Exercise Capacity and Biomarkers Among Children and Adolescents With Sickle Cell Disease.

BACKGROUND: Sickle cell disease is the most common genetic hemoglobinopathy globally and systemically affects body functioning, decreasing exercise capacity. OBJECTIVE: To assess exercise capacity through the 6-minute walk test (6MWT) and biomarkers in children and adolescents with sickle cell disease. MATERIALS AND METHODS: Cross-sectional study involving 20 children and adolescents from Brazil. Demographic and socioeconomic data were obtained. Baseline measurements included biomarkers (red blood cells, hemoglobin, hematocrit, white blood cells, platelets, reticulocytes, lactate dehydrogenase, creatine phosphokinase, C-reactive protein, interleukin 6, and fetal hemoglobin). The following data were obtained before, during, and after the 6MWT: heart rate, blood pressure, and peripheral oxygen saturation. RESULTS: Eighteen children and adolescents ages 5-14 years old were analyzed, 61.1% boys, 100% black or brown, and 61.1% in primary education, with low household income. The average distance walked in 6MWT was 463.8 (137.7) m, significantly less than the predicted value (P < .001). The distance of 6MWT was associated positively with age (P = .042) and inversely with reticulocyte count (P = .42) and interleukin 6 (P = .00). Age modified the effect of interleukin 6 in younger children (P = .038). CONCLUSION: Our findings suggest increased baseline levels of biomarkers of hemolysis and inflammation impact on 6MWT performance.

A Blockchain-Based End-to-End Data Protection Model for Personal Health Records Sharing: A Fully Homomorphic Encryption Approach.

Personal health records (PHR) represent health data managed by a specific individual. Traditional solutions rely on centralized architectures to store and distribute PHR, which are more vulnerable to security breaches. To address such problems, distributed network technologies, including blockchain and distributed hash tables (DHT) are used for processing, storing, and sharing health records. Furthermore, fully homomorphic encryption (FHE) is a set of techniques that allows the calculation of encrypted data, which can help to protect personal privacy in data sharing. In this context, we propose an architectural model that applies a DHT technique called the interplanetary protocol file system and blockchain networks to store and distribute data and metadata separately; two new elements, called data steward and shared data vault, are introduced in this regard. These new modules are responsible for segregating responsibilities from health institutions and promoting end-to-end encryption; therefore, a person can manage data encryption and requests for data sharing in addition to restricting access to data for a predefined period. In addition to supporting calculations on encrypted data, our contribution can be summarized as follows: (i) mitigation of risk to personal privacy by reducing the use of unencrypted data, and (ii) improvement of semantic interoperability among health institutions by using distributed networks for standardized PHR. We evaluated performance and storage occupation using a database with 1.3 million COVID-19 registries, which showed that combining FHE with distributed networks could redefine e-health paradigms.

"pySiRC": Machine Learning Combined with Molecular Fingerprints to Predict the Reaction Rate Constant of the Radical-Based Oxidation Processes of Aqueous Organic Contaminants.

We developed a web application structured in a machine learning and molecular fingerprint algorithm for the automatic calculation of the reaction rate constant of the oxidative processes of organic pollutants by •OH and SO4•- radicals in the aqueous phase-the pySiRC platform. The model development followed the OECD principles: internal and external validation, applicability domain, and mechanistic interpretation. Three machine learning algorithms combined with molecular fingerprints were evaluated, and all the models resulted in high goodness-of-fit for the training set with R2 > 0.931 for the •OH radical and R2 > 0.916 for the SO4•- radical and good predictive capacity for the test set with Rext2 = Qext2 values in the range of 0.639-0.823 and 0.767-0.824 for the •OH and SO4•- radicals. The model was interpreted using the SHAP (SHapley Additive exPlanations) method: the results showed that the model developed made the prediction based on a reasonable understanding of how electron-withdrawing and -donating groups interfere with the reactivity of the •OH and SO4•- radicals. We hope that our models and web interface can stimulate and expand the application and interpretation of kinetic research on contaminants in water treatment units based on advanced oxidative technologies.

Reply to the 'Comment on "Topography of the Free Energy Landscape on the Claisen-Schmidt Condensation: Solvent and Temperature Effect in the Rate-Controlling Step"' by N. D. Coutinho, H. G. Machado, V. H. Carvalho-Silva and W. A. da Silva, Phys. Chem. Chem. Phys., 2021, 23, 6738.

