The Transitivity function, defined in terms of the reciprocal of the apparent activation energy, measures the propensity for a reaction to proceed and can provide a tool for implementing ...phenomenological kinetic models. Applications to systems which deviate from the Arrhenius law at low temperature encouraged the development of a user-friendly graphical interface for estimating the kinetic and thermodynamic parameters of physical and chemical processes. Here, we document the Transitivity code, written in Python, a free open-source code compatible with Windows, Linux and macOS platforms. Procedures are made available to evaluate the phenomenology of the temperature dependence of rate constants for processes from the Arrhenius and Transitivity plots. Reaction rate constants can be calculated by the traditional Transition-State Theory using a set of one-dimensional tunneling corrections (Bell (1935), Bell (1958), Skodje and Truhlar and, in particular, the deformed ( d -TST) approach). To account for the solvent effect on reaction rate constant, implementation is given of the Kramers and of Collins-Kimball formulations. An input file generator is provided to run various molecular dynamics approaches in CPMD code. Examples are worked out and made available for testing. The novelty of this code is its general scope and particular exploit of d
formulations to cope with non-Arrhenius behavior at low temperatures, a topic which is the focus of recent intense investigations. We expect that this code serves as a quick and practical tool for data documentation from electronic structure calculations: It presents a very intuitive graphical interface which we believe to provide an excellent working tool for researchers and as courseware to teach statistical thermodynamics, thermochemistry, kinetics, and related areas.
Biodiesel production is one of the promising strategies to reduce diesel consumption and an important contribution to climate change. However, biodiesel stability remains a challenging problem in ...biofuel use in the global energy matrix. In this context, organic additives have been investigated to minimize these problems and reduce harmful emissions to comply with fuel requirement standards. In this study, we discuss a comprehensive structural description, a behavior of B15 85% volume of diesel and 15% volume of biodiesel (B100) stability in the presence of antioxidants (chalcone analogues), and a theoretical calculation to pave the way for clarifying and expanding the potential of title compounds as an antioxidant additive for diesel-biodiesel blends. Finally, a systematic description of the oxidation stability was undertaken using a specialized machine learning computational pySIRC platform.
Biodiesel production is one of the promising strategies to reduce diesel consumption and an important contribution to climate change.
A number of experimental and theoretical papers accounted almost exclusively for two channels in the reaction of atomic hydrogen with methanol: H-abstraction from the methyl (R1) and hydroxyl (R2) ...functional groups. Recently, several astrochemical studies claimed the importance of another channel for this reaction, which is crucial for kinetic simulations related to the abundance of molecular constituents in planetary atmospheres: methyl radical and water formation (R3 channel). Here, motivated by the lack of and uncertainties about the experimental and theoretical kinetic rate constants for the third channel, we developed first-principles Car-Parrinello molecular dynamics thermalized at two significant temperatures - 300 and 2500 K. Furthermore, the kinetic rate constant of all three channels was calculated using a high-level deformed-transition state theory (d-TST) at a benchmark electronic structure level. d-TST is shown to be suitable for describing the overall rate constant for the CH3OH + H reaction (an archetype of the moderate tunnelling regime) with the precision required for practical applications. Considering the experimental ratios at 1000 K, kR1/kR2 ≈ 0.84 and kR1/kR3 ≈ 15-40, we provided a better estimate when compared with previous theoretical work: 7.47 and 637, respectively. The combination of these procedures explicitly demonstrates the role of the third channel in a significant range of temperatures and indicates its importance considering the thermodynamic control to estimate methyl radical and water formation. We expect that these results can help to shed new light on the fundamental kinetic rate equations for the CH3OH + H reaction.
Chitosan-N-lauroyl (CL) was synthesized from the reaction between chitosan and lauroyl chloride, in two proportions, obtaining the adsorbents CL1P (1:1) and CL2P (2:1). These were used for studies in ...aqueous Cu(II) and Pb(II) solutions on the metal ion adsorption capacity and the metal/adsorbent interaction. The pH, temperature, kinetics, selectivity and adsorption equilibrium were investigated. The feasibility of complexation between the ions and the adsorbent was verified theoretically through a density functional theory (DFT) approach. The theoretical maximum adsorption capacities (qmax) of CL1P and CL2P for Cu(II)/Pb(II) ions were 36.4/41.0 and 48.5/37.6 mg g−1, respectively. The experimental qmax values were lower than the theoretical values and ranged from 31.5–33.0 mg g−1. At the optimum pH value (5.5) the ion adsorption process was spontaneous, endothermic and associated with pseudo-second-order kinetics. Supported by quantum mechanical calculations, the site of ion-chitosan interaction was identified, evidencing the role of carbonyl, hydroxyl and amide groups in the stabilization of the complexes. Considering the scarcity of studies on apolar chitosan-based adsorbents for the removal of heavy metals, the promising results presented herein allow a better understanding of the relation between apolar groups and pH control, which could aid the design of polymeric adsorbents.
