Intramolecular Hydrogen Atom Tunneling in 2-Chlorobenzoic Acid Studied by Low-Temperature Matrix-Isolation Infrared Spectroscopy

Nishino, Satoshi; Nakata, Munetaka

doi:10.1021/jp0717600

Cited by 27 publications

(54 citation statements)

References 23 publications

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“…Hence, it seems possible that these two processes, once occurring simultaneously, lead to a stationary population ratio. The most plausible rationalization for the mechanism of back isomerization of ALA conformer VI to conformer I, in the dark at 14 K, is the occurrence of a tunneling decay, as reported previously for other matrixisolated molecules containing the carboxylic fragment, such as formic, 35 acetic, 29,36 propionic, 37 2-chloropropionic, 38 benzoic 39,40 acids, glycine, 31 and other systems, for example, hydroxycarbene. 41 Actually, if thermal isomerization is involved, form VI could be transformed into form IIa (via forms VIIIa or VIIIb) instead of isomerization into form I, since this process has a much lower energy barrier (i.e., 8-10 kJ mol −1 versus 30 kJ mol −1 , respectively; as compared graphically in Figs.…”

Section: The Decay Mechanism Of L-alanine High-energy Conformer VIsupporting

confidence: 60%

Near-IR laser generation of a high-energy conformer of L-alanine and the mechanism of its decay in a low-temperature nitrogen matrix

Nunes

Lapiński

Fausto

et al. 2013

The Journal of Chemical Physics

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Monomers of L-alanine (ALA) were isolated in cryogenic nitrogen matrices at 14 K. Two conformers were identified for the compound trapped from the gas-phase into the solid nitrogen environment. The potential energy surface (PES) of ALA was theoretically calculated at the MP2 and QCISD levels. Twelve minima were located on this PES. Seven low-energy conformers fall within the 0-10 kJ mol(-1) range and should be appreciably populated in the equilibrium gas phase prior to deposition. Observation of only two forms in the matrices is explained in terms of calculated barriers to conformational rearrangements. All conformers with the O=C-O-H moiety in the cis orientation are separated by low barriers and collapse to the most stable form I during deposition of the matrix onto the low-temperature substrate. The second observed form II has the O=C-O-H group in the trans orientation. The remaining trans forms have very high relative energies (between 24 and 30 kJ mol(-1)) and are not populated. The high-energy trans form VI, that differs from I only by rotation of the OH group, was found to be separated from other conformers by barriers that are high enough to open a perspective for its stabilization in a matrix. The form VI was photoproduced in situ by narrow-band near-infrared irradiation of the samples at 6935-6910 cm(-1), where the first overtone of the OH stretching vibration in form I appears. The photogenerated form VI decays in N2 matrices back to conformer I with a characteristic decay time of ∼15 min. The mechanism of the VI → I relaxation is rationalized in terms of the proton tunneling.

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Section: The Decay Mechanism Of L-alanine High-energy Conformer VIsupporting

confidence: 60%

Near-IR laser generation of a high-energy conformer of L-alanine and the mechanism of its decay in a low-temperature nitrogen matrix

Nunes

Lapiński

Fausto

et al. 2013

The Journal of Chemical Physics

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“…Indeed, the placement of the nearest nitro O relative to the flavin N5 is most compatible with anti transfer of hydride as opposed to the more favorable and common syn transfer (Fig. 6B, (Nishino and Nakata, 2007)). However the geometry allows that the required proton could be acquired from an active site solvent molecule or a proton temporarily resident near N1 via favorable syn proton transfer.…”

Section: Discussionmentioning

confidence: 99%

Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase

et al. 2017

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Summary Nitroreductase from Enterobacter cloacae (NR) reduces diverse nitroaromatics including herbicides, explosives and prodrugs, and holds promise for bioremediation, prodrug activation and enzyme-assisted synthesis. We solved crystal structures of NR complexes with bound substrate or analog for each of its two half-reactions. We complemented these with kinetic isotope effect (KIE) measurements elucidating H-transfer steps essential to each half-reaction. KIEs indicate hydride transfer from NADH to the flavin consistent with our structure of NR with the NADH analog nicotinic acid adenine dinucleotide (NAAD). The KIE on reduction of p-nitrobenzoic acid (p-NBA) also indicates hydride transfer, and requires revision of prior computational mechanisms. Our mechanistic information provided a structural restraint for the orientation of bound substrate, placing the nitro group closer to the flavin N5 in the pocket that binds the amide of NADH. KIEs show that solvent provides a proton, enabling accommodation of different nitro group placements, consistent with NR’s broad repertoire.