In the Comment on our paper on the description of the Gibbs Free energy profile of Claisen-Schmidt condensation, it is claimed that our calculations are flawed due to inconsistencies with experimental isotope effects in aqueous acetonitrile. In this Reply, we presented rigorous arguments, ambiguities in the Comment and new calculations confirming the consistency of our results: (i) small differences in the relative energetic barriers in both experimental and theoretical curves make the assignment of the rate-limiting step debatable, making the concept of RCS questionable; (ii) it is shown how the misinterpretation of the elementary steps and of the overall processes rate constants led the Comment to incorrect conclusions about the behavior of the inverse isotopic effect; (iii) neglect in the Comment of the inverse kinetic isotope effect in step R2 due to the hybridization conversion, and of the inverse equilibrium isotopic effect for step R1 to describe an overall iKIE > 1, (iv) an erroneous suggestion in the Comment that the disagreement between experimental kinetic parameters is due to the fact that acetonitrile is not used in previous experimental works, when contradictorily the literature recommends it as being indispensable to allow kinetic accuracy; and (v) new calculations improved by explicit-implicit hybrid treatment again ensure that step R4, and not step R5, can assume the role of RCS in protic solvents. Recognizing that questioning is an excellent path for promoting understanding, we hope that the answers provided here will help to clarify and expand the pertinent topics under discussion.

Topography of the free energy landscape of Claisen-Schmidt condensation: solvent and temperature effects on the rate-controlling step.

Recent studies have found that hydroxide elimination and the C[double bond, length as m-dash]C bond formation step in base-promoted aldol condensation have a strong influence on the overall rate of the reaction, in contrast to the well-accepted first enolization or C-C bond formation step. Here, applying theoretical models to the prototypical reaction of chalcone formation, the complete free energy profile of Claisen-Schmidt condensation is assessed, revealing how a protic solvent and a slight increase in temperature can induce the second enolization as the rate-controlling step (RCS). It is also observed: i) the nonexistence of a step with a much higher energetic barrier than the others, making the concept of RCS debatable; and ii) that the overall inverse kinetic isotopic effect does not exclude second enolization as a RCS in protic continuum medium. We expect that these results can expand the understanding of the decisive role of physicochemical factors on the choose of the RCS in the aldol condensation.

Exercise for cancer cachexia in adults.

