1
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Kwon T, Kwon S, Sung BJ. The effects of asymmetry in active noises on the efficiency of single colloidal Stirling engines with active noises. SOFT MATTER 2024; 20:2600-2609. [PMID: 38426540 DOI: 10.1039/d3sm01386c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Molecular machines, which operate in highly fluctuating environments far from equilibrium, may benefit from their non-equilibrium environments. It is, however, a topic of controversy how the efficiency of the microscopic engines can be enhanced. Recent experiments showed that microscopic Stirling engines in bacterial reservoirs could show high performance beyond the equilibrium thermodynamics. In this work, we perform overdamped Langevin dynamics simulations for microscopic Stirling heat engines in bacterial reservoirs and show that the temperature dependence of the magnitude of active noises should be responsible for such high efficiency. Only when we introduce temperature-dependent active noises, the efficiency of the microscopic Stirling engines is enhanced significantly as in experiments.
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Affiliation(s)
- Taejin Kwon
- Department of Chemistry and Cosmetics, Jeju National University, Jeju 63243, Republic of Korea
| | - Seulki Kwon
- The Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bong June Sung
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea.
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2
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Qu HC, Yang Y, Cui ZC, Wang D, Xue CD, Qin KR. Temperature-mediated diffusion of nanoparticles in semidilute polymer solutions. Electrophoresis 2023; 44:1899-1906. [PMID: 37736676 DOI: 10.1002/elps.202300054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/07/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023]
Abstract
The temperature is often a critical factor affecting the diffusion of nanoparticles in complex physiological media, but its specific effects are still to be fully understood. Here, we constructed a temperature-regulated model of semidilute polymer solution and experimentally investigated the temperature-mediated diffusion of nanoparticles using the particle tracking method. By examining the ensemble-averaged mean square displacements (MSDs), we found that the MSD grows gradually as the temperature increases while the transition time from sublinear to linear stage in MSD decreases. Meanwhile, the temperature-dependent measured diffusivity of the nanoparticles shows an exponential growth. We revealed that these temperature-mediated changes are determined by the composite effect of the macroscale property of polymer solution and the microscale dynamics of polymer chain as well as nanoparticles. Furthermore, the measured non-Gaussian displacement probability distributions were found to exhibit non-Gaussian fat tails, and the tailed distribution is enhanced as the temperature increases. The non-Gaussianity was calculated and found to vary in the same trend with the tailed distribution, suggesting the occurrence of hopping events. This temperature-mediated non-Gaussian feature validates the recent theory of thermally induced activated hopping. Our results highlight the temperature-mediated changes in diffusive transport of nanoparticles in polymer solutions and may provide the possible strategy to improve drug delivery in physiological media.
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Affiliation(s)
- Heng-Chao Qu
- Affiliated Central Hospital of Dalian University of Technology, Dalian, P. R. China
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, P. R. China
| | - Yi Yang
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, P. R. China
| | - Zhi-Chao Cui
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, P. R. China
| | - Dong Wang
- Affiliated Central Hospital of Dalian University of Technology, Dalian, P. R. China
| | - Chun-Dong Xue
- Affiliated Central Hospital of Dalian University of Technology, Dalian, P. R. China
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, P. R. China
- Faculty of Medicine, Dalian University of Technology, Dalian, P. R. China
| | - Kai-Rong Qin
- Affiliated Central Hospital of Dalian University of Technology, Dalian, P. R. China
- Faculty of Medicine, Dalian University of Technology, Dalian, P. R. China
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3
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Wendering P, Nikoloski Z. Model-driven insights into the effects of temperature on metabolism. Biotechnol Adv 2023; 67:108203. [PMID: 37348662 DOI: 10.1016/j.biotechadv.2023.108203] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/22/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023]
Abstract
Temperature affects cellular processes at different spatiotemporal scales, and identifying the genetic and molecular mechanisms underlying temperature responses paves the way to develop approaches for mitigating the effects of future climate scenarios. A systems view of the effects of temperature on cellular physiology can be obtained by focusing on metabolism since: (i) its functions depend on transcription and translation and (ii) its outcomes support organisms' development, growth, and reproduction. Here we provide a systematic review of modelling efforts directed at investigating temperature effects on properties of single biochemical reactions, system-level traits, metabolic subsystems, and whole-cell metabolism across different prokaryotes and eukaryotes. We compare and contrast computational approaches and theories that facilitate modelling of temperature effects on key properties of enzymes and their consideration in constraint-based as well as kinetic models of metabolism. In addition, we provide a summary of insights from computational approaches, facilitating integration of omics data from temperature-modulated experiments with models of metabolic networks, and review the resulting biotechnological applications. Lastly, we provide a perspective on how different types of metabolic modelling can profit from developments in machine learning and models of different cellular layers to improve model-driven insights into the effects of temperature relevant for biotechnological applications.
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Affiliation(s)
- Philipp Wendering
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany.
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4
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Investigation on the molecular, Electronic, Biological and Spectroscopic properties of a novel cobalt complex: An intuition from an experimental and computational perspective. Polyhedron 2023. [DOI: 10.1016/j.poly.2023.116369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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5
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Makhlouf J, Bakri YE, Saravanan K, Valkonen A, Smirani W. Self-assembly, physico-chemical characterization, biological and computational approach of novel 2-Amino pyridine derivatives. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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6
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Hader JD, Lane T, Boxall ABA, MacLeod M, Di Guardo A. Enabling forecasts of environmental exposure to chemicals in European agriculture under global change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 840:156478. [PMID: 35667426 DOI: 10.1016/j.scitotenv.2022.156478] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/16/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
European agricultural development in the 21st century will be affected by a host of global changes, including climate change, changes in agricultural technologies and practices, and a shift towards a circular economy. The type and quantity of chemicals used, emitted, and cycled through agricultural systems in Europe will change, driven by shifts in the use patterns of pesticides, veterinary pharmaceuticals, reclaimed wastewater used for irrigation, and biosolids. Climate change will also impact the chemical persistence, fate, and transport processes that dictate environmental exposure. Here, we review the literature to identify research that will enable scenario-based forecasting of environmental exposures to organic chemicals in European agriculture under global change. Enabling exposure forecasts requires understanding current and possible future 1.) emissions, 2.) persistence and transformation, and 3.) fate and transport of agricultural chemicals. We discuss current knowledge in these three areas, the impact global change drivers may have on them, and we identify knowledge and data gaps that must be overcome to enable predictive scenario-based forecasts of environmental exposure under global change. Key research gaps identified are: improved understanding of relationships between global change and chemical emissions in agricultural settings; better understanding of environment-microbe interactions in the context of chemical degradation under future conditions; and better methods for downscaling climate change-driven intense precipitation events for chemical fate and transport modelling. We introduce a set of narrative Agricultural Chemical Exposure (ACE) scenarios - augmenting the IPCC's Shared Socio-economic Pathways (SSPs) - as a framework for forecasting chemical exposure in European agriculture. The proposed ACE scenarios cover a plausible range of optimistic to pessimistic 21st century development pathways. Filling the knowledge and data gaps identified within this study and using the ACE scenario approach for chemical exposure forecasting will support stakeholder planning and regulatory intervention strategies to ensure European agricultural practices develop in a sustainable manner.
