1
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Xue C, Xu X, Lyu H, Li Y, Ren Y, Wang J, Mu Y, Mellouki A, Yang Z. Kinetic and reactivity of gas-phase reaction of acyclic dienes with hydroxyl radical in the 273-318 K temperature range. RSC Adv 2024; 14:12303-12312. [PMID: 38633496 PMCID: PMC11019904 DOI: 10.1039/d3ra08750f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/23/2024] [Indexed: 04/19/2024] Open
Abstract
As dienes contain two C[double bond, length as m-dash]C bonds, theoretically, they are much more chemically reactive with hydroxyl radical (˙OH) than alkenes and alkanes, and the reaction with ˙OH is one of the main atmospheric degradation routes of dienes during the daytime. In our work, rate coefficients of three types of acyclic dienes: conjugated as 3-methyl-1,3-pentadiene (3M13PD), isolated as 1,4-hexadiene (14HD), and cumulated as 1,2-pentadiene (12PD) reaction with ˙OH were measured in the temperature range of 273-318 K and 1 atm using the relative rate method. At 298 ± 3 K, the rate coefficients for those reactions were determined to be k3M13PD+OH = (15.09 ± 0.72) × 10-11, k14HD+OH = (9.13 ± 0.62) × 10-11, k12PD+OH = (3.34 ± 0.40) × 10-11 (as units of cm3 per molecule per s), in the excellent agreement with values of previously reported. The first measured temperature dependence for 3M13PD, 14HD and 12PD reaction with ˙OH can be expressed by the following Arrhenius expressions in units of cm3 per molecule per s: k3M13PD+OH = (8.10 ± 2.23) × 10-11 exp[(173 ± 71)/T]; k14HD+OH = (9.82 ± 5.10) × 10-12 exp[(666 ± 123)/T]; k12PD+OH = (1.13 ± 0.87) × 10-12 exp[(1038 ± 167)/T] (as units of cm3 per molecule per s). The kinetic discussion revealed that the relative position between these two C[double bond, length as m-dash]C could significantly affect the reactivity of acyclic dienes toward ˙OH. A simple structure-activity relationship (SAR) method was proposed to estimate the reaction rate coefficients of acyclic dienes with ˙OH.
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Affiliation(s)
- Chenyang Xue
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology Tianjin 300457 China
- Laboratory of Atmospheric Environment and Pollution Control (LAEPC), Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing 100085 China
| | - Xinmiao Xu
- Laboratory of Atmospheric Environment and Pollution Control (LAEPC), Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing 100085 China
- College of Resources and Environment, University of Chinese Academy of Sciences Beijing 100049 China
| | - Han Lyu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University Jinan 250101 China
| | - Yunfeng Li
- School of Mechanical Engineering, Beijing Institute of Petrochemical Technology Beijing 102617 China
| | - Yangang Ren
- Laboratory of Atmospheric Environment and Pollution Control (LAEPC), Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing 100085 China
- College of Resources and Environment, University of Chinese Academy of Sciences Beijing 100049 China
| | - Jinhe Wang
- School of Municipal and Environmental Engineering, Shandong Jianzhu University Jinan 250101 China
| | - Yujing Mu
- Laboratory of Atmospheric Environment and Pollution Control (LAEPC), Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing 100085 China
- College of Resources and Environment, University of Chinese Academy of Sciences Beijing 100049 China
| | - Abdelwahid Mellouki
- Mohammed VI Polytechnic University Lot 660, Hay Moulay Rachid, Ben Guerir 43150 Morocco
- Institut de Combustion Aérothermique Réactivité et Environnement/OSUC-CNRS 45071 Orléans Cedex 2 France
| | - Zongzheng Yang
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology Tianjin 300457 China
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2
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Matarèse BFE, Rusin A, Seymour C, Mothersill C. Quantum Biology and the Potential Role of Entanglement and Tunneling in Non-Targeted Effects of Ionizing Radiation: A Review and Proposed Model. Int J Mol Sci 2023; 24:16464. [PMID: 38003655 PMCID: PMC10671017 DOI: 10.3390/ijms242216464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
It is well established that cells, tissues, and organisms exposed to low doses of ionizing radiation can induce effects in non-irradiated neighbors (non-targeted effects or NTE), but the mechanisms remain unclear. This is especially true of the initial steps leading to the release of signaling molecules contained in exosomes. Voltage-gated ion channels, photon emissions, and calcium fluxes are all involved but the precise sequence of events is not yet known. We identified what may be a quantum entanglement type of effect and this prompted us to consider whether aspects of quantum biology such as tunneling and entanglement may underlie the initial events leading to NTE. We review the field where it may be relevant to ionizing radiation processes. These include NTE, low-dose hyper-radiosensitivity, hormesis, and the adaptive response. Finally, we present a possible quantum biological-based model for NTE.