BACKGROUND: Cancer cachexia is a multifactorial syndrome characterised by an ongoing loss of skeletal muscle mass, with or without a loss of fat mass, leading to progressive functional impairment. Physical exercise may attenuate cancer cachexia and its impact on patient function. This is the first update of an original Cochrane Review published in Issue 11, 2014, which found no studies to include. OBJECTIVES: To determine the effectiveness, acceptability and safety of exercise, compared with usual care, no treatment or active control, for cancer cachexia in adults. SEARCH METHODS: We searched CENTRAL, MEDLINE, Embase, and eight other databases to March 2020. We searched for ongoing studies in trial registries, checked reference lists and contacted experts to seek relevant studies. SELECTION CRITERIA: We sought randomised controlled trials in adults with cancer cachexia, that compared a programme of exercise alone or in combination with another intervention, with usual care, no treatment or an active control group. DATA COLLECTION AND ANALYSIS: Two review authors independently assessed titles and abstracts for relevance and extracted data on study design, participants, interventions and outcomes from potentially relevant articles. We used standard methodological procedures expected by Cochrane. Our primary outcome was lean body mass and secondary outcomes were adherence to exercise programme, adverse events, muscle strength and endurance, exercise capacity, fatigue and health-related quality of life. We assessed the certainty of evidence using GRADE and included two Summary of findings tables. MAIN RESULTS: We included four new studies in this update which overall randomised 178 adults with a mean age of 58 (standard deviation (SD) 8.2) years. Study sample size ranged from 20 to 60 participants and in three studies the proportion of men ranged from 52% to 82% (the fourth study was only available in abstract form). Three studies were from Europe: one in the UK and Norway; one in Belgium and one in Germany. The remaining study was in Canada. The types of primary cancer were head and neck (two studies), lung and pancreas (one study), and mixed (one study). We found two comparisons: exercise alone (strength-based exercise) compared to usual care (one study; 20 participants); and exercise (strength-based exercise/endurance exercise) as a component of a multimodal intervention (pharmacological, nutritional or educational (or a combination) interventions) compared with usual care (three studies, 158 participants). Studies had unclear and high risk of bias for most domains. Exercise plus usual care compared with usual care We found one study (20 participants). There was no clear evidence of a difference for lean body mass (8 weeks: MD 6.40 kg, 95% CI -2.30 to 15.10; very low-certainty evidence). For our secondary outcomes, all participants adhered to the exercise programme and no participant reported any adverse event during the study. There were no data for muscle strength and endurance, or maximal and submaximal exercise capacity. There was no clear evidence of a difference for either fatigue (4 to 20 scale, lower score was better) (8 weeks: MD -0.10, 95% CI -4.00 to 3.80; very low-certainty evidence) or health-related quality of life (0 to 104 scale, higher score was better) (8 weeks: MD 4.90, 95% CI -15.10 to 24.90; very low-certainty evidence). Multimodal intervention (exercise plus other interventions) plus usual care compared with usual care We found three studies but outcome data were only available for two studies. There was no clear evidence of a difference for lean body mass (6 weeks: MD 7.89 kg, 95% CI -9.57 to 25.35; 1 study, 44 participants; very low-certainty evidence; 12 weeks: MD -2.00, 95% CI -8.00 to 4.00; one study, 60 participants; very low-certainty evidence). For our secondary outcomes, there were no data reported on adherence to the exercise programme, endurance, or maximal exercise capacity. In one study (44 participants) there was no clear evidence of a difference for adverse events (patient episode report) (6 weeks: risk ratio (RR) 1.18, 95% CI 0.67 to 2.07; very low-certainty evidence). Another study assessed adverse events but reported no data and the third study did not assess this outcome. There was no clear evidence of a difference in muscle strength (6 weeks: MD 3.80 kg, 95% CI -2.87 to 10.47; 1 study, 44 participants; very low-certainty evidence; 12 weeks MD -5.00 kg, 95% CI -14.00 to 4.00; 1 study, 60 participants; very low-certainty evidence), submaximal exercise capacity (6 weeks: MD -16.10 m walked, 95% CI -76.53 to 44.33; 1 study, 44 participants; very low-certainty evidence; 12 weeks: MD -62.60 m walked, 95% CI -145.87 to 20.67; 1 study, 60 participants; very low-certainty evidence), fatigue (0 to 10 scale, lower score better) (6 weeks: MD 0.12, 95% CI -1.00 to 1.24; 1 study, 44 participants; very low-certainty evidence) or health-related quality of life (0 to 104 scale, higher score better) (12 weeks: MD -2.20, 95% CI -13.99 to 9.59; 1 study, 60 participants; very low-certainty evidence). AUTHORS' CONCLUSIONS: The previous review identified no studies. For this update, our conclusions have changed with the inclusion of four studies. However, we are uncertain of the effectiveness, acceptability and safety of exercise for adults with cancer cachexia. Further high-quality randomised controlled trials are still required to test exercise alone or as part of a multimodal intervention to improve people's well-being throughout all phases of cancer care. We assessed the certainty of the body of evidence as very low, downgraded due to serious study limitations, imprecision and indirectness. We have very little confidence in the results and the true effect is likely to be substantially different from these. The findings of at least three more studies (one awaiting classification and two ongoing) are expected in the next review update.

Deciphering the Dynamics of Organic Nanoaggregates with AIEE Effect and Excited States: Lipophilic Benzothiadiazole Derivatives as Selective Cell Imaging Probes.

An aggregation-induced emission enhancement (AIEE) effect in fluorescent lipophilic 2,1,3-benzothiadiazole (BTD) derivatives and their organic nanoaggregates were studied. A set of techniques such as single-crystal X-ray, dynamic light scattering (DLS), electron paramagnetic resonance (EPR), UV-vis, fluorescence, and density functional theory (DFT) calculations have been used to decipher the formation/break (kinetics), properties, and dynamics of the organic nanoaggregates of three BTD small organic molecules. An in-depth study of the excited-state also revealed the preferential relaxation emissive pathways for the BTD derivatives and the dynamics associated with it. The results described herein, for the first time, explain the formation of fluorescent BTD nanoaggregate derivatives and allow for the understanding of their dynamics in solution as well as the ruling forces of both aggregation and break processes along with the involved equilibrium. One of the developed dyes could be used at a nanomolar concentration to selectively stain lipid droplets emitting an intense and bright fluorescence at the red channel. The other two BTDs could also stain lipid droplets at very low concentrations and were visualized preferentially at the blue channel.