Pesticides are chemical compounds widely used to combat pests in crops, and they thus play a key role in agricultural production. However, due to their persistence in aquatic environments, even at ...low concentrations, their use has been considered an environmental problem and caused concern regarding the adverse effects on human health. This paper reports, for the first time, the mechanisms, kinetics, and an evaluation of the toxicity of picloram degradation initiated by OH radicals in the aqueous environment using quantum chemistry and computational toxicology calculations. The rate constants are calculated using a combination of formulations derived from the Transition State Theory in a realistic temperature range (250–310 K). The results indicate that the two favorable pathways (R1 and R5) of OH -based reactions occur by addition to the pyridine ring. The calculated rate constant at 298 K is compared with the overall second-order reaction rate constant, quantified herein experimentally via the competition kinetics method and data available in the literature showing an excellent agreement. The toxicity assessment and a photolysis study provide important information: i) picloram and the majority of degradation products are estimated as harmful; however, ii) these compounds can suffer photolysis in sunlight. The results of the present study can help understand the mechanism of picloram, also providing important clues regarding risk assessment in aquatic environments as well as novel experimental information.
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•Rate constants were estimated by experimental and theoretical approaches.•Topological analyses and Fukui functions were calculated.•Toxicity assessment was performed using the ECOSAR computational package.•The photolysis study was performed by TD-DFT.
We have developed an algorithm to generate a new spectra-based descriptor, called SpectraFP, in order to digitalize the chemical shifts of
13
C NMR spectra, as well as potentially important data from ...other spectroscopic techniques. This descriptor is a fingerprint vector with defined sizes and values of 0 and 1, with the ability to correct chemical shift fluctuations. To explore the applicability of SpectraFP, we outlined two application scenarios: (1) the prediction of six functional groups by machine learning (ML) models and (2) the search for structures based on the similarity between the query spectrum and spectra in an experimental database, both in the SpectraFP format. For each functional group, five ML models were built and validated following the OECD principles: internal and external validations, applicability domains, and mechanistic interpretations. All the models resulted in high goodness-of-fit for the training and test sets with MCC respectively between 0.626 and 0.909 and 0.653 and 0.917, and
J
ranging from 0.812 to 0.957 and 0.825 to 0.961. Using the SHAP (SHapley Additive exPlanations) approach, the mechanistic interpretations of the models were explored; the results indicated that the most important variables for model decision making were coherent with the expected chemical shifts for each functional group. Several metrics, including Tanimoto, geometric, arithmetic, and Tversky, can be used to perform the similarity calculation for the search algorithm. This algorithm can also incorporate additional variables, such as the correction parameter and the difference between the amount of signals in the query spectrum and the database spectra, while preserving its high performance speed. We hope that our descriptor can link information from spectroscopic/spectrometric techniques with ML models to expand the possibilities in understanding the field of cheminformatics. All databases and algorithms developed for this work are open sources and freely accessible.
We have developed an algorithm to generate a new spectra-based descriptor, called SpectraFP, in order to digitalize the chemical shifts of
13
C NMR spectra, as well as potentially important data from other spectroscopic techniques.
The rate constants of the reactions of OH radicals with atmospheric organic pollutants (AOPs) are crucial physicochemical parameters to guide in the elucidation of the kinetics and mechanisms of the ...reactive landscape. The experimental and theoretical difficulties in revealing the reactivity of these degradation processes motivated us to develop a protocol based on machine learning combining molecular fingerprints to estimate their rate constants. The present workflow is based on Organization for Economic Cooperation and Development (OECD) guidelines and state-of-the-art techniques involving (i) data collection including 903 AOPs cataloged in the literature, (ii) pre-processing and structuring of data, (iii) development of models based on three machine learning algorithms, (iv) the standard reference of validation, and (v) mechanistic interpretation. The results show that the built model has a high predictive capacity – Rcv2 > 0.959 and RMSEcv < 0.090 for the training set and Rext2 and Qext2 > 0.889 and RMSEext < 0.084 for the test set. Additionally, through the SHapley Additive exPlanations (SHAP) method, it was possible to establish insight into the contribution of chemical classes to reaction kinetics and mechanism and to discuss it consistently with current experimental and theoretical observations. The availability of the evaluated reaction rate constants permitted to elucidate the role of AOPs in the photochemical ozone balance. Finally, to disseminate use of our results, we have presented them in a user-friendly web application that permits compilation of kinetic parameters, and that permits future implementations to account for the temperature dependence in the environmental relevant range, and the consideration of a wider class of chemicals and processes in the mechanistic networks of atmospheric reactivity.