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Affiliation(s)
- Bruno F. E. Matarèse
- Department of Haematology, University of Cambridge, Cambridge CB2 1TN, UK;
- Department of Physics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Andrej Rusin
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
| | - Colin Seymour
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
| | - Carmel Mothersill
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
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3
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Knight AL, Widjaja V, Lisi GP. Temperature as a modulator of allosteric motions and crosstalk in mesophilic and thermophilic enzymes. Front Mol Biosci 2023; 10:1281062. [PMID: 37877120 PMCID: PMC10591084 DOI: 10.3389/fmolb.2023.1281062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
Mesophilic and thermophilic enzyme counterparts are often studied to understand how proteins function under harsh conditions. To function well outside of standard temperature ranges, thermophiles often tightly regulate their structural ensemble through intra-protein communication (via allostery) and altered interactions with ligands. It has also become apparent in recent years that the enhancement or diminution of allosteric crosstalk can be temperature-dependent and distinguish thermophilic enzymes from their mesophilic paralogs. Since most studies of allostery utilize chemical modifications from pH, mutations, or ligands, the impact of temperature on allosteric function is comparatively understudied. Here, we discuss the biophysical methods, as well as critical case studies, that dissect temperature-dependent function of mesophilic-thermophilic enzyme pairs and their allosteric regulation across a range of temperatures.
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Affiliation(s)
| | | | - George P. Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
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4
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Tesnim D, Hedi BA, Simal-Gandara J. Sustainable and Green Synthesis of Iron Nanoparticles Supported on Natural Clays via Palm Waste Extract for Catalytic Oxidation of Crocein Orange G Mono Azoic Dye. ACS OMEGA 2023; 8:34364-34376. [PMID: 37780026 PMCID: PMC10534912 DOI: 10.1021/acsomega.3c01333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/05/2023] [Indexed: 10/03/2023]
Abstract
In this study, the removal of Crocein Orange G dye (COG) from aqueous solution was investigated using an innovative green catalyst to overcome problems with chemical techniques. Clay bentonite El Hamma (HB)-supported nanoscale zero-valent iron (NZVI) was used as a heterogeneous Fenton-like catalyst for the oxidation of harmful COG. Palm waste extract was herein used as a reducing and capping agent to synthesize NZVI, and HB clay was employed, which was obtained from the El Hamma bentonite deposit in the Gabes province of Tunisia. HB and HB-NZVI were characterized by various techniques such as scanning electron microscopy (SEM), transmission electron microscopy (TEM), Brunauer, Emmett, and Teller (BET), Fourier transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), X-ray diffraction (XRD), and zeta potential. Under optimal conditions, total degradation of COG was attained within 180 min. Kinetic studies showed that the dye degradation rate followed well the pseudo-second-order model. The apparent activation energy was 33.11 kJ/mol, which is typical of a physically controlled reaction. The degradation pathways and mineralization study revealed that the adsorption-Fenton-like reaction was the principal mechanism that demonstrated 100% degradation efficiency of COG even after three successive runs. Obtained results suggest that HB-NZVI is an affective heterogeneous catalyst for the degradation of COG by H2O2 and may constitute a sustainable green catalyst for azoic dye removal from industrial wastewaters.