Exercise versus no exercise for the occurrence, severity, and duration of acute respiratory infections.

BACKGROUND: Acute respiratory infections (ARIs) last for less than 30 days and are the most common acute diseases affecting people. Exercise has been shown to improve health generally, but it is uncertain whether exercise may be effective in reducing the occurrence, severity, and duration of ARIs. This is an update of our review published in 2015. OBJECTIVES: To evaluate the effectiveness of exercise for altering the occurrence, severity, or duration of acute respiratory infections. SEARCH METHODS: We searched CENTRAL (2020, Issue 2), MEDLINE (1948 to March week 1, 2020), Embase (1974 to 05 March 2020), CINAHL (1981 to 05 March 2020), LILACS (1982 to 05 March 2020), SPORTDiscus (1985 to 05 March 2020), PEDro (searched 05 March 2020), OTseeker (searched 05 March 2020), and the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) and ClinicalTrials.gov (searched 05 March 2020). SELECTION CRITERIA: Randomised controlled trials (RCTs) and quasi-RCTs (method of allocation that is not truly random, e.g. based on date of birth, medical record number) of exercise for ARIs in the general population. DATA COLLECTION AND ANALYSIS: Two review authors independently extracted data from the included trials using a standard form. One review author entered data, which a second review author checked. We contacted trial authors to request missing data. There were sufficient differences in the populations trialed and in the nature of the interventions to use the random-effects model (which makes fewer assumptions than the fixed-effect model) in the analysis. MAIN RESULTS: We included three new trials for this update (473 participants) for a total of 14 trials involving 1377 adults, published between 1990 and 2018. Nine trials were conducted in the USA, and one each in Brazil, Canada, Portugal, Spain, and Turkey. Sample sizes ranged from 16 to 419 participants, aged from 18 to 85 years. The proportion of female participants ranged from 52% to 100%. Follow-up duration ranged from 1 to 36 weeks (median = 12 weeks). Moderate-intensity aerobic exercise (walking, bicycling, treadmill, or a combination) was evaluated in 11 trials, and was most commonly prescribed at least three times a week for 30 to 45 minutes. There was no difference between exercise and no exercise in the number of ARI episodes per person per year (risk ratio (RR) 1.00, 95% confidence interval (CI) 0.77 to 1.30; 4 trials; 514 participants; low-certainty evidence); proportion of participants who experienced at least one ARI over the study period (RR 0.88, 95% CI 0.72 to 1.08; 5 trials; 520 participants; low-certainty evidence); and the number of symptom days per episode of illness (mean difference (MD) -0.44 day, 95% CI -2.33 to 1.46; 6 trials; 557 participants; low-certainty evidence). Exercise reduced the severity of ARI symptoms measured on the Wisconsin Upper Respiratory Symptom Survey (WURSS-24) (MD -103.57, 95% CI -198.28 to -8.87; 2 trials; 373 participants; moderate-certainty evidence) and the number of symptom days during follow-up period (MD -2.24 days, 95% CI -3.50 to -0.98; 4 trials; 483 participants; low-certainty evidence). Excercise did not have a significant effect on laboratory parameters (blood lymphocytes, salivary secretory immunoglobulin, and neutrophils), quality of life outcomes, cost-effectiveness, and exercise-related injuries. There was no difference in participant dropout between the intervention and control groups. Overall, the certainty of the evidence was low, downgraded mainly due to limitations in study design and implementation, imprecision, and inconsistency. Seven trials were funded by public agencies; five trials did not report funding; and two trials were funded by private companies. AUTHORS' CONCLUSIONS: Exercise did not reduce the number of ARI episodes, proportion of participants experiencing at least one ARI during the study, or the number of symptom days per episode of illness. However, exercise reduced the severity of ARI symptoms (two studies) and the number of symptom days during the study follow-up period (four studies). Small study size, risk of bias, and heterogeneity in the populations studied contributed to the uncertainty of the findings. Larger trials that are designed to avoid risk of bias associated with participant selection, blinding of outcomes assessors, and with adequate reporting of all outcomes proposed for measurement in trials, would help to provide more robust evidence.

