same. The overall F(-) + CH3I rate constant at Erel of both 0.32 and 1.53 eV is in good agreement with experiment and negligibly affected by the treatment of CH2I(-) ZPE, since the SN2 reaction is the major contributor to the total reaction rate constant. The potential energy surface and reaction dynamics for F(-) + CH3I proton transfer are compared with those reported previously (J. Phys. Chem. A 2013, 117, 7162-7178) for the isoelectronic OH(-) + CH3I reaction.

Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments.

In this study we have coupled mixed quantum-classical (quantum mechanics/molecular mechanics) direct chemical dynamics simulations with electrospray ionization/tandem mass spectrometry experiments in order to achieve a deeper understanding of the fragmentation mechanisms occurring during the collision induced dissociation of gaseous protonated uracil. Using this approach, we were able to successfully characterize the fragmentation pathways corresponding to ammonia loss (m/z 96), water loss (m/z 95) and cyanic or isocyanic acid loss (m/z 70). Furthermore, we also performed experiments with isotopic labeling completing the fragmentation picture. Remarkably, fragmentation mechanisms obtained from chemical dynamics simulations are consistent with those deduced from isotopic labeling.

Comparison of direct dynamics simulations with different electronic structure methods. F(-) + CH3I with MP2 and DFT/B97-1.

In previous work, ion imaging experiments and direct chemical dynamics simulations with DFT/B97-1 were performed to study the atomic-level dynamics of the F(-) + CH3I → FCH3 + I(-) SN2 nucleophilic substitution reaction at different collision energies. Overall, the simulations are in quite good agreement with experiment at the low collision energy of 0.32 eV, however there are differences between experiment and simulation at the high collision energy of 1.53 eV. A recent CCSD(T) study of the potential energy surface for the F(-) + CH3I → FCH3 + I(-) SN2 reaction shows that it has both a traditional C3v and a hydrogen-bond entrance channel. They are represented by MP2 but not by B97-1, which has only the latter channel. On the other hand, B97-1 gives a reaction exothermicity in excellent agreement with experiment, while MP2 is in error by 24.3 kJ mol(-1). In the work presented here, direct dynamics simulations using MP2/aug-cc-pvdz/ECP/d were performed for the F(-) + CH3I → FCH3 + I(-) reaction at a 1.53 eV collision energy. The same direct rebound and stripping and indirect atomistic reaction mechanisms are found in the B97-1 and MP2 simulations. Both the B97-1 and MP2 simulations agree with the experimental fraction of the available product energy partitioned to CH3F internal energy, i.e. fint = 0.59 ± 0.08. However, the MP2 fint distribution is broader and in better agreement with experiment than B97-1. The two simulations methods give the same product energy partitioning for the stripping mechanism, but different partitionings for the rebound and indirect mechanisms. Compared to experiment, the principal difference between the B97-1 and MP2 results is the differential cross section which is nearly isotropic for B97-1. For MP2 backward scattering is more important than forward, as found in the experiments. Though there is no overall barrier for the reaction, B97-1 gives a reaction cross section appreciably larger than that for MP2, i.e. 8.6 ± 2.2 Å(2)versus 1.8 ± 0.3 Å(2). For B97-1 59% of the reaction consists of indirect mechanisms, while for MP2 the indirect mechanisms only comprise 11% of the reaction. The experimental differential cross section is more consistent with the atomistic mechanisms for MP2 than for B97-1.

Galactose-6-Sulfate collision induced dissociation using QM + MM chemical dynamics simulations and ESI-MS/MS experiments

This work combines theoretical and experimental approaches to explore the fragmentation mechanisms occurring during the collision-induced dissociation (CID) of Galactose-6-Sulfate (Gal-6S). This compound is a building block of sulfated sugars and its study can shed light on fragmentation mechanisms occurring for other related systems. In particular, to understand in detail the fragmentation mechanisms at the molecular level, we have coupled mixed quantum/classical (QM+MM) direct chemical dynamics simulations with tandem mass spectrometry (MS/MS) experiments. Our results, on one hand, are in a good agreement with the “charge-remote” picture, which is usually proposed in the literature as fragmentation mechanism to account for the formation of many fragment ions. On the other hand, to reproduce some of the fragments ions obtained during our experiments, alternate dissociation pathways are proposed.

ChemInform Abstract: Direct Chemical Dynamics Simulations: Coupling of Classical and Quasiclassical Trajectories with Electronic Structure Theory

AbstractReview: 123 refs.