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Affiliation(s)
- John D Hader
- Department of Environmental Science, Stockholm University, 10691 Stockholm, Sweden
| | - Taylor Lane
- Department of Environment and Geography, University of York, Heslington, York, North Yorkshire YO10 5NG, United Kingdom
| | - Alistair B A Boxall
- Department of Environment and Geography, University of York, Heslington, York, North Yorkshire YO10 5NG, United Kingdom
| | - Matthew MacLeod
- Department of Environmental Science, Stockholm University, 10691 Stockholm, Sweden.
| | - Antonio Di Guardo
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, CO, Italy
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7
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Emran KM, Omar IMA, Arab ST, Ouerfelli N. On the pseudo-hyperbolic behavior of charge transfer resistance-temperature dependence in corrosion behavior of Nickel based glass alloy. Sci Rep 2022; 12:6432. [PMID: 35440686 PMCID: PMC9019006 DOI: 10.1038/s41598-022-10462-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/09/2022] [Indexed: 11/25/2022] Open
Abstract
Temperature plays an important role in promoting the corrosion of metals. The Arrhenius plot can interpret the corrosion rate-temperature dependence, where the Arrhenius behavior gives a geometrical meaning and makes explicit a positive or negative linear dependence of charge transitivity and temperature. In addition, according to the Arrhenius interpretation, it represents the energy that the molecule in the initial state of the process must acquire before it can take part in the reaction, whether it is a physical, or a chemical process. Taking into account the deviation from the linearity, we have extended the Arrhenius-type expression by one term in 1/T2 and we have given some physical meaning to the new related coefficients for which it is found that they depend closely on the number of acid hydrogen atoms in the polyacid for the corrosion and passivation of the Nickel based metallic glass alloy of the composition Ni82.3Cr7Fe3Si4.5B3.2. Moreover, we can consider that the deviation to the Arrhenius linear behavior as a super-Arrhenius behavior In addition, a mathematical analysis of the trend of experimental scatter points of the charge transfer resistance with temperature permits us to reveal an interesting homographic behavior which leads us to suggest an original empirical model with only two optimal adjustable parameters, as well as a new pseudo-power dependence of the number of hydrogen atoms in the polyacid.
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Affiliation(s)
- Khadijah M Emran
- Chemistry Department, College of Science, Taibah University, Al-Madinah, Saudi Arabia.
| | - Inam M A Omar
- Chemistry Department, College of Science, Taibah University, Al-Madinah, Saudi Arabia
| | - Sanaa T Arab
- Chemistry Department, Faculty of Sciences, Al-Faisaliah, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noureddine Ouerfelli
- Institut Supérieur des Technologies Médicales de Tunis, LR13SE07, Laboratoire de Biophysique et Technologies Médicales, Université de Tunis El Manar, Tunis, Tunisia
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8
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Mustakim M, Kumar AVA. Depletion Induced Demixing and Crystallization in Binary Colloids Subjected to an External Potential Barrier. J Phys Chem B 2021; 126:327-335. [PMID: 34961314 DOI: 10.1021/acs.jpcb.1c08591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Depletion interaction plays an important role in determining the structural and dynamical properties of binary colloidal mixtures. We have investigated the effect of the attractive depletion interaction between an external potential barrier and larger species in the binary mixture on the phase behavior of a binary colloidal mixture using canonical-isokinetic ensemble molecular dynamics simulations. The demixing of the binary mixture due to this depletion interaction increases as the volume fraction increases, and a pure phase of larger particles forms in the region of the potential barrier. The local density of this pure phase is high enough that a face centered cubic crystalline domain is formed at this region. This crystalline phase diffuses perpendicular to the external potential barrier, indicating that moving crystals can be obtained in an equilibrium system. The temperature dependence of diffusivity of larger particles is non-Arrhenius and changes from sub-Arrhenius to super-Arrhenius as the volume fraction increases. This crossover from sub-Arrhenius to super-Arrhenius diffusion coincides with the crystalline formation near the potential barrier.
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Affiliation(s)
- Mahammad Mustakim
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - A V Anil Kumar
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
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9
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Sanches-Neto FO, Ramos B, Lastre-Acosta AM, Teixeira ACSC, Carvalho-Silva VH. Aqueous picloram degradation by hydroxyl radicals: Unveiling mechanism, kinetics, and ecotoxicity through experimental and theoretical approaches. CHEMOSPHERE 2021; 278:130401. [PMID: 33839382 DOI: 10.1016/j.chemosphere.2021.130401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/09/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
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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Affiliation(s)
- Flávio O Sanches-Neto
- Instituto de Química, Universidade de Brasília, Caixa Postal 4478, 70904-970, Brasília, Brazil.
| | - Bruno Ramos
- Research Group in Advanced Oxidation Processes (AdOx), Department of Chemical Engineering, Escola Politécnica, University of São Paulo, São Paulo, 05508-010, Brazil
| | - Arlen M Lastre-Acosta
- Research Group in Advanced Oxidation Processes (AdOx), Department of Chemical Engineering, Escola Politécnica, University of São Paulo, São Paulo, 05508-010, Brazil
| | - Antonio Carlos S C Teixeira
- Research Group in Advanced Oxidation Processes (AdOx), Department of Chemical Engineering, Escola Politécnica, University of São Paulo, São Paulo, 05508-010, Brazil
| | - Valter H Carvalho-Silva
- Instituto de Química, Universidade de Brasília, Caixa Postal 4478, 70904-970, Brasília, Brazil; Modeling of Physical and Chemical Transformations Division, Theoretical and Structural Chemistry Group, Research and Postgraduate Center, Goiás State University, 75132-903, Anápolis, Brazil.
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10
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Coutinho ND, Machado HG, Carvalho-Silva VH, da Silva WA. Topography of the free energy landscape of Claisen-Schmidt condensation: solvent and temperature effects on the rate-controlling step. Phys Chem Chem Phys 2021; 23:6738-6745. [PMID: 33710206 DOI: 10.1039/d0cp05659f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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.
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Affiliation(s)
- Nayara Dantas Coutinho
- Laboratory of Bioactive Compounds Synthesis N.T.S., University of Brasilia (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, Brazil.
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11
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Mairet F, Gouzé JL, de Jong H. Optimal proteome allocation and the temperature dependence of microbial growth laws. NPJ Syst Biol Appl 2021; 7:14. [PMID: 33686098 PMCID: PMC7940435 DOI: 10.1038/s41540-021-00172-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 01/15/2021] [Indexed: 11/14/2022] Open
Abstract
Although the effect of temperature on microbial growth has been widely studied, the role of proteome allocation in bringing about temperature-induced changes remains elusive. To tackle this problem, we propose a coarse-grained model of microbial growth, including the processes of temperature-sensitive protein unfolding and chaperone-assisted (re)folding. We determine the proteome sector allocation that maximizes balanced growth rate as a function of nutrient limitation and temperature. Calibrated with quantitative proteomic data for Escherichia coli, the model allows us to clarify general principles of temperature-dependent proteome allocation and formulate generalized growth laws. The same activation energy for metabolic enzymes and ribosomes leads to an Arrhenius increase in growth rate at constant proteome composition over a large range of temperatures, whereas at extreme temperatures resources are diverted away from growth to chaperone-mediated stress responses. Our approach points at risks and possible remedies for the use of ribosome content to characterize complex ecosystems with temperature variation.
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Affiliation(s)
- Francis Mairet
- Ifremer, Physiology and Biotechnology of Algae laboratory, Nantes, France.
| | - Jean-Luc Gouzé
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France
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12
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Yadav S, Kunwar A. Temperature-Dependent Activity of Motor Proteins: Energetics and Their Implications for Collective Behavior. Front Cell Dev Biol 2021; 9:610899. [PMID: 33732692 PMCID: PMC7959718 DOI: 10.3389/fcell.2021.610899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/11/2021] [Indexed: 12/27/2022] Open
Abstract
Molecular motor proteins are an extremely important component of the cellular transport system that harness chemical energy derived from ATP hydrolysis to carry out directed mechanical motion inside the cells. Transport properties of these motors such as processivity, velocity, and their load dependence have been well established through single-molecule experiments. Temperature dependent biophysical properties of molecular motors are now being probed using single-molecule experiments. Additionally, the temperature dependent biochemical properties of motors (ATPase activity) are probed to understand the underlying mechanisms and their possible implications on the enzymatic activity of motor proteins. These experiments in turn have revealed their activation energies and how they compare with the thermal energy available from the surrounding medium. In this review, we summarize such temperature dependent biophysical and biochemical properties of linear and rotary motor proteins and their implications for collective function during intracellular transport and cellular movement, respectively.