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“…For several molecules containing a carboxylic group, and where high-energy conformers could be successfully produced in situ in cryogenic matrices by near-IR pumping of a lower energy precursor conformer, it has been observed that back-isomerization can take place spontaneously in the dark, by tunneling. 57,[66][67][68][69][70][71] In the present study, we have also investigated this possibility for TAA.…”

Section: Spontaneous Decay (By Tunneling) Of the High-energy Conformementioning

confidence: 99%

Tetrazole acetic acid: Tautomers, conformers, and isomerization

Araujo-Andrade

Reva

Fausto

2014

The Journal of Chemical Physics

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Monomers of (tetrazol-5-yl)-acetic acid (TAA) were obtained by sublimation of the crystalline compound and the resulting vapors were isolated in cryogenic nitrogen matrices at 13 K. The conformational and tautomeric composition of TAA in the matrix was characterized by infrared spectroscopy and vibrational calculations carried out at the B3LYP/6-311++G(d,p) level. TAA may adopt two tautomeric modifications, 1H- and 2H-, depending on the position of the annular hydrogen atom. Two-dimensional potential energy surfaces (PESs) of TAA were theoretically calculated at the MP2/6-311++G(d,p) level, for each tautomer. Four and six symmetry-unique minima were located on these PESs, for 1H- and 2H-TAA, respectively. The energetics of the detected minima was subsequently refined by calculations at the QCISD level. Two 1H- and three 2H-conformers fall within the 0-8 kJ mol(-1) energy range and should be appreciably populated at the sublimation temperature (∼330 K). Observation of only one conformer for each tautomer (1ccc and 2pcc) is explained in terms of calculated barriers to conformational rearrangements. All conformers with the cis O=COH moiety are separated by low barriers (less than 10 kJ mol(-1)) and collapse to the most stable 1ccc (1H-) and 2pcc (2H-) forms during deposition of the matrix. On the trans O=COH surfaces, the relative energies are very high (between 12 and 27 kJ mol(-1)). The trans forms are not thermally populated at the sublimation conditions and were not detected in matrices. One high-energy form in each tautomer, 1cct (1H-) and 2pct (2H-), was found to differ from the most stable form only by rotation of the OH group and separated from other forms by high barriers. This opened a perspective for their stabilization in a matrix. 1cct and 2pct were generated in the matrices selectively by means of narrow-band near-infrared (NIR) irradiations of the samples at 6920 and 6937 cm(-1), where the first OH stretching overtone vibrations of 1ccc and 2pcc occur. The reverse transformations could be induced by irradiations at 7010 and 7030 cm(-1), transforming 1cct and 2pct back to 1ccc and 2pcc, also selectively. Besides the NIR-induced transformations, the photogenerated 1cct and 2pct forms also decay in N2 matrices back to 1ccc and 2pcc spontaneously, with characteristic decay times of hours (1H) and tens of minutes (2H). The decay mechanism is rationalized in terms of the proton tunneling. In crystals, TAA exists exclusively as 1H-tautomer. By contrast, the tautomeric composition of the matrix-isolated monomers was found to consist of both 1H- and 2H-tautomers, in comparable amounts. A mechanistic discussion of the tautomerization process occurring during sublimation, accounting also for the observed minor decomposition of TAA leading to CO2 and 5-methyl-tetrazole, is proposed.

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Intramolecular Hydrogen Atom Tunneling in 2-Chlorobenzoic Acid Studied by Low-Temperature Matrix-Isolation Infrared Spectroscopy

Cited by 27 publications

References 23 publications

Near-IR laser generation of a high-energy conformer of L-alanine and the mechanism of its decay in a low-temperature nitrogen matrix

Near-IR laser generation of a high-energy conformer of L-alanine and the mechanism of its decay in a low-temperature nitrogen matrix

Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase

Tetrazole acetic acid: Tautomers, conformers, and isomerization

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