Temperature Dependence of Rate Processes Beyond Arrhenius and Eyring: Activation and Transitivity

Carvalho-Silva, Valter H.; Coutinho, Nayara D.; Aquilanti, Vincenz̊o

doi:10.3389/fchem.2019.00380

Cited by 81 publications

(83 citation statements)

References 98 publications

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“…We find that several laboratories have reported rate coefficients (mostly involving reactions with atomic chlorine) that are considerably larger than would be expected from a simple collision theory calculation. For reactants with large dipole moments such as Criegee intermediates, rate coefficients in excess of the collision limit have been rationalized (Chhantyal-Pun et al, 2017, 2018. However, it is more difficult to explain such high rate coefficients in the chlorine reactions, and it is possible that further measurements and theoretical work may be helpful in this regard.…”

Section: Scientific Backgroundmentioning

confidence: 99%

Database for the kinetics of the gas-phase atmospheric reactions of organic compounds

McGillen

Carter

Mellouki

et al. 2020

Earth Syst. Sci. Data

120

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Abstract. We present a digital, freely available, searchable, and evaluated compilation of rate coefficients for the gas-phase reactions of organic compounds with OH, Cl, and NO3 radicals and with O3. Although other compilations of many of these data exist, many are out of date, most have limited scope, and all are difficult to search and to load completely into a digitized form. This compilation uses results of previous reviews, though many recommendations are updated to incorporate new or omitted data or address errors, and includes recommendations on many reactions that have not been reviewed previously. The database, which incorporates over 50 years of measurements, consists of a total of 2765 recommended bimolecular rate coefficients for the reactions of 1357 organic substances with OH, 709 with Cl, 310 with O3, and 389 with NO3, and is much larger than previous compilations. Many compound types are present in this database, including naturally occurring chemicals formed in or emitted to the atmosphere and anthropogenic compounds such as halocarbons and their degradation products. Recommendations are made for rate coefficients at 298 K and, where possible, the temperature dependences over the entire range of the available data. The primary motivation behind this project has been to provide a large and thoroughly evaluated training dataset for the development of structure–activity relationships (SARs), whose reliability depends fundamentally upon the availability of high-quality experimental data. However, there are other potential applications of this work, such as research related to atmospheric lifetimes and fates of organic compounds, or modelling gas-phase reactions of organics in various environments. This database is freely accessible at https://doi.org/10.25326/36 (McGillen et al., 2019).

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Section: Scientific Backgroundmentioning

confidence: 99%

Database for the kinetics of the gas-phase atmospheric reactions of organic compounds

McGillen

Carter

Mellouki

et al. 2020

Earth Syst. Sci. Data

120

View full text Add to dashboard Cite

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“…2). Although this parameterization is arbitrary and n, A and B do not have any clear physical or chemical meaning (Carvalho-Silva et al, 2019), it works well in fitting kinetic data for most compounds over wide temperature ranges with only one additional parameter. This is shown, for example, in Figure 2, which gives an Arrhenius plot for rate coefficient measurements for the reaction of OH with dimethyl ether over a temperature range of 195-1470 K. The dashed blue line is the standard Arrhenius expression derived from the data for 230-300K, k(T)=5.7×10 -12 exp(-215/T) cm 3 molecule -1 s -1 , while the solid line shows the extended expression, k(T)=1.02×10 -12 (T/300) 2.09 exp(308/T) cm 3 molecule -1 s -1 , which fits the data over the full range of 195-1470 K.…”

Section: Scientific Backgroundmentioning

confidence: 99%

Database for the kinetics of the gas-phase atmospheric reactions of organic compounds

