Theoretical investigation on the reaction mechanism and kinetics of benzyl alcohol with OH radical

Sun, Cuihong; Lv, Liqiang; Zhang, Shaowen

doi:10.1007/s00214-016-1811-2

Cited by 7 publications

(7 citation statements)

References 42 publications

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“…Kinetic data on the rate of production of hydrated electrons is not observable from our experiments, but other work has shown this to be on the picosecond or shorter time scale: the reactions of eqs 1 and 2 are expected to proceed very rapidly indeed, 12 and the reaction of hydroxyl radicals with cryoprotectants is also expected to be fast relative to the time scales of our experiment. 25 In agreement with these expectations, our data on varying the photon flux density suggest that the production and breakdown of hydrated electrons has reached a kinetic steady state, with only a minor perturbation caused by the photoreduction of Cu(II) in the sample. Thus, under steady-state conditions varying the photon flux density will be reflected by a change in the steady-state level of hydrated electrons, with k eff being proportional to the flux density, as indeed we observe (Table 2).…”

supporting

confidence: 86%

Cryoprotectants Severely Exacerbate X-ray-Induced Photoreduction

Nienaber

Pushie

Cotelesage

et al. 2018

J. Phys. Chem. Lett.

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Approximately 11% of enzymes contain a transition metal ion that is essential for catalytic function. Such metalloenzymes catalyze much of the most chemically challenging and biologically essential chemistry carried out by life. X-ray-based methods, predominantly macromolecular crystallography (MX) and also X-ray absorption spectroscopy (XAS), have proved essential for determining structures of transition metal ion-containing active sites in order to deduce enzyme catalytic mechanisms. However, X-ray irradiation can induce change in both the oxidation state and structure of the metal, which is problematic in structure determination. We present an XAS study of whether cryoprotectants such as polyethylene glycol (PEG) or glycerol, routinely added to MX or XAS samples to improve data quality, affect photoreduction. Our data demonstrate a remarkable 10-fold exacerbation in rate of photoreduction of Cu(II) to Cu(I) when alcohol or ether cryoprotectants are present. Our results suggest that widespread use of cryoprotectants may increase the potential for erroneous structures.

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supporting

confidence: 86%

Cryoprotectants Severely Exacerbate X-ray-Induced Photoreduction

Nienaber

Pushie

Cotelesage

et al. 2018

J. Phys. Chem. Lett.

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“…1,2 The processes of oxidation of alcohols have become the subject of numerous studies, 3 in particular the oxidation of benzyl alcohol, the main oxidation product of which-benzaldehyde-is of great importance for the industry. 4,5 In addition, the study of the oxidation of benzyl alcohols is important for the following reason: Benzyl alcohol groups are critical to reactions in lignin, the most abundant renewable macromolecule in Nature, since its degradation includes -O-4 cleavage, and oxidation is an alternative for the selective depolymerization. 6,7 However, when oxidized by stoichiometric oxidants, dichromate or permanganate, toxic, and harmful by-products are formed.…”

Section: Introductionmentioning

confidence: 99%

“…Selective oxidation of alcohols to carbonyl compounds is an important process of organic synthesis in both academic studies and industrial production . The processes of oxidation of alcohols have become the subject of numerous studies, in particular the oxidation of benzyl alcohol, the main oxidation product of which—benzaldehyde—is of great importance for the industry . In addition, the study of the oxidation of benzyl alcohols is important for the following reason: Benzyl alcohol groups are critical to reactions in lignin, the most abundant renewable macromolecule in Nature, since its degradation includes β ‐O‐4 cleavage, and oxidation is an alternative for the selective depolymerization .…”

Section: Introductionmentioning

confidence: 99%

Kinetics of oxidation of benzyl alcohols with molecular oxygen catalyzed by N‐hydroxyphthalimide: Role of hydroperoxyl radicals

Opeida

Sheparovych

Hrynda

et al. 2019

Int J of Chemical Kinetics

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A kinetic study of the initiated oxidation of benzyl alcohol and cumene by molecular oxygen was performed. The oxidation rate was more enhanced with N‐hydroxyphthalimide (NHPI) in the case of cumene than that of benzyl alcohol. HOOH inhibits cumene oxidation and does not affect the rate of oxidation of benzyl alcohol. It was shown that termination chain reactions of phthalimid‐N‐oxyl radicals (PINO•) does not occur with RОО• and proceeds with HOO•. A kinetic scheme of the process and an equation describing the kinetics of oxidation of benzyl alcohol in the presence of NHPI are proposed. Using the PM7 method, the thermodynamic characteristics of elementary steps of oxidation explaining the obtained results were calculated.