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Affiliation(s)
- Dhiss Tesnim
- National
School of Engineers of Gabes, Laboratory of Research: Processes, Energy,
Environment & Electrical Systems PEESE (LR18ES34), University of Gabes, Rue Omar Ibn Alkhattab, 6029 Gabes, Tunisia
| | - Ben Amor Hedi
- National
School of Engineers of Gabes, Laboratory of Research: Processes, Energy,
Environment & Electrical Systems PEESE (LR18ES34), University of Gabes, Rue Omar Ibn Alkhattab, 6029 Gabes, Tunisia
| | - Jesus Simal-Gandara
- Nutrition
and Bromatology Group, Analytical Chemistry and Food Science Department,
Faculty of Science, Universidade de Vigo, E32004 Ourense, Spain
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5
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Ballotta B, Martínez-Núñez E, Rampino S, Barone V. New prebiotic molecules in the interstellar medium from the reaction between vinyl alcohol and CN radicals: unsupervised reaction mechanism discovery, accurate electronic structure calculations and kinetic simulations. Phys Chem Chem Phys 2023; 25:22840-22850. [PMID: 37584420 DOI: 10.1039/d3cp02571c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Vinyl alcohol (VyA) and cyanide (CN) radicals are relatively abundant in the interstellar medium (ISM). VyA is the enolic tautomer of acetaldehyde and has two low-lying conformers, characterized by the syn or anti placement of hydroxyl hydrogen with respect to the double bond. In this paper, we present a gas-phase model of the barrierless reactions of both VyA's conformers with CN employing accurate quantum chemical computations in the framework of a master equation approach based on the transition state theory. Our results indicate that both VyA conformers feature a similar reactivity with CN, starting with a barrierless addition to the double bond and followed by different isomerization, dissociation, and/or hydrogen elimination steps. The rate constants computed for temperatures up to 600 K show that several reaction channels are open even under the harsh conditions of the ISM, with the favoured one providing the first feasible formation route of a prebiotic molecule not yet detected in the ISM, namely cyanoacetaldehyde. This finding suggests looking for cyanoacetaldehyde in regions where both VyA and CN have already been detected, like, e.g., Sagittarius B2N or G+0.693-0.027.
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Affiliation(s)
- Bernardo Ballotta
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Emilio Martínez-Núñez
- Departamento de Química Física, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, Avenida das Ciencias s/n, 15782, Santiago de Compostela, Spain
| | - Sergio Rampino
- Università degli Studi di Padova, Dipartimento di Scienze Chimiche, Via Marzolo 1, 35131 Padova, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
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6
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Piskulich ZA, Borkowski AK, Thompson WH. A Maxwell relation for dynamical timescales with application to the pressure and temperature dependence of water self-diffusion and shear viscosity. Phys Chem Chem Phys 2023; 25:12820-12832. [PMID: 37129891 DOI: 10.1039/d3cp01386c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A Maxwell relation for a reaction rate constant (or other dynamical timescale) obtained under constant pressure, p, and temperature, T, is introduced and discussed. Examination of this relationship in the context of fluctuation theory provides insight into the p and T dependence of the timescale and the underlying molecular origins. This Maxwell relation motivates a suggestion for the general form of the timescale as a function of pressure and temperature. This is illustrated by accurately fitting simulation results and existing experimental data on the self-diffusion coefficient and shear viscosity of liquid water. A key advantage of this approach is that each fitting parameter is physically meaningful.
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Affiliation(s)
- Zeke A Piskulich
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.
| | | | - Ward H Thompson
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.
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7
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Weaver RL, Lee S. Slow dynamics in a single bead with mechanical conditioning and transient heating. Phys Rev E 2023; 107:044902. [PMID: 37198830 DOI: 10.1103/physreve.107.044902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 03/17/2023] [Indexed: 05/19/2023]
Abstract
The contact stiffness of an aluminum bead confined between two slabs diminishes upon mechanical conditioning, and then recovers as log(t) after the conditioning ceases. Here that structure is evaluated for its response to transient heating and cooling, with and without accompanying conditioning vibrations. It is found that, under heating or cooling alone, stiffness changes are mostly consistent with temperature-dependent material moduli; there is little or no slow dynamics. Hybrid tests in which vibration conditioning is followed by heating or cooling lead to recoveries that begin as log(t) and then become more complex. On subtracting the known response to heating or cooling alone we discern the influence of higher or lower temperatures on slow dynamic recovery from vibrations. It is found that heating accelerates the initial log(t) recovery, but by an amount more than predicted by an Arrhenius model of thermally activated barrier penetrations. Transient cooling has no discernible effect, in contrast to the Arrhenius prediction that it slows recovery.