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Affiliation(s)
- Saumya Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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13
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Singh J, Mustakim M, Anil Kumar AV. Super-Arrhenius diffusion in a binary colloidal mixture at low volume fraction: an effect of depletion interaction due to an asymmetric barrier. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:125101. [PMID: 33463528 DOI: 10.1088/1361-648x/abd428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We report results from the molecular dynamics simulations of a binary colloidal mixture subjected to an external potential barrier along one of the spatial directions at low volume fraction, ϕ = 0.2. The variations in the asymmetry of the external potential barrier do not change the dynamics of the smaller particles, showing Arrhenius diffusion. However, the dynamics of the larger particles shows a crossover from sub-Arrhenius to super-Arrhenius diffusion with the asymmetry in the external potential at the low temperatures and low volume fraction. Super-Arrhenius diffusion is generally observed in the high density systems where the transient cages are present due to dense packing, e.g., supercooled liquids, jammed systems, diffusion through porous membranes, dynamics within the cellular environment, etc. This model can be applied to study the molecular transport across cell membranes, nano-, and micro-channels which are characterized by spatially asymmetric potentials.
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Affiliation(s)
- Jalim Singh
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Jatni, Bhubaneswar 752050, India
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14
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Temperature effect on water dynamics in tetramer phosphofructokinase matrix and the super-arrhenius respiration rate. Sci Rep 2021; 11:383. [PMID: 33431895 PMCID: PMC7801438 DOI: 10.1038/s41598-020-79271-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 11/26/2020] [Indexed: 11/08/2022] Open
Abstract
Advances in understanding the temperature effect on water dynamics in cellular respiration are important for the modeling of integrated energy processes and metabolic rates. For more than half a century, experimental studies have contributed to the understanding of the catalytic role of water in respiration combustion, yet the detailed water dynamics remains elusive. We combine a super-Arrhenius model that links the temperature-dependent exponential growth rate of a population of plant cells to respiration, and an experiment on isotope labeled 18O2 uptake to H218O transport role and to a rate-limiting step of cellular respiration. We use Phosphofructokinase (PFK-1) as a prototype because this enzyme is known to be a pacemaker (a rate-limiting enzyme) in the glycolysis process of respiration. The characterization shows that PFK-1 water matrix dynamics are crucial for examining how respiration (PFK-1 tetramer complex breathing) rates respond to temperature change through a water and nano-channel network created by the enzyme folding surfaces, at both short and long (evolutionary) timescales. We not only reveal the nano-channel water network of PFK-1 tetramer hydration topography but also clarify how temperature drives the underlying respiration rates by mapping the channels of water diffusion with distinct dynamics in space and time. The results show that the PFK-1 assembly tetramer possesses a sustainable capacity in the regulation of the water network toward metabolic rates. The implications and limitations of the reciprocal-activation-reciprocal-temperature relationship for interpreting PFK-1 tetramer mechanisms are briefly discussed.
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15
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Non-conservation of activation energy barriers in the same chemical process: a cooperative (effect) proton transfer on (HF)n molecular aggregates. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02681-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Meynet P, Davenport RJ, Fenner K. Understanding the Dependence of Micropollutant Biotransformation Rates on Short-Term Temperature Shifts. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:12214-12225. [PMID: 32897072 DOI: 10.1021/acs.est.0c04017] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Temperature is a key factor that influences chemical biotransformation potential and rates, on which exposure and fate models rely to predict the environmental (micro)pollutant fate. Arrhenius-based models are currently implemented in environmental exposure assessment to adapt biotransformation rates to actual temperatures, assuming validity in the 0-30 °C range. However, evidence on how temperature shifts affect the physicochemical and microbial features in biological systems is scarce, questioning the validity of the existing modeling approaches. In this work, laboratory-scale batch assays were designed to investigate how a mixed microbial community responds to short-term temperature shifts, and how this impacts its ability to biotransform a range of structurally diverse micropollutants. Our results revealed three distinct kinetic responses at temperatures above 20 °C, mostly deviating from the classic Arrhenius-type behavior. Micropollutants with similar temperature responses appeared to undergo mostly similar initial biotransformation reactions, with substitution-type reactions maintaining Arrhenius-type behavior up to higher temperatures than oxidation-type reactions. Above 20 °C, the microbial community also showed marked shifts in both composition and activity, which mostly correlated with the observed deviations from Arrhenius-type behavior, with compositional changes becoming a more relevant factor in biotransformations catalyzed by more specific enzymes (e.g., oxidation reactions). Our findings underline the need to re-examine and further develop current environmental fate models by integrating biological aspects, to improve accuracy in predicting the environmental fate of micropollutants.
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Affiliation(s)
- Paola Meynet
- School of Engineering, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
- Department of Environmental Chemistry, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Russell J Davenport
- School of Engineering, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Kathrin Fenner
- Department of Environmental Chemistry, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
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17
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Sodre ER, Guido BC, de Souza PEN, Machado DFS, Carvalho-Silva VH, Chaker JA, Gatto CC, Correa JR, Fernandes TDA, Neto BAD. Deciphering the Dynamics of Organic Nanoaggregates with AIEE Effect and Excited States: Lipophilic Benzothiadiazole Derivatives as Selective Cell Imaging Probes. J Org Chem 2020; 85:12614-12634. [PMID: 32876447 DOI: 10.1021/acs.joc.0c01805] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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.
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Affiliation(s)
- Elaine R Sodre
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal 70904-900, Brazil
| | - Bruna C Guido
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal 70904-900, Brazil
| | - Paulo E N de Souza
- Laboratory of Software and Instrumentation in Applied Physics and Laboratory of Electron Paramagnetic Resonance, Institute of Physics, Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal 70904-970, Brazil
| | - Daniel F S Machado
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal 70904-900, Brazil
| | - Valter H Carvalho-Silva
- Divisão de Modelagem de Transformações Físicas e Químicas, Grupo de Química Teo'rica e Estrutural de Ana'polis, Centro de Pesquisa e Pos-Graduação, Universidade Estadual de Goia's,, Ana'polis, Goia's 75001-970, Brazil
| | - Juliano A Chaker
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal 70904-900, Brazil
| | - Claudia C Gatto
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal 70904-900, Brazil
| | - Jose R Correa
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal 70904-900, Brazil
| | - Talita de A Fernandes
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal 70904-900, Brazil
| | - Brenno A D Neto
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal 70904-900, Brazil
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18
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Temperature coefficient (Q10) and its applications in biological systems: Beyond the Arrhenius theory. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2020.109127] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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19
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Maglinao RL, Wagner TJ, Duff K. Effects of Temperature, Antioxidants, and
High‐Vacuum
Distillation on the Oxidation of Biodiesel Derived from Waste Vegetable Oil. J AM OIL CHEM SOC 2020. [DOI: 10.1002/aocs.12391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Randy L. Maglinao
- Advanced Fuels Center Montana State University‐Northern Havre Montana 59501 USA
| | - Torrey J. Wagner
- Department of Systems Engineering and Management Air Force Institute of Technology Wright‐Patterson Air Force Base Ohio 45433 USA
| | - Keegan Duff
- US Department of Agriculture Agricultural Research Service Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center Hilo Hawaii 96720 USA
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20
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Alsaffar MA, Rashid SA, Ayodele BV, Hamidon MN, Yasin FM, Ismail I, Hosseini S, Babadi FE. Response Surface Optimization of Multilayer Graphene Growth on Alumina-Supported Bimetallic Cobalt–Nickel Substrate. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2020. [DOI: 10.1007/s13369-020-04586-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Kushwaha VS, Peterman EJG. The temperature dependence of kinesin motor-protein mechanochemistry. Biochem Biophys Res Commun 2020; 529:812-818. [PMID: 32620235 DOI: 10.1016/j.bbrc.2020.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/03/2020] [Indexed: 11/27/2022]
Abstract
Biophysical studies of the mechanochemical cycle of kinesin motors are essential for understanding the mechanism of energy conversion. Here, we report a systematic study of the impact of temperature on velocity and run length of homodimeric Drosophila kinesin-1, homodimeric C. elegans OSM-3 and heterodimeric C. elegans kinesin-II motor proteins using in vitro single-molecule motility assays. Under saturated ATP conditions, kinesin-1 and OSM-3 are fast and processive motors compared to kinesin-II. From in vitro motility assays employing single-molecule fluorescence microscopy, we extracted single-motor velocities and run lengths in a temperature range from 15 °C to 35 °C. Both parameters showed a non-Arrhenius temperature dependence for all three motors, which could be quantitatively modeled using a simplified, two-state kinetic model of the mechanochemistry of the three motors, providing new insights in the temperature dependence of their mechanochemistry.