From the Kinetic Theory of Gases to the Kinetics of Rate Processes: On the Verge of the Thermodynamic and Kinetic Limits.

A variety of current experiments and molecular dynamics computations are expanding our understanding of rate processes occurring in extreme environments, especially at low temperatures, where deviations from linearity of Arrhenius plots are revealed. The thermodynamic behavior of molecular systems is determined at a specific temperature within conditions on large volume and number of particles at a given density (the thermodynamic limit): on the other side, kinetic features are intuitively perceived as defined in a range between the extreme temperatures, which limit the existence of each specific phase. In this paper, extending the statistical mechanics approach due to Fowler and collaborators, ensembles and partition functions are defined to evaluate initial state averages and activation energies involved in the kinetics of rate processes. A key step is delayed access to the thermodynamic limit when conditions on a large volume and number of particles are not fulfilled: the involved mathematical analysis requires consideration of the role of the succession for the exponential function due to Euler, precursor to the Poisson and Boltzmann classical distributions, recently discussed. Arguments are presented to demonstrate that a universal feature emerges: Convex Arrhenius plots (super-Arrhenius behavior) as temperature decreases are amply documented in progressively wider contexts, such as viscosity and glass transitions, biological processes, enzymatic catalysis, plasma catalysis, geochemical fluidity, and chemical reactions involving collective phenomena. The treatment expands the classical Tolman's theorem formulated quantally by Fowler and Guggenheim: the activation energy of processes is related to the averages of microscopic energies. We previously introduced the concept of "transitivity", a function that compactly accounts for the development of heuristic formulas and suggests the search for universal behavior. The velocity distribution function far from the thermodynamic limit is illustrated; the fraction of molecules with energy in excess of a certain threshold for the description of the kinetics of low-temperature transitions and of non-equilibrium reaction rates is derived. Uniform extension beyond the classical case to include quantum tunneling (leading to the concavity of plots, sub-Arrhenius behavior) and to Fermi and Bose statistics has been considered elsewhere. A companion paper presents a computational code permitting applications to a variety of phenomena and provides further examples.

Analyzing the performance of a blockchain-based personal health record implementation.

BACKGROUND: The Personal Health Record (PHR) and Electronic Health Record (EHR) play a key role in more efficient access to health records by health professionals and patients. It is hard, however, to obtain a unified view of health data that is distributed across different health providers. In particular, health records are commonly scattered in multiple places and are not integrated. OBJECTIVE: This article presents the implementation and evaluation of a PHR model that integrates distributed health records using blockchain technology and the openEHR interoperability standard. We thus follow OmniPHR architecture model, which describes an infrastructure that supports the implementation of a distributed and interoperable PHR. METHODS: Our method involves implementing a prototype and then evaluating the integration and performance of medical records from different production databases. In addition to evaluating the unified view of records, our evaluation criteria also focused on non-functional performance requirements, such as response time, CPU usage, memory occupation, disk, and network usage. RESULTS: We evaluated our model implementation using the data set of more than 40 thousand adult patients anonymized from two hospital databases. We tested the distribution and reintegration of the data to compose a single view of health records. Moreover, we profiled the model by evaluating a scenario with 10 superpeers and thousands of competing sessions transacting operations on health records simultaneously, resulting in an average response time below 500 ms. The blockchain implemented in our prototype achieved 98% availability. CONCLUSION: Our performance results indicated that data distributed via a blockchain could be recovered with low average response time and high availability in the scenarios we tested. Our study also demonstrated how OmniPHR model implementation can integrate distributed data into a unified view of health records.

Physical activity for lower urinary tract symptoms secondary to benign prostatic obstruction.