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Affiliation(s)
- Richard L Weaver
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - SangMin Lee
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
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8
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Waste additives as biopolymers for the modification of bitumen: Mechanical performance and structural analysis characterization. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2023.131079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Benjamin I, Louis H, Okon GA, Qader SW, Afahanam LE, Fidelis CF, Eno EA, Ejiofor EE, Manicum ALE. Transition Metal-Decorated B 12N 12-X (X = Au, Cu, Ni, Os, Pt, and Zn) Nanoclusters as Biosensors for Carboplatin. ACS OMEGA 2023; 8:10006-10021. [PMID: 36969422 PMCID: PMC10035017 DOI: 10.1021/acsomega.2c07250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/09/2023] [Indexed: 06/02/2023]
Abstract
Theoretical studies on the adsorption, sensibility, and reactivity of a boron nitride nanocage decorated with Au, Cu, Ni, Os, Pt, and Zn metals as a biosensor material were carried out for the adsorption of carboplatin by applying the density functional theory computation at the B3LYP-GD3BJ/def2svp level of theory. All the optimized structures, as well as the calculations as regards the studied objective including electronic properties, geometry optimization parameters, adsorption energy studies, natural bond orbital analysis, topology studies, sensor mechanistic parameters, and thermodynamic properties (ΔG and ΔH), were investigated herein. As a result, the noticeable change in the energy gap of the studied surfaces when interacting with carboplatin accounted for the surfaces' reactivity, stability, conductivity, work function, and overall adsorption ability, implying that the studied decorated surfaces are good sensor materials for sensing carboplatin. Furthermore, the negative adsorption energies obtained for interacting surfaces decorated with Cu, Ni, Os, and Zn suggest that the surface has a superior ability to sense carboplatin as chemisorption was seen. Substantially, the geometric short adsorption bond length after adsorption, thermodynamically spontaneous reactions, and acceptable sensor mechanism results demonstrate that the investigated surfaces have strong sensing characteristics for sensing carboplatin.
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Affiliation(s)
- Innocent Benjamin
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540221, Nigeria
| | - Gideon A. Okon
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Chemical Sciences, Clifford University, Owerrinta 451101, Nigeria
| | - Suhailah W. Qader
- Department
of Medical Laboratory Science, Knowledge
University, Erbil 44001, Iraq
| | - Lucy E. Afahanam
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - Chidera F. Fidelis
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540221, Nigeria
| | - Ededet A. Eno
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540221, Nigeria
| | - Emmanuel E. Ejiofor
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Chemical Sciences, Clifford University, Owerrinta 451101, Nigeria
| | - Amanda-Lee E. Manicum
- Department
of Chemistry, Tshwane University of Technology, Pretoria 0183, South Africa
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10
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Długosz O. Natural Deep Eutectic Solvents in the Synthesis of Inorganic Nanoparticles. MATERIALS (BASEL, SWITZERLAND) 2023; 16:627. [PMID: 36676363 PMCID: PMC9862785 DOI: 10.3390/ma16020627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/23/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Natural deep eutectic solvents (NDESs), as a new type of green solvent, are used in many fields, including industry in extraction processes, medicine, pharmaceuticals, metallurgy, electrodeposition, separations, gas capture, biocatalysis and nanotechnology. Mainly due to their properties, such as simple preparation, environmental friendliness, biocompatibility and multifunctionality, they are being used in various fields of industry. This review aims to provide insight into the applications of natural deep eutectic solvents, specifically in nanotechnology processes. It focuses on the description of NDES and how their physicochemical properties are used to obtain functional nanomaterials, including metals, metal oxides and salts. It highlights how the use of NDESs to obtain a wide range of inorganic nanoparticles enables the elimination of disadvantages of traditional methods of obtaining them, including reducing energy consumption and functionalising nanoparticles in situ. In conclusion, recent advances and future directions in the development and applications of NDESs in nanotechnology are discussed with the aim of identifying unexplained scientific questions that can be investigated in the future.