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Affiliation(s)
- Vandana S Kushwaha
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, 1081 HV, Amsterdam, the Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, 1081 HV, Amsterdam, the Netherlands.
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22
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Lin CH, Wu LX, Chen KH, Lo HF, Lin KC, Kasai T, Chen CC, Shih CH, Manzano MC, Santos GN, Manzano E, Yu DE. Non-invasive and Time-dependent Blood-sugar Monitoring via Breath-derived CO 2 Correlation Using Gas Chromatograph with a Milli-whistle Gas Analyzer. ANAL SCI 2020; 36:739-743. [PMID: 31932522 DOI: 10.2116/analsci.19p407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A clear and positive correlation between the CO2 concentration and the blood-sugar level has been observed via a non-invasive and time-dependent monitoring of CO2 concentration from human breath, which is carried out by using a home-made gas chromatography (GC)/milli-whistle compact analyzer. The time-dependent sampling of the CO2 concentration correlated between 5.0 to 5.6% (1% = 104 ppm) in accordance with blood-sugar level variations of 80 to 110 mg/dL. The analytical method results in a rapid, continuous and non-invasive determination of blood-sugar level via measurement of the CO2 concentration exhaled from the lungs.
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Affiliation(s)
| | - Luo-Xian Wu
- Department of Chemistry, National Taiwan Normal University
| | - Kuan-Hao Chen
- Department of Chemistry, National Taiwan Normal University
| | - Hsu-Feng Lo
- Department of Chemistry, National Taiwan Normal University
| | | | - Toshio Kasai
- Department of Chemistry, National Taiwan University.,Institute of Scientific and industrial Research, Osaka University
| | - Chien-Chung Chen
- Graduate Institute of Biomedical Materials and Tissue Engineering, Taipei Medical University
| | - Chung-Hung Shih
- School of Respiratory Therapy, Taipei Medical University.,Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University Hospital
| | | | | | - Enrique Manzano
- Physics Department, De La Salle University.,Electronics and Communications Engineering Department, De La Salle University
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23
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From the Kinetic Theory of Gases to the Kinetics of Rate Processes: On the Verge of the Thermodynamic and Kinetic Limits. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25092098. [PMID: 32365840 PMCID: PMC7248839 DOI: 10.3390/molecules25092098] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 11/24/2022]
Abstract
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.
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24
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Zaia DAM, de Carvalho PCG, Samulewski RB, de Carvalho Pereira R, Zaia CTBV. Unexpected Thiocyanate Adsorption onto Ferrihydrite Under Prebiotic Chemistry Conditions. ORIGINS LIFE EVOL B 2020; 50:57-76. [PMID: 32266585 DOI: 10.1007/s11084-020-09594-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/10/2020] [Indexed: 02/02/2023]
Abstract
The most crucial role played by minerals was in the preconcentration of biomolecules or precursors of biomolecules in prebiotic seas. If this step had not occurred, molecular evolution would not have occurred. Thiocyanate is an important molecule in the formation of biomolecules as well as a catalyst for prebiotic reactions. The adsorption of thiocyanate onto ferrihydrite was carried out under pH and ion composition conditions in seawater that resembled those of prebiotic Earth. The seawater used in this work had high Mg2+, Ca2+ and SO42- concentrations. The most important result of this work was that ferrihydrite adsorbed thiocyanateata pH value (7.2 ± 0.2) that usually does not adsorb thiocyanate. The high adsorptivity of Mg2+, Ca2+ and SO42-onto ferrihydrite showed that seawater ions can act as carriers of thiocyanate to the ferrihydrite surface, creating a huge outer-sphere complex. Kinetic adsorption and isotherm experiments showed the best fit for the pseudo-second-order model and an activation energy of 23.8 kJ mol-1forthe Langmuir-Freundlich model, respectively. Thermodynamic data showed positive ΔG values, which apparently contradict the adsorption isotherm data and kinetic data that was obtained. The adsorption of thiocyanate onto ferrihydrite could be explained by coupling with the exergonic SO42- adsorption onto ferrihydrite. The FTIR spectra showed no difference between the C≡N stretching peaks of adsorbed thiocyanate and free thiocyanate, corroborating the formation of an outer-sphere complex. All the results demonstrated the importance of the artificial seawater composition for the adsorption of thiocyanate and for understanding prebiotic chemistry.
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Affiliation(s)
- Dimas A M Zaia
- Departamento de Química, Laboratório de Química Prebiótica-LQP, Universidade Estadual de Londrina, Londrina, PR, CEP 86 057-970, Brazil.
