More Like this

1. Sub-Doppler infrared spectroscopy of resonance-stabilized hydrocarbon intermediates: ν 3 / ν 4 CH stretch modes and CH 2 internal rotor dynamics of benzyl radical

   https://doi.org/10.1039/c7cp05776h  

   Kortyna, A. ; Samin, A. J. ; Miller, T. A. ; Nesbitt, D. J. ( January 2017 , Physical Chemistry Chemical Physics)

   Highly reactive benzyl radicals are generated by electron dissociative attachment to benzyl chloride doped into a neon–hydrogen–helium discharge and immediately cooled to T rot = 15 K in a high density, supersonic slit expansion environment. The sub-Doppler spectra are fit to an asymmetric-top rotational Hamiltonian, thereby yielding spectroscopic constants for the ground ( v = 0) and first excited ( v = 1, ν 3 , ν 4 ) vibrational levels of the ground electronic state. The rotational constants obtained for the ground state are in good agreement with previous laser induced fluorescence measurements (LIF), with vibrational band origins ( ν 3 = 3073.2350 ± 0.0006 cm −1 , ν 4 = 3067.0576 ± 0.0006 cm −1 ) in agreement with anharmonically corrected density functional theory calculations. To assist in detection of benzyl radical in the interstellar medium, we have also significantly improved the precision of the ground state rotational constants through combined analysis of the ground state IR and LIF combination differences. Of dynamical interest, there is no evidence in the sub-Doppler spectra for tunneling splittings due to internal rotation of the CH 2 methylene subunit, which implies a significant rotational barrier consistent with partial double bond character in the CC bond. This is further confirmed with high level ab initio calculations at the CCSD(T)-f12b/ccpVdZ-f12 level, which predict a zero-point energy corrected barrier to internal rotation of Δ E tun ≈ 11.45 kcal mol −1 or 4005 cm −1 . In summary, the high-resolution infrared spectra are in excellent agreement with simple physical organic chemistry pictures of a strongly resonance-stabilized benzyl radical with a nearly rigid planar structure due to electron delocalization around the aromatic ring. 

   more » « less
2. Hidden complexities in the reaction of H 2 O 2 and HNO revealed by ab initio quantum chemical investigations

   https://doi.org/10.1039/c7cp05883g  

   Beckett, Daniel ; Edelmann, Marc ; Raff, Jonathan D. ; Raghavachari, Krishnan ( January 2017 , Physical Chemistry Chemical Physics)

   Nitroxyl (HNO) and hydrogen peroxide have both been implicated in a variety of reactions relevant to environmental and physiological processes and may contribute to a unique, unexplored, pathway for the production of nitrous acid (HONO) in soil. To investigate the potential for this reaction, we report an in-depth investigation of the reaction pathway of H 2 O 2 and HNO forming HONO and water. We find the breaking of the peroxide bond and a coupled proton transfer in the first step leads to hydrogen nitryl (HNO 2 ) and an endogenous water, with an extrapolated NEVPT2 (multireference perturbation theory) barrier of 29.3 kcal mol −1 . The first transition state is shown to possess diradical character linking the far peroxide oxygen to the bridging, reacting, peroxide oxygen. The energy of this first step, when calculated using hybrid density functional theory, is shown to depend heavily on the amount of Hartree–Fock exchange in the functional, with higher amounts leading to a higher barrier and more diradical character. Additionally, high amounts of spin contamination cause CCSD(T) to significantly overestimate the TS1 barrier with a value of 36.2 kcal mol −1 when using the stable UHF wavefunction as the reference wavefunction. However, when using the restricted Hartree–Fock reference wavefunction, the TS1 CCSD(T) energy is lowered to yield a barrier of 31.2 kcal mol −1 , in much better agreement with the NEVPT2 result. The second step in the reaction is the isomerization of HNO 2 to trans -HONO through a Grotthuss-like mechanism accepting a proton from and donating a proton to the endogenous water. This new mechanism for the isomerization of HNO 2 is shown to have an NEVPT2 barrier of 23.3 kcal mol −1 , much lower than previous unimolecular estimates not including an explicit water. Finally, inclusion of an additional explicit water is shown to lower the HNO 2 isomerization barrier even further. 

   more » « less
3. High-resolution CH stretch spectroscopy of jet-cooled cyclopentyl radical: First insights into equilibrium structure, out-of-plane puckering, and IVR dynamics

   https://doi.org/10.1063/5.0096946  

   Kortyna, Andrew ; Reber, Melanie A. ; Nesbitt, David J. ( July 2022 , The Journal of Chemical Physics)