BACKGROUND: Lower urinary tract symptoms caused by benign prostatic obstruction (LUTS/BPO) represents one of the most common clinical complaints in men. Physical activity might represent a viable first-line intervention for treating LUTS/BPO. OBJECTIVES: To assess the effects of physical activity for lower urinary tract symptoms caused by benign prostatic obstruction (LUTS/BPO). SEARCH METHODS: We performed a comprehensive search of multiple databases (CENTRAL, MEDLINE, Embase, Web of Science, LILACS, ClinicalTrials.gov, and WHO ICTRP); checked the reference lists of retrieved articles; and handsearched abstract proceedings of conferences with no restrictions on the language of publication or publication status from database inception to 6 November 2018. SELECTION CRITERIA: We included published and unpublished randomised controlled and controlled clinical trials that included men diagnosed with LUTS/BPO. We excluded studies in which medical history suggested non-BPO causes of LUTS or prior invasive therapies to physical activity or that used electrical stimulation. DATA COLLECTION AND ANALYSIS: Two review authors independently assessed study eligibility, extracted data, and assessed the risk of bias of included studies. We assessed primary outcomes (symptom score for LUTS; response rate, defined as 20% improvement in symptom score; withdrawal due to adverse events) and secondary outcomes (change of medication use; need for an invasive procedure; postvoid residual urine). We assessed the quality of the evidence using the GRADE approach. MAIN RESULTS: We included six studies that randomised 652 men over 40 years old with moderate or severe LUTS. The four different comparisons were as follows:Physical activity versus watchful waitingTwo RCTs randomised 119 participants. The interventions included tai chi and pelvic floor exercise. The evidence was overall of very low quality, and we are uncertain about the effects of physical activity on symptom score for LUTS (mean difference (MD) -8.1, 95% confidence interval (CI) -13.2 to -3.1); response rate (risk ratio (RR) 1.80, 95% CI 0.81 to 4.02; 286 more men per 1000, 95% CI 68 fewer to 1079 more); and withdrawal due to adverse events (RR 1.00, 95% CI 0.59 to 1.69; 0 fewer men per 1000, 95% CI 205 fewer to 345 more).Physical activity as part of self-management programme versus watchful waitingTwo RCTs randomised 362 participants. Pelvic floor exercise was one of multiple intervention components. The evidence was of very low quality, and we are uncertain about the effects of physical activity for symptom score for LUTS (MD -6.2, 95% CI -9.9 to -2.5); response rate (RR 2.36, 95% CI 1.32 to 4.21; 424 more men per 1000, 95% CI 100 more to 1000 more); and withdrawal due to adverse events (risk difference 0.00, 95% CI -0.05 to 0.06; 65 fewer men per 1000, 95% CI 65 fewer to 65 fewer).Physical activity as part of weight reduction programme versus watchful waitingOne RCT randomised 130 participants. An unclear type of intense exercise was one of multiple intervention components. The evidence was of very low quality, and we are uncertain about the effects for symptom score for LUTS (MD -1.1, 95% CI -3.5 to 1.3); response rate (RR 1.20, 95% CI 0.74 to 1.94; 67 more men per 1000, 95% CI 87 fewer to 313 more); and withdrawal due to adverse events (RR 1.63, 95% CI 1.03 to 2.57; 184 more men per 1000, 95% CI 9 more to 459 more).Physical activity versus alpha-blockersOne RCT randomised 41 participants to pelvic floor exercise or alpha-blockers. The evidence was of very low quality, and we are uncertain about the effects for symptom score for LUTS (MD 2.8, 95% CI -0.9 to 6.4) and response rate (RR 0.80, 95% CI 0.55 to 1.15; 167 fewer men per 1000, 95% CI 375 fewer to 125 more). The evidence was of low quality for withdrawal due to adverse events; the effects for this outcome may be similar between interventions (RR 0.86, 95% CI 0.06 to 12.89; 7 fewer men per 1000, 95% CI 49 fewer to 626 more). AUTHORS' CONCLUSIONS: We rated the quality of the evidence for most of the effects of physical activity for LUTS/BPO as very low. We are therefore uncertain whether physical activity affects symptom scores for LUTS, response rate, and withdrawal due to adverse events. Our confidence in the estimates was lowered due to study limitations, inconsistency, indirectness, and imprecision. Additional high-quality research is necessary.

"Transitivity": A Code for Computing Kinetic and Related Parameters in Chemical Transformations and Transport Phenomena.

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.

Kinetics of the OH+HCl→H2 O+Cl reaction: Rate determining roles of stereodynamics and roaming and of quantum tunneling.