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Affiliation(s)
- Olga Długosz
- Faculty of Chemical Engineering and Technology, Cracow University of Technology, 31-155 Cracow, Poland
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11
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Yewdall NA, André AAM, van Haren MHI, Nelissen FHT, Jonker A, Spruijt E. ATP:Mg 2+ shapes material properties of protein-RNA condensates and their partitioning of clients. Biophys J 2022; 121:3962-3974. [PMID: 36004782 PMCID: PMC9674983 DOI: 10.1016/j.bpj.2022.08.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/29/2022] [Accepted: 08/19/2022] [Indexed: 11/26/2022] Open
Abstract
Many cellular condensates are heterotypic mixtures of proteins and RNA formed in complex environments. Magnesium ions (Mg2+) and ATP can impact RNA folding, and local intracellular levels of these factors can vary significantly. However, the effect of ATP:Mg2+ on the material properties of protein-RNA condensates is largely unknown. Here, we use an in vitro condensate model of nucleoli, made from nucleophosmin 1 (NPM1) proteins and ribosomal RNA (rRNA), to study the effect of ATP:Mg2+. While NPM1 dynamics remain unchanged at increasing Mg2+ concentrations, the internal RNA dynamics dramatically slowed until a critical point, where gel-like states appeared, suggesting the RNA component alone forms a viscoelastic network that undergoes maturation driven by weak multivalent interactions. ATP reverses this arrest and liquefies the gel-like structures. ATP:Mg2+ also influenced the NPM1-rRNA composition of condensates and enhanced the partitioning of two clients: an arginine-rich peptide and a small nuclear RNA. By contrast, larger ribosome partitioning shows dependence on ATP:Mg2+ and can become reversibly trapped around NPM1-rRNA condensates. Lastly, we show that dissipative enzymatic reactions that deplete ATP can be used to control the shape, composition, and function of condensates. Our results illustrate how intracellular environments may regulate the state and client partitioning of RNA-containing condensates.
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Affiliation(s)
- N Amy Yewdall
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
| | - Alain A M André
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Aafke Jonker
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
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12
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Rizk F, Gelin S, Biance AL, Joly L. Microscopic Origins of the Viscosity of a Lennard-Jones Liquid. PHYSICAL REVIEW LETTERS 2022; 129:074503. [PMID: 36018701 DOI: 10.1103/physrevlett.129.074503] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Unlike crystalline solids or ideal gases, transport properties remain difficult to describe from a microscopic point of view in liquids, whose dynamics result from complex energetic and entropic contributions at the atomic scale. Two scenarios are generally proposed: one represents the dynamics in a fluid as a series of energy-barrier crossings, leading to Arrhenius-like laws, while the other assumes that atoms rearrange themselves by collisions, as exemplified by the free volume model. To assess the validity of these two views, we computed, using molecular dynamics simulations, the transport properties of the Lennard-Jones fluid and tested to what extent the Arrhenius equation and the free volume model describe the temperature dependence of the viscosity and of the diffusion coefficient at fixed pressure. Although both models reproduce the simulation results over a wide range of pressure and temperature covering the liquid and supercritical states of the Lennard-Jones fluid, we found that the parameters of the free volume model can be estimated directly from local structural parameters, also obtained in the simulations. This consistency of the results gives more credibility to the free volume description of transport properties in liquids.
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Affiliation(s)
- Farid Rizk
- Univ Lyon, Univ Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 VILLEURBANNE, France
| | - Simon Gelin
- Univ Lyon, Univ Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 VILLEURBANNE, France
| | - Anne-Laure Biance
- Univ Lyon, Univ Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 VILLEURBANNE, France
| | - Laurent Joly
- Univ Lyon, Univ Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 VILLEURBANNE, France
- Institut Universitaire de France (IUF), 1 rue Descartes, 75005 Paris, France
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13
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Calandra P, Quaranta S, Apolo Miranda Figueira B, Caputo P, Porto M, Oliviero Rossi C. Mining wastes to improve bitumen performances: An example of circular economy. J Colloid Interface Sci 2022; 614:277-287. [DOI: 10.1016/j.jcis.2022.01.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
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14
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Cellulose nanocrystal (CNC)-stabilized Pickering emulsion for improved curcumin storage stability. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Farantos SC. Hamiltonian chemical kinetics for studying roaming in formaldehyde dissociation: Linear and nonlinear models. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Stavros C. Farantos
- Department of Chemistry University of Crete Heraklion Greece
- Institute of Electronic Structure and Laser, Foundation for Research and Technology‐Hellas Heraklion Greece
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16
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Thermal Input/Concentration Output Systems Processed by Chemical Reactions of Helicene Oligomers. REACTIONS 2022. [DOI: 10.3390/reactions3010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This article describes thermal input/concentration output systems processed by chemical reactions. Various sophisticated thermal inputs can be converted into concentration outputs through the double-helix formation of helicene oligomers exhibiting thermal hysteresis. The inputs include high or low temperature, cooling or heating state, slow or fast cooling state, heating state, and cooling history. The chemical basis for the properties of the chemical reactions includes the reversibility out of chemical equilibrium, sigmoidal relationship and kinetics, bistability involving metastable states, positive feedback by self-catalytic chemical reactions, competitive chemical reactions, and fine tunability for parallel processing. The interfacing of concentration outputs in other systems is considered, and biological cells are considered to have been utilizing such input/output systems processed by chemical reactions.