McGillen¹,

Carter²,

Mellouki³

et al. 2020

Preprint

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Abstract. We present a digital, freely available, searchable and evaluated compilation of rate coefficients for the gas-phase reactions of organic compounds with OH, Cl and NO3 radicals and with O3 (McGillen et al., 2019). Although other compilations of much of these data exist, many are out-of-date, most have limited scope, and all are difficult to search and to load completely into a digitized form. This compilation uses results of previous reviews, though many recommendations are updated to incorporate new or omitted data or address errors, and includes recommendations on many reactions that have not been reviewed previously. The database, which incorporates over 50 years of measurements, consists of a total of 2765 recommended bimolecular rate coefficients for the reactions of 1357 organic substances with OH, 709 with Cl, 310 with O3, and 389 with NO3, and is much larger than previous compilations. A large variety of functional groups is present in this database, including naturally occurring chemicals formed in or emitted to the atmosphere and anthropogenic compounds such as halocarbons and their degradation products. Recommendations were made for rate coefficients at 298 K and, where possible, the temperature dependences over the entire range of the available data. The primary motivation behind this project has been to provide a large and thoroughly evaluated training dataset for the development of structure-activity relationships (SARs), whose reliability depends fundamentally upon the availability of high-quality experimental data. However, there are other potential applications of this work, such as research related to atmospheric lifetimes and fates of organic compounds, or modelling gas-phase reactions of organics in various environments. This database is freely accessible at https://doi.org/10.25326/36 (McGillen et al., 2019).

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“…In particular, it will be important to verify August 26, 2020 15/26 that unfolding rates can still be well-fit to the Arrhenius equation. The presence of explicit solvent may introduce a temperature-dependence to the unfolding-rate prefactors and activation energies, in which case an alternative model should be used for rate extrapolation [57]. However, it is worth noting that the small simulation timesteps used in MD render these simulations much slower to run than MC simulations.…”

Section: Use Of Dbfold To Generate Experimentally-testable Predictionsmentioning

confidence: 99%

DBFOLD: An efficient algorithm for computing folding pathways of complex proteins

Bitran

Jacobs²,

Shakhnovich

2020

Preprint

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Atomistic simulations can provide valuable, experimentally-verifiable insights into protein folding mechanisms, but existing ab initio simulation methods are restricted to only the smallest proteins due to severe computational speed limits. The folding of larger proteins has been studied using native-centric potential functions, but such models omit the potentially crucial role of non-native interactions.Here, we present an algorithm, entitled DBFOLD, which can predict folding pathways for a wide range of proteins while accounting for the effects of non-native contacts. In addition, DBFOLD can predict the relative rates of different transitions within a protein’s folding pathway. To accomplish this, rather than directly simulating folding, our method combines equilibrium Monte-Carlo simulations, which deploy enhanced sampling, with unfolding simulations at high temperatures. We show that under certain conditions, trajectories from these two types of simulations can be jointly analyzed to compute unknown folding rates from detailed balance. This requires inferring free energies from the equilibrium simulations, and extrapolating transition rates from the unfolding simulations to lower, physiologically-reasonable temperatures at which the native state is marginally stable. As a proof of principle, we show that our method can accurately predict folding pathways and Monte-Carlo rates for the well-characterized Streptococcal protein G. We then show that our method significantly reduces the amount of computation time required to compute the folding pathways of large, misfolding-prone proteins that lie beyond the reach of existing direct simulation methods. Our algorithm, which is available online, can generate detailed atomistic models of protein folding mechanisms while shedding light on the role of non-native intermediates which may crucially affect organismal fitness and are frequently implicated in disease.Author summaryMany proteins must adopt a specific structure in order to function. Computational simulations have been used to shed light on the mechanisms of protein folding, but unfortunately, realistic simulations can typically only be run for small proteins, due to severe limits in computational speed. Here, we present a method to solve this problem, whereby instead of directly simulating folding from an unfolded state, we run simulations that allow for computation of equilibrium folding free energies, alongside high temperature simulations to compute unfolding rates. From these quantities, folding rates can be computed using detailed balance. Importantly, our method can account for the effects of nonnative contacts which transiently form during folding and must be broken prior to adoption of the native state. Such contacts, which are often excluded from simple models of folding, may crucially affect real protein folding pathways and are often observed in folding intermediates implicated in disease.

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Temperature Dependence of Rate Processes Beyond Arrhenius and Eyring: Activation and Transitivity

Cited by 81 publications

References 98 publications

Database for the kinetics of the gas-phase atmospheric reactions of organic compounds

Database for the kinetics of the gas-phase atmospheric reactions of organic compounds

Database for the kinetics of the gas-phase atmospheric reactions of organic compounds

DBFOLD: An efficient algorithm for computing folding pathways of complex proteins

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