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•Six machine learning models were developed.•The half-life time and POCP of the reaction is reported for OH radical.•Workflow was fitted with experimental data to train ML models using of AOPs.•The models development followed the OECD principles.
A number of experimental and theoretical papers accounted almost exclusively for two channels in the reaction of atomic hydrogen with methanol: H-abstraction from the methyl (R1) and hydroxyl (R2) ...functional groups. Recently, several astrochemical studies claimed the importance of another channel for this reaction, which is crucial for kinetic simulations related to the abundance of molecular constituents in planetary atmospheres: methyl radical and water formation (R3 channel). Here, motivated by the lack of and uncertainties about the experimental and theoretical kinetic rate constants for the third channel, we developed first-principles Car-Parrinello molecular dynamics thermalized at two significant temperatures - 300 and 2500 K. Furthermore, the kinetic rate constant of all three channels was calculated using a high-level deformed-transition state theory (d-TST) at a benchmark electronic structure level. d-TST is shown to be suitable for describing the overall rate constant for the CH
OH + H reaction (an archetype of the moderate tunnelling regime) with the precision required for practical applications. Considering the experimental ratios at 1000 K, k
/k
≈ 0.84 and k
/k
≈ 15-40, we provided a better estimate when compared with previous theoretical work: 7.47 and 637, respectively. The combination of these procedures explicitly demonstrates the role of the third channel in a significant range of temperatures and indicates its importance considering the thermodynamic control to estimate methyl radical and water formation. We expect that these results can help to shed new light on the fundamental kinetic rate equations for the CH
OH + H reaction.
The efforts of contrasting the effects caused by the Covid-19 (coronavirus disease 2019) pandemic increased the disposal of active pharmaceutical ingredients. This paper reports the mechanisms and ...kinetics of the degradation in aqueous environments induced by OH of two drugs, among those most widely probed at the outbreak of coronavirus, nitazoxanide and hydroxychloroquine. The investigation exploits quantum chemistry techniques and a reaction rate theory combined with diffusion-controlled processes and quantum mechanical tunneling. The reaction rate constants are obtained in an environmentally relevant temperature range. The results show that (i) the deacetylation of nitazoxanide with formation of tizoxanide is kinetically the most favorable channel, in agreement with experimental work; (ii) for hydroxychloroquine, the present theoretical calculations show that the most favorable channel is the addition of OH at the aromatic ring. The half-life time degradation products are for both cases in the range between 12 to 138 days. Both drugs presented toxicities between harmful and toxic as obtained by computational toxicology calculations: The toxicity is also calculated for the degradation products: (i) in the nitazoxanide degradation process, tizoxanide was characterized as more toxic, while (ii) in the case of hydroxychloroquine, the major degradation product showed a decrease in the toxicity.
The excessive use of pesticides and the demand for environmentally friendly compounds have driven the focus to detailed studies of the environmental destination of these compounds. Degradation by ...hydrolysis of pesticides, when released into the soil, can result in the formation of metabolites with potentially adverse effects on the environment. Moving in this direction, we investigated the mechanism of acid hydrolysis of the herbicide ametryn (AMT) and predicted the toxicities of metabolites through experimental and theoretical approaches. The formation of ionized hydroxyatrazine (HA) occurs with the release of the SCH3- group and the addition of H3O+ to the triazine ring. The tautomerization reactions privileged the conversion of AMT into HA. Furthermore, the ionized HA is stabilized by an intramolecular reaction that provides the molecule in two tautomeric states. Experimentally, the hydrolysis of AMT was obtained under acidic conditions and at room temperature with HA as the main product. HA was isolated in a solid state through its crystallization as organic counterions. The mechanism of conversion of AMT to HA and the experimental investigation of the reaction kinetics allowed us to determine the dissociation of CH3SH as the rate-controlling step in the degradation process that culminates in a half-life between 7 and 24 months under typical acid soil conditions of the Brazilian Midwest – region with strong agricultural and livestock vocation. The keto and hydroxy metabolites showed substantial thermodynamic stability and a decrease in toxicity compared to AMT. We hope that this comprehensive study will support the understanding of the degradation of s-triazine-based pesticides.
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•Mechanism of the acid hydrolysis of Ametryn (AMT) herbicide into the hydroxiatrazine (HA).•Due to tautomerism, the HA occurs as a stable and versatile product when AMT is delivered in an acidic medium.•The conversion of AMT in HA occurs as an apparent pseudo-first-order reaction with low kinetic rates.•HA was isolated by forming salts with chloride, nitrate, mesylate, and oxalate anions.
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