   First, high-resolution sub-Doppler infrared spectroscopic results for cyclopentyl radical (C 5 H 9 ) are reported on the α-CH stretch fundamental with suppression of spectral congestion achieved by adiabatic cooling to T rot ≈ 19(4) K in a slit jet expansion. Surprisingly, cyclopentyl radical exhibits a rotationally assignable infrared spectrum, despite 3N − 6 = 36 vibrational modes and an upper vibrational state density (ρ ≈ 40–90 #/cm −1 ) in the critical regime (ρ ≈ 100 #/cm −1 ) necessary for onset of intramolecular vibrational relaxation (IVR) dynamics. Such high-resolution data for cyclopentyl radical permit detailed fits to a rigid-rotor asymmetric top Hamiltonian, initial structural information for ground and vibrationally excited states, and opportunities for detailed comparison with theoretical predictions. Specifically, high level ab initio calculations at the coupled-cluster singles, doubles, and perturbative triples (CCSD(T))/ANO0, 1 level are used to calculate an out-of-plane bending potential, which reveals a C 2 symmetry double minimum 1D energy surface over a C 2v transition state. The inversion barrier [V barrier ≈ 3.7(1) kcal/mol] is much larger than the effective moment of inertia for out-of-plane bending, resulting in localization of the cyclopentyl wavefunction near its C 2 symmetry equilibrium geometry and tunneling splittings for the ground state too small (<1 MHz) to be resolved under sub-Doppler slit jet conditions. The persistence of fully resolved high-resolution infrared spectroscopy for such large cyclic polyatomic radicals at high vibrational state densities suggests a “deceleration” of IVR for a cycloalkane ring topology, much as low frequency torsion/methyl rotation degrees of freedom have demonstrated a corresponding “acceleration” of IVR processes in linear hydrocarbons. 

   more » « less
4. Semiclassical transition state theory/master equation kinetics of HO + CO: Performance evaluation

   https://doi.org/10.1002/kin.21420  

   Barker, John R. ; Stanton, John F. ; Nguyen, Thanh Lam ( September 2020 , International Journal of Chemical Kinetics)

   Previously, master equation (ME) simulations using semiclassical transition state theory (SCTST) and high‐accuracy extrapolated ab initio thermochemistry (HEAT) predicted rate constants in excellent agreement with published experimental data over a wide range of pressure and temperatures ≳250 K, but the agreement was not as good at lower temperatures. Possible reasons for this reduced performance are investigated by (a) critically evaluating the published experimental data and by investigating; (b) three distinct ME treatments of angular momentum, including one that is exact at the zero‐ and infinite‐pressure limits; (c) a hindered‐rotor model for HOCO that implicitly includes the cis‐ and trans‐conformers; (d) possible empirical adjustments of the thermochemistry; (e) possible empirical adjustments to an imaginary frequency controlling tunneling; (f) including or neglecting the prereaction complex PRC1; and (g) its possible bimolecular reactions. Improvements include better approximations to factors in SCTST and using the Hill and van Vleck treatment of angular momentum coupling. Evaluation of literature data does not reveal any specific shortcomings, but the stated uncertainties may be underestimated. All ME treatments give excellent fits to experimental data atT≥ 250 K, but the discrepancy atT < 250 K persists. Note that each ME model requires individual empirical energy transfer parameters. Thermochemical adjustments were unable to match the experimental H/D kinetic isotope effects. Adjusting an imaginary frequency can achieve good fits, but the adjustments are unacceptably large. Whether PRC1 and its possible bimolecular reactions are included had little effect. We conclude that none of the adjustments is an improvement over the unadjusted theory. Note that only one set of experimental data exists in the regime of the discrepancy with theory, and data for DO + CO are scanty.

    

   more » « less
5. Isomerization of trans ‐3‐methylglutaconic acid

   https://doi.org/10.1002/jmd2.12185  

   Jones, Dylan E. ; Ricker, J. David ; Geary, Laina M. ; Kosma, Dylan K. ; Ryan, Robert O. ( November 2020 , JIMD Reports)

   3‐Methylglutaconic (3MGC) aciduria is a common phenotypic feature of a growing number of inborn errors of metabolism. “Primary” 3MGC aciduria is caused by deficiencies in leucine pathway enzymes while “secondary” 3MGC aciduria results from inborn errors of metabolism that impact mitochondrial energy production. The metabolic precursor of 3MGC acid istrans‐3MGC CoA, an intermediate in the leucine catabolism pathway. Gas chromatography‐mass spectrometry (GC‐MS) analysis of commercially availabletrans‐3MGC acid yielded a mixture ofcisandtransisomers while¹H‐NMR spectroscopy oftrans‐3MGC acid at 25°C provided no evidence for thecisisomer. Whentrans‐3MGC acid was incubated under conditions used for sample derivatization prior to GC‐MS (but with no trimethylsilane added),¹H‐NMR spectroscopy provided evidence oftranstocisisomerization. Incubation oftrans‐3MGC acid at 37°C resulted in time‐dependent isomerization tocis‐3MGC acid.Cis‐3MGC acid behaved in a similar manner except that, under identical incubation conditions, less isomerization occurred. In agreement with these experimental results, molecular modeling studies provided evidence that the energy minimized structure ofcis‐3MGC acid is 4 kJ/mol more stable than that fortrans‐3MGC acid. Once generated in vivo,trans‐3MGC acid is proposed to isomerize via a mechanism involving π electron delocalization with formation of a resonance structure that permits bond rotation. The data presented are consistent with the occurrence of both diastereomers in urine samples of subjects with 3MGC aciduria.

    

   more » « less