| | - Paulo C G de Carvalho
- Departamento de Química, Laboratório de Química Prebiótica-LQP, Universidade Estadual de Londrina, Londrina, PR, CEP 86 057-970, Brazil
| | - Rafael B Samulewski
- Departamento de Química, Laboratório de Química Prebiótica-LQP, Universidade Estadual de Londrina, Londrina, PR, CEP 86 057-970, Brazil
| | - Rodrigo de Carvalho Pereira
- Departamento de Química, Laboratório de Química Prebiótica-LQP, Universidade Estadual de Londrina, Londrina, PR, CEP 86 057-970, Brazil
| | - Cássia Thaïs B V Zaia
- Departamento de Ciências Fisiológicas, Laboratório de Fisiologia Neuroendocrina--LaFiNen, Universidade Estadual de Londrina, Londrina, PR, CEP 86 057-970, Brazil
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25
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Veloso AC, Rodrigues N, Ouarouer Y, Zaghdoudi K, Pereira JA, Peres AM. A Kinetic‐Thermodynamic Study of the Effect of the Cultivar/Total Phenols on the Oxidative Stability of Olive Oils. J AM OIL CHEM SOC 2020. [DOI: 10.1002/aocs.12351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ana C.A. Veloso
- Instituto Politécnico de CoimbraISEC, DEQB Rua Pedro Nunes, Quinta da Nora 3030‐199 Coimbra Portugal
- CEB—Centre of Biological EngineeringUniversity of Minho Campus de Gualtar 4710‐057 Braga Portugal
| | - Nuno Rodrigues
- Centro de Investigação de Montanha (CIMO), ESAInstituto Politécnico de Bragança Campus Santa Apolónia 5300‐253 Bragança Portugal
| | - Yosra Ouarouer
- Centro de Investigação de Montanha (CIMO), ESAInstituto Politécnico de Bragança Campus Santa Apolónia 5300‐253 Bragança Portugal
- Département Génie Chimique, Université Libre de Tunis Avenue Khéreddine—Pacha Tunis, 30, 1002 Tunis Tunisia
| | - Khalil Zaghdoudi
- Département Génie Chimique, Université Libre de Tunis Avenue Khéreddine—Pacha Tunis, 30, 1002 Tunis Tunisia
| | - José A. Pereira
- Centro de Investigação de Montanha (CIMO), ESAInstituto Politécnico de Bragança Campus Santa Apolónia 5300‐253 Bragança Portugal
| | - António M. Peres
- Centro de Investigação de Montanha (CIMO), ESAInstituto Politécnico de Bragança Campus Santa Apolónia 5300‐253 Bragança Portugal
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26
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Sanches-Neto FO, Coutinho ND, Palazzetti F, Carvalho-Silva VH. Temperature dependence of rate constants for the H(D) + CH4 reaction in gas and aqueous phase: deformed Transition-State Theory study including quantum tunneling and diffusion effects. Struct Chem 2019. [DOI: 10.1007/s11224-019-01437-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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de Castro DG, Poveda LA, Crispim LWS, Ballester MY. Quasi-Classical Trajectory Study of NH( 3∑ -) + NH( 3∑ -) Reactive Collisions. J Phys Chem A 2019; 123:9113-9122. [PMID: 31573199 DOI: 10.1021/acs.jpca.9b08278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A full-dimension quasi-classical trajectory study of collisions between two NH radicals is presented. Interatomic interactions are represented by a previously reported global six-dimensional potential energy surface for singlet electronic state of the N2H2 system. This study suggests that the formation of N2 from the collision of two NH radicals may occur via a one-step (NH + NH → N2 + H + H) or two-step (NH + NH → N2H + H → N2 + H + H) microscopic reaction mechanism. A fast vibrational energy redistribution is observed in the four-body complex in the latter mechanism. Excitation functions are presented and discussed. A variant of the vibrational energy quantum mechanical threshold method was used to correct the zero-point energy leakage in the classical calculations. The influence of reactant's rotational and vibrational energy on reactivity was investigated by state-specific calculations with one or both reactants excited. Reaction rate constants for the ground and some rotationally excited states are presented using an Arrhenius-Kooij-like functional form.
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Affiliation(s)
| | - Luis A Poveda
- Centro Federal de Educação Tecnológica de Minas Gerais , Belo Horizonte 36700-000 , MG , Brazil
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28
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Rosa Junior ACP, Cruz C, Santana WS, Moret MA. Characterization of the non-Arrhenius behavior of supercooled liquids by modeling nonadditive stochastic systems. Phys Rev E 2019; 100:022139. [PMID: 31574742 DOI: 10.1103/physreve.100.022139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Indexed: 11/07/2022]
Abstract
The characterization of the formation mechanisms of amorphous solids is a large avenue for research, since understanding its non-Arrhenius behavior is challenging to overcome. In this context, we present one path toward modeling the diffusive processes in supercooled liquids near glass transition through a class of nonhomogeneous continuity equations, providing a consistent theoretical basis for the physical interpretation of its non-Arrhenius behavior. More precisely, we obtain the generalized drag and diffusion coefficients that allow us to model a wide range of non-Arrhenius processes. This provides a reliable measurement of the degree of fragility of the system and an estimation of the fragile-to-strong transition in glass-forming liquids, as well as a generalized Stokes-Einstein equation, leading to a better understanding of the classical and quantum effects on the dynamics of nonadditive stochastic systems.
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Affiliation(s)
- A C P Rosa Junior
- Grupo de Informação Quântica, Centro de Ciências Exatas e das Tecnologias, Universidade Federal do Oeste da Bahia, Rua Bertioga, 892, Morada Nobre I, 47810-059 Barreiras, Bahia, Brazil
| | - C Cruz
- Grupo de Informação Quântica, Centro de Ciências Exatas e das Tecnologias, Universidade Federal do Oeste da Bahia, Rua Bertioga, 892, Morada Nobre I, 47810-059 Barreiras, Bahia, Brazil
| | - W S Santana
- Grupo de Informação Quântica, Centro de Ciências Exatas e das Tecnologias, Universidade Federal do Oeste da Bahia, Rua Bertioga, 892, Morada Nobre I, 47810-059 Barreiras, Bahia, Brazil
| | - M A Moret
- Programa de Modelagem Computacional-SENAI-CIMATEC, 41650-010 Salvador, Bahia, Brazil.,Universidade do Estado da Bahia (UNEB), 41150-000 Salvador, Bahia, Brazil
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29
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Machado HG, Sanches-Neto FO, Coutinho ND, Mundim KC, Palazzetti F, Carvalho-Silva VH. "Transitivity": A Code for Computing Kinetic and Related Parameters in Chemical Transformations and Transport Phenomena. Molecules 2019; 24:E3478. [PMID: 31557893 PMCID: PMC6803931 DOI: 10.3390/molecules24193478] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/04/2019] [Accepted: 09/08/2019] [Indexed: 12/25/2022] Open
Abstract
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.
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Affiliation(s)
- Hugo G Machado
- Grupo de Química Teórica e Estrutural de Anápolis, Centro de Pesquisa e Pós-Graduação. Universidade Estadual de Goiás, 75132-400 Anápolis, GO, Brazil.
- Instituto de Química, Universidade de Brasília, Caixa Postal 4478, 70904-970 Brasília, Brazil.
| | - Flávio O Sanches-Neto
- Grupo de Química Teórica e Estrutural de Anápolis, Centro de Pesquisa e Pós-Graduação. Universidade Estadual de Goiás, 75132-400 Anápolis, GO, Brazil.
- Instituto de Química, Universidade de Brasília, Caixa Postal 4478, 70904-970 Brasília, Brazil.
| | - Nayara D Coutinho
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy.
| | - Kleber C Mundim
- Instituto de Química, Universidade de Brasília, Caixa Postal 4478, 70904-970 Brasília, Brazil.
| | - Federico Palazzetti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy.
| | - Valter H Carvalho-Silva
- Grupo de Química Teórica e Estrutural de Anápolis, Centro de Pesquisa e Pós-Graduação. Universidade Estadual de Goiás, 75132-400 Anápolis, GO, Brazil.
- Instituto de Química, Universidade de Brasília, Caixa Postal 4478, 70904-970 Brasília, Brazil.
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30
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Artificial Intelligence Modelling Approach for the Prediction of CO-Rich Hydrogen Production Rate from Methane Dry Reforming. Catalysts 2019. [DOI: 10.3390/catal9090738] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This study investigates the applicability of the Leven–Marquardt algorithm, Bayesian regularization, and a scaled conjugate gradient algorithm as training algorithms for an artificial neural network (ANN) predictively modeling the rate of CO and H2 production by methane dry reforming over a Co/Pr2O3 catalyst. The dataset employed for the ANN modeling was obtained using a central composite experimental design. The input parameters consisted of CH4 partial pressure, CO2 partial pressure, and reaction temperature, while the target parameters included the rate of CO and H2 production. A neural network architecture of 3 13 2, 3 15 2, and 3 15 2 representing the input layer, hidden neuron layer, and target (output) layer were employed for the Leven–Marquardt, Bayesian regularization, and scaled conjugate gradient training algorithms, respectively. The ANN training with each of the algorithms resulted in an accurate prediction of the rate of CO and H2 production. The best prediction was, however, obtained using the Bayesian regularization algorithm with the lowest standard error of estimates (SEE). The high values of coefficient of determination (R2 > 0.9) obtained from the parity plots are an indication that the predicted rates of CO and H2 production were strongly correlated with the observed values.