Indirect Dynamics in a Highly Exoergic Substitution Reaction

The highly exoergic nucleophilic substitution reaction F(-) + CH3I shows reaction dynamics strikingly different from that of substitution reactions of larger halogen anions. Over a wide range of collision energies, a large fraction of indirect scattering via a long-lived hydrogen-bonded complex is found both in crossed-beam imaging experiments and in direct chemical dynamics simulations. Our measured differential scattering cross sections show large-angle scattering and low product velocities for all collision energies, resulting from efficient transfer of the collision energy to internal energy of the CH3F reaction product. Both findings are in strong contrast to the previously studied substitution reaction of Cl(-) + CH3I [Science 2008, 319, 183-186] at all but the lowest collision energies, a discrepancy that was not captured in a subsequent study at only a low collision energy [J. Phys. Chem. Lett. 2010, 1, 2747-2752]. Our direct chemical dynamics simulations at the DFT/B97-1 level of theory show that the reaction is dominated by three atomic-level mechanisms, an indirect reaction proceeding via an F(-)-HCH2I hydrogen-bonded complex, a direct rebound, and a direct stripping reaction. The indirect mechanism is found to contribute about one-half of the overall substitution reaction rate at both low and high collision energies. This large fraction of indirect scattering at high collision energy is particularly surprising, because the barrier for the F(-)-HCH2I complex to form products is only 0.10 eV. Overall, experiment and simulation agree very favorably in both the scattering angle and the product internal energy distributions.

Gas-phase collision induced dissociation mechanisms of peptides: Theoretical and experimental study of N-formylalanylamide fragmentation

In order to shed light on the fragmentation mechanisms occurring during the collision induced dissociation (CID) of peptides in the gas phase, we have studied a model system, the N-formylalanylamide (HCO-Ala-NH2), by coupling experimental and theoretical methods. In particular, we have addressed two different questions arising in such experiments: (i) what is (are) the structure(s) of the ion before collision, and (ii) what are the fragmentation mechanisms occurring after collision with the target gas. For the first question, we coupled the potential energy surface (PES) study done by means of density functional theory (DFT), with Infra Red Multiple Photon Dissociation (IRMPD) spectroscopy. For the second problem, which is actually the main topic of the present work, we coupled quantum mechanics plus molecular mechanics (QM+MM) direct chemical dynamics simulations with tandem mass spectrometry (MS/MS). In addition, in order to better delineate the fragmentation mechanisms and validate those proposed by simulations, isotopic labeling experiments using 2H and 13C were performed. Thanks to the interplay between simulations and experiments, it was possible to successfully identify the fragmentation pathways leading to b1, y1, a1 and immonium ions. Our mechanisms support the “mobile proton” picture that is supposed to trigger the peptide fragmentation in the gas phase, confirming, from a chemical dynamics point of view, previous theoretical and experimental studies on similar systems.

Direct chemical dynamics simulations: coupling of classical and quasiclassical trajectories with electronic structure theory

AbstractIn classical and quasiclassical trajectory chemical dynamics simulations, the atomistic dynamics of collisions, chemical reactions, and energy transfer are studied by solving the classical equations of motion. These equations require the potential energy and its gradient for the chemical system under study, and they may be obtained directly from an electronic structure theory. This article reviews such direct dynamics simulations. The accuracy of classical chemical dynamics is considered, with simulations highlighted for the F− + CH3OOH reaction and of energy transfer in collisions of CO2 with a perfluorinated self‐assembled monolayer (F‐SAM) surface. Procedures for interfacing chemical dynamics and electronic structure theory computer codes are discussed. A Hessian‐based predictor–corrector algorithm and high‐accuracy Hessian updating algorithm, for enhancing the efficiency of direct dynamics simulations, are described. In these simulations, an ensemble of trajectories is calculated which represents the experimental and chemical system under study. Algorithms are described for selecting the appropriate initial conditions for bimolecular and unimolecular reactions, gas‐surface collisions, and initializing trajectories at transition states and conical intersections. Illustrative direct dynamics simulations are presented for the Cl− + CH3I SN2 reaction, unimolecular decomposition of the epoxy resin constituent CH3NHCHCHCH3 versus temperature, collisions and reactions of N‐protonated diglycine with a F‐SAM surface that has a reactive head group, and the product energy partitioning for the post‐transition state dynamics of C2H5F → HF + C2H4 dissociation. © 2012 John Wiley & Sons, Ltd.This article is categorized under: Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics