Chemical dynamics trajectory simulations were used to study the atomic-level mechanisms of the OH- + CH3F --> CH3OH + F- SN2 nucleophilic substitution reaction. The reaction dynamics, from the [OH...CH3...F]- central barrier to the reaction products, are simulated by ab initio direct dynamics. The reaction's potential energy surface has a deep minimum in the product exit channel arising from the CH3OH...F- hydrogen-bonded complex. Statistical theories of unimolecular reaction rates assume that the reactive system becomes trapped in this minimum and forms an intermediate, with random redistribution of its vibrational energy, but the majority of the trajectories (90%) avoided this potential energy minimum and instead dissociated directly to products. This finding is discussed in terms of intramolecular vibrational energy redistribution (IVR) and the relation between IVR and molecular structure. The finding of this study may be applicable to other reactive systems where there is a hierarchy of time scales for intramolecular motions and thus inefficient IVR.

https://science.sciencemag.org/content/sci/296/5569/875.full.pdf

A SN2 Reaction That Avoids Its Deep Potential Energy Minimum

Blackbody infrared radiative dissociation (BIRD) describes the observation of ion-dissociation reactions at essentially zero pressure by the ambient blackbody radiation field, which is usually studied in the ion-trapping ion cyclotron resonance (ICR) mass spectrometer. A brief summary of the historical context and evolution is provided. Focussing on the quantitative observation of the temperature dependence of BIRD rates, methods are developed for connecting BIRD observations with activation parameters and dissociation thermochemistry. Three regimes are differentiated and described, comprising large molecules, small molecules, and intermediate-sized molecules. The different approaches to interpreting BIRD kinetics in those three regimes are discussed. In less than a decade since its inception, this approach to studying gas-phase ions has spread over a wide variety of applications, which are surveyed. Some major areas of activity are: the characterization of solvent-molecule detachment from solvated ions; dissociation reactions of biomolecules (polypeptides, oligonucleotides, complexes involving polysaccharides) and the structural information to be deduced from them; and dissociations of proton-bound and metal-ion-containing complexes. Studies of blackbody-radiation-driven evaporation of water molecules from large water-cluster ions are surveyed briefly. Several techniques related to BIRD are noted, including collisional dissociation in the FT-ICR ion trap; high-pressure thermal dissociation in quadrupole ion traps and in heated inlet capillary regions; hot-filament-assisted dissociation; and infrared multiphoton dissociation (IRMPD).

BIRD (blackbody infrared radiative dissociation): evolution, principles, and applications.

Molecular activation by blackbody photons, first postulated in 1919 by Perrin, plays a dominant role in the unimolecular dissociation of large ions trapped at low pressure in a Fourier-transform mass spectrometer. Under readily achievable experimental conditions, molecular ions of the protein ubiquitin equilibrate with the blackbody radiation field inside the vacuum chamber. The internal energy of a population of these ions is given by a Boltzmann distribution. From the temperature dependence of unimolecular dissociation rate constants measured in the zero-pressure limit, Arrhenius activation parameters equal to those in the high-pressure limit are obtained.

/pdf/unimolecular-reaction-kinetics-in-the-high-pressure-limit-4l43qvppfo.pdf

Unimolecular reaction kinetics in the high-pressure limit without collisions.

FT-ICR Studies of Solvation Effects in Ionic Water Cluster Reactions.

Extensive classical chemical dynamics simulations of gas-phase X(-) + CH(3)Y → XCH(3) + Y(-) S(N)2 nucleophilic substitution reactions are reviewed and discussed and compared with experimental measurements and predictions of theoretical models. The primary emphasis is on reactions for which X and Y are halogen atoms. Both reactions with the traditional potential energy surface (PES), which include pre- and postreaction potential energy minima and a central barrier, and reactions with nontraditional PESs are considered. These S(N)2 reactions exhibit important nonstatistical atomic-level dynamics. The X(-) + CH(3)Y → X(-)---CH(3)Y association rate constant is less than the capture model as a result of inefficient energy transfer from X(-)+ CH(3)Y relative translation to CH(3)Y rotation and vibration. There is weak coupling between the low-frequency intermolecular modes of the X(-)---CH(3)Y complex and higher frequency CH(3)Y intramolecular modes, resulting in non-RRKM kinetics for X(-)---CH(3)Y unimolecular decomposition. Recrossings of the [X--CH(3)--Y](-) central barrier is important. As a result of the above dynamics, the relative translational energy and temperature dependencies of the S(N)2 rate constants are not accurately given by statistical theory. The nonstatistical dynamics results in nonstatistical partitioning of the available energy to XCH(3) +Y(-) reaction products. Besides the indirect, complex forming atomic-level mechanism for the S(N)2 reaction, direct mechanisms promoted by X(-) + CH(3)Y relative translational or CH(3)Y vibrational excitation are possible, e.g., the roundabout mechanism.

Chemical dynamics simulations of X- + CH3Y → XCH3 + Y- gas-phase S(N)2 nucleophilic substitution reactions. Nonstatistical dynamics and nontraditional reaction mechanisms.

The unimolecular dissociation of the molecular ion of acetophenone induced by thermal radiation

Stationary points for the OH− + CH3F → CH3OH + F− potential energy surface

Unimolecular dissociation reactions of gas-phase partially solvated transition metal complex ions, diamminebis(2,2‘-bipyridine)ruthenium(II), [Ru(NH3)2(bipy)2]2+, tetraammine(2,2‘-bipyridine)ruthenium(II), [Ru(NH3)4bipy]2+, and pentaammine(2-methylpyrazine)ruthenium(II), [Ru(NH3)5MePyz]3+, have been investigated with electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI−FTICR/MS) under low pressure (<10-8 mbar) conditions. Under these conditions, dissociation of solvent from the complex ions is driven primarily by absorption of blackbody photons from the FTICR analyzer cell walls, that is, via blackbody infrared radiative dissociation (BIRD), with little collisional contribution at pressures below 10-8 mbar. The replacement of ammine hydrogens with deuterium increases measured BIRD rate constants. Optimized geometries, vibrational frequencies, and IR absorption band intensities have been calculated for the complexes by semiempirical and ab initio methods. These calculate...

Blackbody Infrared Radiative Dissociation of Partially Solvated Mixed Ligand Ru(II) Complex Ions

Electrospray ionization Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry has been utilized to study solvates of tris(2,2‘-bipyridine)ruthenium(II). Spontaneous dissociation of solvent (acetonitrile, acetone, or methyl ethyl ketone) from the solvation shell occurs when these ions are trapped for extended periods of time in the ICR cell. The pressures employed in these experiments are low enough (10-9 to 10-8 mbar) to neglect (or partially neglect) collisional activation as a means for dissociation. Therefore, it is suggested that the solvated ruthenium species undergo dissociation following the absorption of blackbody infrared radiation. Solvent−complex dissociation has been studied at several pressures ranging from 10-9 to 10-8 mbar to provide a range of dissociation data in the low-pressure regime. The results reported here demonstrate the consistency of the dissociation rate constants at pressures that differ by an order of magnitude. Temperature dependence studies were performed ...

Blackbody Infrared Radiative Dissociation of Partially Solvated Tris(2,2‘-bipyridine)ruthenium(II) Complex Ions†

Three important aspects are still at the forefront of gas-phase ion chemistry: structure and energetics, mechanisms of gas-phase reactions relevant to condensed phases, and bridging the gap between gas-phase and solution. In this paper, we review some recent results of our laboratories: 1) The use of incoherent infrared radiation to promote multiphoton dissociation of ions is shown to be an efficient and convenient method to determine the energetics of ions and provide structural information of ions. 2) New experimental and theoretical data provide some interesting comparison between nucleophilic reactions at carbon, silicon and germanium centers. In the latter cases, the mechanism involves primarily an attachment-detachment process. 3) The ability to make gas-phase anions attached to neutral molecules provides an interesting approach towards the study of the stability, reactivity, structure and spectroscopy of gas-phase solvated ions.

/pdf/recent-advances-in-the-energetics-and-mechanisms-of-gas-1zbo94xxo6.pdf

Marcelo Sena

Papers

The unimolecular dissociation of the molecular ion of acetophenone induced by thermal radiation

Stationary points for the OH− + CH3F → CH3OH + F− potential energy surface

Blackbody Infrared Radiative Dissociation of Partially Solvated Mixed Ligand Ru(II) Complex Ions

Blackbody Infrared Radiative Dissociation of Partially Solvated Tris(2,2‘-bipyridine)ruthenium(II) Complex Ions†

Recent advances in the energetics and mechanisms of gas-phase ionic reactions