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31
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Garcia E, Jambrina PG, Laganà A. Kinetics Of The H + CH 2 → CH + H 2 Reaction At Low Temperature. J Phys Chem A 2019; 123:7408-7419. [PMID: 31373813 DOI: 10.1021/acs.jpca.9b06212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A quasiclassical trajectory study of the kinetics of the title astrochemical reaction in a range of temperatures varying from 5 to 1000 K (corresponding to both the outer and the inner regions of the protostar and the circumstellar envelopes) was carried out and a clear dependence of the rate coefficient on the temperature is given, in contrast with the constant value adopted in kinetics astrochemical databases. Levering the massive nature of the performed calculations and of the detailed dynamical investigation of the reactive process, a rationalization of the temperature dependence of the released translational energy and of the rovibrational population of the CH and H2 diatomic products is also provided. Furthermore, the effect of the initial rovibrational energy of CH2 on the state-specific rate coefficients and cross sections is analyzed in order to single out the role played by the different regions of the potential energy surface on the dynamical outcomes and on the modeling the temperature dependence of the reactive efficiency of the investigated process. This led to a parametrization of the computed rate in terms of the following double Arrhenius expression (in cm3 s-1), k(T) = 2.50 × 10-10 exp(- 1.67/T) + 5.98 × 10-11 exp(- 280.5/T), alternative to the piecewise formulation into the three subintervals of temperature in which the overall 5-1000 K interval can be divided.
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Affiliation(s)
- Ernesto Garcia
- Departamento de Química Física , Universidad del País Vasco (UPV/EHU) , Paseo de la Universidad 7 , 01006 Vitoria , Spain
| | - Pablo G Jambrina
- Departamento de Química Física , Universidad de Salamanca , Plaza de los Caı́dos , 37008 Salamanca , Spain
| | - Antonio Laganà
- UOS Perugia , CNR ISTM , via Elce di sotto 8 , I-06123 Perugia , Italy.,Master UP srl , Strada Sperandio 15 , I-06125 Perugia , Italy
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32
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Sarkar D, Kang P, Nielsen SO, Qin Z. Non-Arrhenius Reaction-Diffusion Kinetics for Protein Inactivation over a Large Temperature Range. ACS NANO 2019; 13:8669-8679. [PMID: 31268674 PMCID: PMC7384293 DOI: 10.1021/acsnano.9b00068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding protein folding and unfolding has been a long-standing fundamental question and has important applications in manipulating protein activity in biological systems. Experimental investigations of protein unfolding have been predominately conducted by small temperature perturbations (e.g., temperature jump), while molecular simulations are limited to small time scales (microseconds) and high temperatures to observe unfolding. Thus, it remains unclear how fast a protein unfolds irreversibly and loses function (i.e., inactivation) across a large temperature range. In this work, using nanosecond pulsed heating of individual plasmonic nanoparticles to create precise localized heating, we examine the protein inactivation kinetics at extremely high temperatures. Connecting this with protein inactivation measurements at low temperatures, we observe that the kinetics of protein unfolding is less sensitive to temperature change at the higher temperatures, which significantly departs from the Arrhenius behavior extrapolated from low temperatures. To account for this effect, we propose a reaction-diffusion model that modifies the temperature-dependence of protein inactivation by introducing a diffusion limit. Analysis of the reaction-diffusion model provides general guidelines in the behavior of protein inactivation (reaction-limited, transition, diffusion-limited) across a large temperature range from physiological temperature to extremely high temperatures. We further demonstrate that the reaction-diffusion model is particularly useful for designing optimal operating conditions for protein photoinactivation. The experimentally validated reaction-diffusion kinetics of protein unfolding is an important step toward understanding protein-inactivation kinetics over a large temperature range. It has important applications including molecular hyperthermia and calls for future studies to examine this model for other protein molecules.
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Affiliation(s)
- Daipayan Sarkar
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Peiyuan Kang
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Steven O. Nielsen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Zhenpeng Qin
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Surgery, The University of Texas at Southwestern Medical Center, Dallas, TX 75390, USA
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33
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Albernaz AF, da Silva WB, Barreto PRP, Correa E. Thermal rate constant for the C(
3
P) + OH(X
2
Π) → CO(X
1
Σ) + H(
2
S) reaction using stochastic energy grained master equation method. INT J CHEM KINET 2019. [DOI: 10.1002/kin.21279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Washington B. da Silva
- Instituto Federal de EducaçãoCiência e Tecnologia de Brasília – IFBCeilândia Distrito Federal Brazil
| | - Patricia R. P. Barreto
- Laboratório Associado de Plasma -- LAPInstituto Nacional de Pesquisas Espaciais -- INPE/MCTSão José dos CamposSão Paulo Brazil
| | - Eberth Correa
- Universidade de BrasíliaCampus Gama, Gama Distrito Federal Brazil
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34
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Nucleophilic substitution vs elimination reaction of bisulfide ions with substituted methanes: exploration of chiral selectivity by stereodirectional first-principles dynamics and transition state theory. J Mol Model 2019; 25:227. [PMID: 31317347 DOI: 10.1007/s00894-019-4126-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/07/2019] [Indexed: 10/26/2022]
Abstract
Control of molecular orientation is emerging as crucial for the characterization of the stereodynamics of kinetics processes beyond structural stereochemistry. The special role played in chiral discrimination phenomena has been particularly emphasized by Aquilanti and collaborators after their extensive probes of experimental control of molecular alignment and orientation. In this work, the manifestation of the Aquilanti mechanism has been demonstrated for the first time in first-principles molecular dynamics simulations: stationary points characterized on potential energy surfaces have been calculated for the study of chemical reactions occurring between the bisulfide anion HS- and oriented prototypical chiral molecules CHFXY (where X = CH3 or CN and Y = Cl or I). The important reaction channels are those corresponding to bimolecular nucleophilic substitution (SN2) and to bimolecular elimination (E2): their relative role has been assessed and alternative pathways due to the mirror forms of the oriented chiral molecule are revealed by the different reactivity of the two enantiomers of CHFCNI in SN2 reaction.
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35
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Carvalho-Silva VH, Coutinho ND, Aquilanti V. Temperature Dependence of Rate Processes Beyond Arrhenius and Eyring: Activation and Transitivity. Front Chem 2019; 7:380. [PMID: 31192196 PMCID: PMC6548831 DOI: 10.3389/fchem.2019.00380] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/10/2019] [Indexed: 12/02/2022] Open
Abstract
Advances in the understanding of the dependence of reaction rates from temperature, as motivated from progress in experiments and theoretical tools (e. g., molecular dynamics), are needed for the modeling of extreme environmental conditions (e.g., in astrochemistry and in the chemistry of plasmas). While investigating statistical mechanics perspectives (Aquilanti et al., 2017b, 2018), the concept of transitivity was introduced as a measure for the propensity for a reaction to occur. The Transitivity plot is here defined as the reciprocal of the apparent activation energy vs. reciprocal absolute temperature. Since the transitivity function regulates transit in physicochemical transformations, not necessarily involving reference to transition-state hypothesis of Eyring, an extended version is here proposed to cope with general types of transformations. The transitivity plot permits a representation where deviations from Arrhenius behavior are given a geometrical meaning and make explicit a positive or negative linear dependence of transitivity for sub- and super-Arrhenius cases, respectively. To first-order in reciprocal temperature, the transitivity function models deviations from linearity in Arrhenius plots as originally proposed by Aquilanti and Mundim: when deviations are increasingly larger, other phenomenological formulas, such as Vogel-Fulcher-Tammann, Nakamura-Takayanagi-Sato, and Aquilanti-Sanches-Coutinho-Carvalho are here rediscussed from the transitivity concept perspective and with in a general context. Emphasized is the interest of introducing into this context modifications to a very successful tool of theoretical kinetics, Eyring's Transition-State Theory: considering the behavior of the transitivity function at low temperatures, in order to describe deviation from Arrhenius behavior under the quantum tunneling regime, a "d-TST" formulation was previously introduced (Carvalho-Silva et al., 2017). In this paper, a special attention is dedicated to a derivation of the temperature dependence of viscosity, making explicit reference to feature of the transitivity function, which in this case generally exhibits a super-Arrhenius behavior. This is of relevance also for advantages of using the transitivity function for diffusion-controlled phenomena.