The OH + HCl → H2 O + Cl reaction is one of the most studied four-body systems, extensively investigated by both experimental and theoretical approaches. Here, as a continuation of our previous work on the OH + HBr and OH + HI reactions, which manifest an anti-Arrhenius behavior that was explained by stereodynamic and roaming effects, we extend the strategy to understand the transition to the sub-Arrhenius behavior occurring for the HCl case. As previously, we perform first-principles on-the-fly Born-Oppenheimer molecular dynamics calculations, thermalized at four temperatures (50, 200, 350, and 500 K), but this time we also apply a high-level transition-state-theory, modified to account for tunneling conditions. We find that the theoretical rate constants calculated with Bell tunneling corrections are in good agreement with extensive experimental data available for this reaction in the ample temperature range: (i) simulations show that the roles of molecular orientation in promoting this reaction and of roaming in finding the favorable path are minor than in the HBr and HI cases, and (ii) dominating is the effect of quantum mechanical penetration through the energy barrier along the reaction path on the potential energy surface. The discussion of these results provides clarification of the origin on different non-Arrhenius mechanisms observed along this series of reactions. © 2018 Wiley Periodicals, Inc.

Combined Role of the Asymmetric Counteranion-Directed Catalysis (ACDC) and Ionic Liquid Effect for the Enantioselective Biginelli Multicomponent Reaction.

This work describes new chiral task-specific ionic liquids bearing chiral anions as the catalysts for the enantioselective multicomponent Biginelli reaction. For the first time, the combined role of asymmetric counteranion-directed catalysis (ACDC) and ionic liquid effect (ILE) for the chiral induction in the Biginelli multicomponent reaction is demonstrated. The chiral induction arises from a supramolecular aggregate where the anion and the cation of the catalyst are alongside with a key cationic intermediate of the reaction. Each component of the new catalyst had a vital role for the chiral induction success. The mechanism of an asymmetric version of this multicomponent reaction is in addition demonstrated for the first time using electrospray (tandem) mass spectrometry, ESI-MS(/MS). The analyses indicated the reaction takes place preferentially and exclusively through the iminium mechanism. Unprecedented supramolecular aggregates were detected by ESI-MS and characterized by ESI-MS/MS. No intermediate of the other two possible reactions pathways could be detected. Theoretical calculations shed light on the transition state of the transformation during the key step of the chiral induction and helped to elucidate the roles of the chiral anion (ACDC contribution) and of the imidazolium-containing nonchiral cation derivative (ILE contribution) in the molecular reaction process.

Deformed transition-state theory: Deviation from Arrhenius behavior and application to bimolecular hydrogen transfer reaction rates in the tunneling regime.

A formulation is presented for the application of tools from quantum chemistry and transition-state theory to phenomenologically cover cases where reaction rates deviate from Arrhenius law at low temperatures. A parameter d is introduced to describe the deviation for the systems from reaching the thermodynamic limit and is identified as the linearizing coefficient in the dependence of the inverse activation energy with inverse temperature. Its physical meaning is given and when deviation can be ascribed to quantum mechanical tunneling its value is calculated explicitly. Here, a new derivation is given of the previously established relationship of the parameter d with features of the barrier in the potential energy surface. The proposed variant of transition state theory permits comparison with experiments and tests against alternative formulations. Prescriptions are provided and implemented to three hydrogen transfer reactions: CH4 + OH → CH3 + H2 O, CH3 Cl + OH → CH2 Cl + H2 O and H2 + CN → H + HCN, widely investigated both experimentally and theoretically. © 2016 Wiley Periodicals, Inc.

A novel assessment of the role of the methyl radical and water formation channel in the CH3OH + H reaction.

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.

Rovibrational spectroscopic constants of the interaction between ammonia and metallo-phthalocyanines: a theoretical protocol for ammonia sensor design.

In the present contribution, we develop an adapted theoretical approach based on DFT calculations (B3LYP functional) and solution of the nuclear Schrödinger equation by using the Discrete Variable Representation method to model the interaction of ammonia with metallo-phthalocyanines (MPcs, where M = Fe2+, Co2+, Ni2+, Cu2+ or Zn2+). This approach is intended to be a general protocol for the rational design of chemical sensors. The as-obtained binding energy curves, obtained from ab initio points, permitted us to calculate rovibrational energies and spectroscopic constants, as well as to establish the relative population of rovibrational states in different types of MPc-NH3 thermodynamic systems. Simulated binding energy curves show that the binding energy in MPc-NH3 systems is dependent on the type of M central ion, decreasing in the order FePc > ZnPc > CoPc > CuPc > NiPc, with values spanning from -170 to -16 kJ mol-1. Also, MPc-NH3 systems have at least 16 rovibrational levels, which confirms that they are all bound systems (chemically or physically). Despite that, only the interaction between ammonia and FePc, CoPc or ZnPc is spontaneous within the studied temperature range (200-700 K). NiPc and CuPc show a change between spontaneous and non-spontaneous behaviours at ∼400 K and ∼500 K, respectively. Less bound systems should more efficiently guarantee the sensors' signal reset, while they are also less specific than sensors built with medium to strongly bound systems. Moreover, the intermediate energy and spontaneous binding of ammonia to NiPc and CuPc at operation temperatures, as determined with our theoretical approach, suggests that these MPcs are most promising for ammonia sensors.