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“…To better characterize the kinetics of the H2′-abstraction reaction by the carbon-centered radical and its corresponding peroxyl species, thermal tunneling-corrected canonical transition-state theory was implemented to calculate the rate constants of the major paths from the following equation: − where σ, K B , h , and T are the reaction symmetry number, Boltzmann’s constant, Planck’s constant, and temperature (Kelvin), respectively. k ( T ) is the thermal tunneling coefficient, which was obtained through calculation of the one-dimensional tunneling probability.…”

Section: Computational Model and Methodsmentioning

confidence: 99%

“…Q TS ( T ) and Q R ( T ) represent the partition function calculated, respectively, for the transition state (TS) and the reactant (R). For the practical use in chemical kinetic modeling, three kinetic parameters A , n , and E a for each reaction of the major thermal decomposition paths were obtained by fitting the calculated rate constants over the temperature range of 273–313 K to a modified Arrhenius expression: − …”

Section: Computational Model and Methodsmentioning

confidence: 99%

Theoretical Insights on the Inefficiency of RNA Oxidative Damage under Aerobic Conditions

2017

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Oxidative damage to RNA has been linked to change or loss of RNA function and development of many human age-related diseases. However, knowledge on the nature of RNA oxidative damage is relatively limited. In this study, oxidative damage to RNA is investigated under anaerobic and aerobic conditions by exploring the properties and reactions of 5-hydroxyl-2'-uridin-6-yl and its peroxyl diastereoisomers in the RNA strand, respectively. Selective addition of OH to the nucleic base from the 5'-end is studied at the molecular level for the first time, explaining the large number of the 5S-isomer available for further reactions. Our results provide clear evidence that the efficiency of C2'-H2' bond activation in the peroxyl isomers is lower than in the carbon radical species. An exception is observed for the isomer cis-(5S,6R)-A1, whose internucleotidyl H2'-abstraction barrier is far smaller than that in the corresponding C6-yl radical. However, analysis of the equilibrium species distribution reveals that the amount of cis-(5S,6R)-A1 is very small among the peroxyl diastereoisomers, and hence the resulting products from direct strand scission should be a less important component in RNA oxidative damage. The species with maximum distribution is the cis-(5S,6R)-B1 isomer, which is derived from cis-(5S,6R)-A1 and has a moderate intranucleotidyl H2'-abstraction barrier. More importantly, the reaction is mildly exothermic. These results show that the main fraction of the intranucleotidyl H2'-abstraction intermediates can be formed from the cis-(5S,6R)-B1 isomer. The absolute reduction potentials, the hydrogen atom binding energies, and the key structural parameters of the C6-peroxyl species are used to understand the diverse reactivity of the cis-(5S,6R) diastereoisomers toward the C2'-H2' bonds activation. The present study shows that in addition to the selectivity of the OH radical addition, there is a strong correlation between the conformation of the modified uracil base and its reactivity in RNA oxidative damage.

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Theoretical investigation on the reaction mechanism and kinetics of benzyl alcohol with OH radical

Cited by 7 publications

References 42 publications

Cryoprotectants Severely Exacerbate X-ray-Induced Photoreduction

Cryoprotectants Severely Exacerbate X-ray-Induced Photoreduction

Kinetics of oxidation of benzyl alcohols with molecular oxygen catalyzed by N‐hydroxyphthalimide: Role of hydroperoxyl radicals

Theoretical Insights on the Inefficiency of RNA Oxidative Damage under Aerobic Conditions

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