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Affiliation(s)
- Valter H. Carvalho-Silva
- Grupo de Química Teórica e Estrutural de Anápolis, Campus de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, Anápolis, Brazil
| | - Nayara D. Coutinho
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Vincenzo Aquilanti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy
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36
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Capitelli M, Pietanza LD. Past and present aspects of Italian plasma chemistry. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2019. [DOI: 10.1007/s12210-019-00781-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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37
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Só YADO, Neto PHDO, de Macedo LGM, Gargano R. Theoretical Investigation on H 2O 2-Ng (He, Ne, Ar, Kr, Xe, and Rn) Complexes Suitable for Stereodynamics: Interactions and Thermal Chiral Rate Consequences. Front Chem 2019; 6:671. [PMID: 30713840 PMCID: PMC6345723 DOI: 10.3389/fchem.2018.00671] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/24/2018] [Indexed: 11/29/2022] Open
Abstract
Although molecular collisions of noble gases (Ng) can be theoretically used to distinguish between the enantiomers of hydrogen peroxide - H2O2 (HP), little is known about the effects of HP-Ng interactions on the chiral rate. In this work, the chiral rate as a function of temperature (CRT) between enantiomeric conformations of HP and Ng (Ng=He, Ne, Ar, Kr, Xe, and Rn) are presented at MP2(full)/aug-cc-pVTZ level of theory through a fully basis set superposition error (BSSE) corrected potential energy surface. The results show that: (a) the CRT is highly affected even at a small decrease in the height of trans-barrier; (b) its smallest values occur with Ne for all temperatures between 100 and 4,000 K; (c) that the decrease of CRT shows an inverse correlation with respect to the average valence electron energy of the Ng and (d) Ne and He may be the noble gases more suitable for study the oriented collision dynamics of HP. In addition to binding energies, the electron density ρ and its Laplacian ∇2ρ topological analyses were also performed within the atoms in molecules (AIM) theory in order to determine the nature of the HP-Ng interactions. The results of this work provide a more complete foundation on experiments to study HP's chirality using Ng in crossed molecular beams without a light source.
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Affiliation(s)
| | | | | | - Ricardo Gargano
- Institute of Physics, University of Brasília, Brasília, Brazil
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38
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From statistical thermodynamics to molecular kinetics: the change, the chance and the choice. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2018. [DOI: 10.1007/s12210-018-0749-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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39
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Firaha DS, Döntgen M, Berkels B, Leonhard K. Pressure-Dependent Rate Constant Predictions Utilizing the Inverse Laplace Transform: A Victim of Deficient Input Data. ACS OMEGA 2018; 3:8212-8219. [PMID: 31458958 PMCID: PMC6644344 DOI: 10.1021/acsomega.8b00311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/07/2018] [Indexed: 06/10/2023]
Abstract
k(E) can be calculated either from the Rice-Ramsperger-Kassel-Marcus theory or by inverting macroscopic rate constants k(T). Here, we elaborate the inverse Laplace transform approach for k(E) reconstruction by examining the impact of k(T) data fitting accuracy. For this approach, any inaccuracy in the reconstructed k(E) results from inaccurate/incomplete k(T) description. Therefore, we demonstrate how an improved mathematical description of k(T) data leads to accurate k(E) data. Refitting inaccurate/incomplete k(T), hence, allows for recapturing k(T) information that yields more accurate k(E) reconstructions. The present work suggests that accurate representation of experimental and theoretical k(T) data in a broad temperature range could be used to obtain k(T,p). Thus, purely temperature-dependent kinetic models could be converted into fully temperature- and pressure-dependent kinetic models.
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Affiliation(s)
- Dzmitry S. Firaha
- AICES
Graduate School, Rheinisch-Westfälische
Technische Hochschule Aachen, Schinkelstr. 2, D-52062 Aachen, Germany
- Chair
of Technical Thermodynamics, Rheinisch-Westfälische
Technische Hochschule Aachen, Schinkelstr. 8, D-52062 Aachen, Germany
| | - Malte Döntgen
- Chair
of Technical Thermodynamics, Rheinisch-Westfälische
Technische Hochschule Aachen, Schinkelstr. 8, D-52062 Aachen, Germany
| | - Benjamin Berkels
- AICES
Graduate School, Rheinisch-Westfälische
Technische Hochschule Aachen, Schinkelstr. 2, D-52062 Aachen, Germany
| | - Kai Leonhard
- AICES
Graduate School, Rheinisch-Westfälische
Technische Hochschule Aachen, Schinkelstr. 2, D-52062 Aachen, Germany
- Chair
of Technical Thermodynamics, Rheinisch-Westfälische
Technische Hochschule Aachen, Schinkelstr. 8, D-52062 Aachen, Germany
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40
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Sanches-Neto FO, Coutinho ND, Carvalho-Silva VH. A novel assessment of the role of the methyl radical and water formation channel in the CH 3OH + H reaction. Phys Chem Chem Phys 2018; 19:24467-24477. [PMID: 28890979 DOI: 10.1039/c7cp03806b] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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.
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Affiliation(s)
- Flávio O Sanches-Neto
- Grupo de Química Teórica de Anápolis Campus de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, Caixa Postal 459, 75001-970, Anápolis, GO, Brazil.