Stereodirectional Origin of anti-Arrhenius Kinetics for a Tetraatomic Hydrogen Exchange Reaction: Born-Oppenheimer Molecular Dynamics for OH + HBr.

Among four-atom processes, the reaction OH + HBr → H2O + Br is one of the most studied experimentally: its kinetics has manifested an unusual anti-Arrhenius behavior, namely, a marked decrease of the rate constant as the temperature increases, which has intrigued theoreticians for a long time. Recently, salient features of the potential energy surface have been characterized and most kinetic aspects can be considered as satisfactorily reproduced by classical trajectory simulations. Motivation of the work reported in this paper is the investigation of the stereodirectional dynamics of this reaction as the prominent reason for the peculiar kinetics: we started in a previous Letter ( J. Phys. Chem. Lett. 2015 , 6 , 1553 - 1558 ) a first-principles Born-Oppenheimer "canonical" molecular dynamics approach. Trajectories are step-by-step generated on a potential energy surface quantum mechanically calculated on-the-fly and are thermostatically equilibrated to correspond to a specific temperature. Here, refinements of the method permitted a major increase of the number of trajectories and the consideration of four temperatures -50, +200, +350, and +500 K, for which the sampling of initial conditions allowed us to characterize the stereodynamical effect. The role is documented of the adjustment of the reactants' mutual orientation to encounter the entrance into the "cone of acceptance" for reactivity. The aperture angle of this cone is dictated by a range of directions of approach compatible with the formation of the specific HOH angle of the product water molecule; and consistently the adjustment is progressively less effective the higher the kinetic energy. Qualitatively, this emerging picture corroborates experiments on this reaction, involving collisions of aligned and oriented molecular beams, and covering a range of energies higher than the thermal ones. The extraction of thermal rate constants from this molecular dynamics approach is discussed and the systematic sampling of the canonical ensemble is indicated as needed for quantitative comparison with the kinetic experiments.

Investigation of the Abstraction and Dissociation Mechanism in the Nitrogen Trifluoride Channels: Combined Post-Hartree-Fock and Transition State Theory Approaches.

The present paper concludes our series of kinetics studies on the reactions involved in the complex mechanism of nitrogen trifluoride decomposition. Two other related reactions that, along with this mechanism, take part in an efficient boron nitride growth process are also investigated. We report results concerning two abstraction reactions, namely NF2 + N ⇄ 2NF and NF3 + NF ⇄ 2NF2, and two dissociations, N2F4 ⇄ 2NF2 and N2F3 ⇄ NF2 + NF. State-of-the-art electronic structure calculations at the CCSD(T)/cc-pVTZ level of theory were considered to determine geometries and frequencies of reactants, products, and transition states. Extrapolation of the energies to the complete basis set limit was used to obtain energies of all the species. We applied transition state theory to compute thermal rate constants including Wigner, Eckart, Bell, and deformed theory corrections in order to take tunneling effects into account. The obtained results are in good agreement with the experimental data available in the literature and are expected to provide a better phenomenological understanding of the NF3 decomposition role in the boron nitride growth for a wide range of temperature values.

Scientometrics: Nature Index and Brazilian science.

A recent published newspaper article commented on the (lack of) quality of Brazilian science and its (in) efficiency. The newspaper article was based on a special issue of Nature and on a new resource for scientometrics called Nature Index. I show here arguments and sources of bias that, under the light of the principle in dubio pro reo, it is questionable to dispute the quality and efficiency of the Brazilian science on these grounds, as it was commented on the referred article. A brief overview of Brazilian science is provided for readers to make their own judgment.