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41
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Mandal A, Das RS, Singh B, Banerjee R, Mukhopadhyay S. Penicillamine and captopril: mechanistic exploration of defensive actions of thiol drugs against a metal bound-superoxo complex. J COORD CHEM 2017. [DOI: 10.1080/00958972.2017.1303488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Arabinda Mandal
- Department of Chemistry, Bidhannagar College, Kolkata, India
| | | | - Bula Singh
- Department of Chemistry, Visva-Bharati, Santiniketan, India
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42
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Spezia R, Martínez-Nuñez E, Vazquez S, Hase WL. Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:20170035. [PMID: 28320909 PMCID: PMC5360905 DOI: 10.1098/rsta.2017.0035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, CEA CNRS Université Paris Saclay, 91025 Evry, France
- LAMBE, Université d'Evry, 91025 Evry, France
| | - Emilio Martínez-Nuñez
- Departamento de Química Física and Centro Singular de Investigación en Química, Biológica y Materiales Moleculares (CIQUS), Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Saulo Vazquez
- Departamento de Química Física and Centro Singular de Investigación en Química, Biológica y Materiales Moleculares (CIQUS), Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - William L Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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43
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Aquilanti V, Coutinho ND, Carvalho-Silva VH. Kinetics of low-temperature transitions and a reaction rate theory from non-equilibrium distributions. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0201. [PMID: 28320904 PMCID: PMC5360900 DOI: 10.1098/rsta.2016.0201] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/14/2016] [Indexed: 05/14/2023]
Abstract
This article surveys the empirical information which originated both by laboratory experiments and by computational simulations, and expands previous understanding of the rates of chemical processes in the low-temperature range, where deviations from linearity of Arrhenius plots were revealed. The phenomenological two-parameter Arrhenius equation requires improvement for applications where interpolation or extrapolations are demanded in various areas of modern science. Based on Tolman's theorem, the dependence of the reciprocal of the apparent activation energy as a function of reciprocal absolute temperature permits the introduction of a deviation parameter d covering uniformly a variety of rate processes, from those where quantum mechanical tunnelling is significant and d < 0, to those where d > 0, corresponding to the Pareto-Tsallis statistical weights: these generalize the Boltzmann-Gibbs weight, which is recovered for d = 0. It is shown here how the weights arise, relaxing the thermodynamic equilibrium limit, either for a binomial distribution if d > 0 or for a negative binomial distribution if d < 0, formally corresponding to Fermion-like or Boson-like statistics, respectively. The current status of the phenomenology is illustrated emphasizing case studies; specifically (i) the super-Arrhenius kinetics, where transport phenomena accelerate processes as the temperature increases; (ii) the sub-Arrhenius kinetics, where quantum mechanical tunnelling propitiates low-temperature reactivity; (iii) the anti-Arrhenius kinetics, where processes with no energetic obstacles are rate-limited by molecular reorientation requirements. Particular attention is given for case (i) to the treatment of diffusion and viscosity, for case (ii) to formulation of a transition rate theory for chemical kinetics including quantum mechanical tunnelling, and for case (iii) to the stereodirectional specificity of the dynamics of reactions strongly hindered by the increase of temperature.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Vincenzo Aquilanti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
- Instituto de Física, Universidade Federal da Bahia, 40210 Salvador, Brazil
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, 00016 Rome, Italy
| | - Nayara Dantas Coutinho
- Instituto de Química, Universidade de Brasília, Caixa Postal 4478, 70904-970 Brasília, Brazil
| | - Valter Henrique Carvalho-Silva
- Grupo de Química Teórica e Estrutural de Anápolis, Campus de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, CP 459, 75001-970 Anápolis, GO, Brazil
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44
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Non-linear van't Hoff behavior in pulmonary surfactant model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1133-1143. [PMID: 28336314 DOI: 10.1016/j.bbamem.2017.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/14/2017] [Accepted: 03/18/2017] [Indexed: 11/22/2022]
Abstract
Pulmonary surfactant exhibits phase coexistence over a wide range of surface pressure and temperature. Less is known about the effect of temperature on pulmonary surfactant models. Given the lack of studies on this issue, we used electron paramagnetic resonance (EPR) and nonlinear least-squares (NLLS) simulations to investigate the thermotropic phase behavior of the matrix that mimics the pulmonary surfactant lipid complex, i.e., the lipid mixture composed of dipalmitoyl phosphatidylcholine (DPPC), palmitoyl-oleoyl phosphatidylcholine (POPC) and palmitoyl-oleoyl phosphatidylglycerol (POPG). Irrespective of pH, the EPR spectra recorded from 5°C to 25°C in the DPPC/POPC/POPG (4:3:1) model membrane contain two spectral components corresponding to lipids in gel-like and fluid-like phases, indicating a coexistence of two domains in that range. The temperature dependence of the distribution of spin labels between the domains yielded nonlinear van't Hoff plots. The thermodynamic parameters evaluated were markedly different for DPPC and for the ternary DPPC/POPC/POPG (4:3:1) membranes and exhibited a dependence on chemical environment. While enthalpy and entropy changes for DPPC were always positive and presented a quadratic behavior with temperature, those of the ternary mixture were linearly dependent on temperature and changed from negative to positive values. Despite that, enthalpy-entropy compensation takes place in the two systems. The thermotropic process associated with the coexistence of the two domains is entropically-driven in DPPC and either entropically- or enthalpically-driven in the pulmonary surfactant membrane depending on the pH, ionic strength and temperature. The significance of these results to the structure and function of the pulmonary surfactant lipid matrix is discussed.
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45
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Rampino S, Suleimanov YV. Thermal Rate Coefficients for the Astrochemical Process C + CH+ → C2+ + H by Ring Polymer Molecular Dynamics. J Phys Chem A 2016; 120:9887-9893. [DOI: 10.1021/acs.jpca.6b10592] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sergio Rampino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italia
| | - Yury V. Suleimanov
- Computation-based
Science and Technology Research Center, Cyprus Institute, 20
Kavafi Street, Nicosia 2121, Cyprus
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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46
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Carvalho-Silva VH, Aquilanti V, de Oliveira HCB, Mundim KC. Deformed transition-state theory: Deviation from Arrhenius behavior and application to bimolecular hydrogen transfer reaction rates in the tunneling regime. J Comput Chem 2016; 38:178-188. [PMID: 27859380 DOI: 10.1002/jcc.24529] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/24/2016] [Accepted: 10/10/2016] [Indexed: 12/14/2022]
Abstract
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.
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Affiliation(s)
- Valter H Carvalho-Silva
- Grupo de Química Teórica e Estrutural de Anápolis, Unidade Universitária de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, P.O. Box 459, 75001-970, Anápolis, GO, Brazil
| | - Vincenzo Aquilanti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy. Instituto de Física, Universidade Federal da Bahia, 40210, Salvador, Brazil.,Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, 00016, Rome, Italy
| | - Heibbe C B de Oliveira
- Instituto de Química, Universidade de Brasília, Caixa Postal 4478, 70904-970, Brasília, Brazil
| | - Kleber C Mundim
- Instituto de Química, Universidade de Brasília, Caixa Postal 4478, 70904-970, Brasília, Brazil
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47
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48
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Coutinho ND, Aquilanti V, Silva VHC, Camargo AJ, Mundim KC, de Oliveira HCB. Stereodirectional Origin of anti-Arrhenius Kinetics for a Tetraatomic Hydrogen Exchange Reaction: Born-Oppenheimer Molecular Dynamics for OH + HBr. J Phys Chem A 2016; 120:5408-17. [PMID: 27205872 DOI: 10.1021/acs.jpca.6b03958] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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.
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Affiliation(s)
- Nayara D Coutinho
- Instituto de Química, Universidade de Brasília , 4478, 70904-970 Brasília, Brazil
| | - Vincenzo Aquilanti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , Via Elce di Sotto 8, 06123, Perugia, Italy.,Instituto de Física, Universidade Federal da Bahia , 40210 Salvador, Brazil.,Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche , 00016 Rome, Italy
| | - Valter H C Silva
- Grupo de Química Teórica e Estrutural de Anápolis, Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás , 0459, 75001-970 Anápolis, GO Brazil
| | - Ademir J Camargo
- Grupo de Química Teórica e Estrutural de Anápolis, Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás , 0459, 75001-970 Anápolis, GO Brazil
| | - Kleber C Mundim
- Instituto de Química, Universidade de Brasília , 4478, 70904-970 Brasília, Brazil
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49
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Cortes Patino SA, Bonilla RR. Polymers selection for a liquid inoculant of Azospirillum brasilense based on the Arrhenius thermodynamic model. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/ajb2015.14777] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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50
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Collins P, Kramer ZC, Carpenter BK, Ezra GS, Wiggins S. Nonstatistical dynamics on the caldera. J Chem Phys 2015; 141:034111. [PMID: 25053305 DOI: 10.1063/1.4889780] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We explore both classical and quantum dynamics of a model potential exhibiting a caldera: that is, a shallow potential well with two pairs of symmetry related index one saddles associated with entrance/exit channels. Classical trajectory simulations at several different energies confirm the existence of the "dynamical matching" phenomenon originally proposed by Carpenter, where the momentum direction associated with an incoming trajectory initiated at a high energy saddle point determines to a considerable extent the outcome of the reaction (passage through the diametrically opposing exit channel). By studying a "stretched" version of the caldera model, we have uncovered a generalized dynamical matching: bundles of trajectories can reflect off a hard potential wall so as to end up exiting predominantly through the transition state opposite the reflection point. We also investigate the effects of dissipation on the classical dynamics. In addition to classical trajectory studies, we examine the dynamics of quantum wave packets on the caldera potential (stretched and unstretched). These computations reveal a quantum mechanical analogue of the "dynamical matching" phenomenon, where the initial expectation value of the momentum direction for the wave packet determines the exit channel through which most of the probability density passes to product.
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Affiliation(s)
- Peter Collins
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Zeb C Kramer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, USA
| | - Barry K Carpenter
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Gregory S Ezra
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, USA
| | - Stephen Wiggins
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
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