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17
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Mallick S, Kumar P. Effect of microsolvation on the mode specificity of the OH˙(H 2O) + HCl reaction. Phys Chem Chem Phys 2021; 23:25246-25255. [PMID: 34734608 DOI: 10.1039/d1cp01300a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present study investigates the mode specificity in the microsolvated OH˙(H2O) + HCl reaction using on-the-fly direct dynamics simulation. To the best of our knowledge, this is the first study which aims to gain insights into the effect of microsolvation on the mode selectivity. Our investigation reveals that, similar to the gas phase OH˙ + HCl reaction, the microsolvated reaction is also predominantly affected by the vibrational excitation of the HCl mode, whereas the OH vibrational mode behaves as a spectator. Interestingly, in contrast to the behavior of the bare reaction, the integral cross section at the ground state of the microsolvated reaction decreases with an increase in translational energy. However, for the vibrational excited states, the reactivity of the microsolvated reaction is found to be higher than that of the bare reaction within the selected range of translational energies.
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Affiliation(s)
- Subhasish Mallick
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, 302017, India.
| | - Pradeep Kumar
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, 302017, India.
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Pringle V, Merritt K, Vaclaw C, Whitaker N, Volkin DB, Ogunyankin MO, Pace S, Dhar P. Evaluating the combined impact of temperature and application of interfacial dilatational stresses on surface-mediated protein particle formation in monoclonal antibody formulations. J Pharm Sci 2021; 111:680-689. [PMID: 34742729 DOI: 10.1016/j.xphs.2021.10.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/31/2021] [Accepted: 10/31/2021] [Indexed: 10/19/2022]
Abstract
Formation of submicron and subvisible protein particles (0.1-100 μm) present a major obstacle during processing and storage of therapeutic proteins. While protein aggregation resulting in particle formation is well-understood in bulk solution, the mechanisms of aggregation due to interfacial stresses is less understood. Particularly, in this study, we focus on understanding the combined effect of temperature and application of interfacial dilatational stresses, on interface-induced protein particle formation, using two industrially relevant monoclonal antibodies (mAbs). The surface activity of Molecule C (MC) and Molecule B (MB) were measured at room temperature (RT) and 4°C in the absence and presence of interfacial dilatation stress using a Langmuir trough. These results were correlated with Micro-flow imaging (MFI) to characterize formation of subvisible protein particles at the interface and in the bulk solution. Our results show that the surface activity for both proteins is temperature dependent. However, the extent of the impact of temperature on the mechanical properties of the monomolecular protein films when subjected to dilatational stresses is protein dependent. Protein particle analysis provided evidence that protein particles formed in bulk solution originate at the interface and are dependent on both application of thermal stresses and interfacial dilatational stresses. In the absence of any interfacial stresses, more and larger protein particles were formed at the interface at RT than at 4°C. When mAb formulations are subjected to interfacial dilatational stresses, protein particle formation in bulk solution was found to be temperature dependent. Together our results validate that mAb solutions maintained at 4°C can lower the surface activity of proteins and reduce their tendency to form interface-induced protein particles both in the absence and presence of interfacial dilatational stresses.
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Affiliation(s)
- Valerie Pringle
- Department of Chemical and Petroleum Engineering, The University of Kansas, 1530 W 15(th) Street, Lawrence, Kansas 66045, USA
| | - Kimberly Merritt
- Bioengineering Program, School of Engineering, The University of Kansas, 1530 W 15(th) Street, Lawrence, Kansas 66045, USA
| | - Coleman Vaclaw
- Bioengineering Program, School of Engineering, The University of Kansas, 1530 W 15(th) Street, Lawrence, Kansas 66045, USA
| | - Neal Whitaker
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, USA
| | - David B Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, USA
| | - Maria Olu Ogunyankin
- Department of Drug Product Development, Bristol-Myers Squibb, Inc., One Squibb Drive, New Brunswick, New Jersey, 08901, USA
| | - Samantha Pace
- Department of Drug Product Development, Bristol-Myers Squibb, Inc., One Squibb Drive, New Brunswick, New Jersey, 08901, USA
| | - Prajnaparamita Dhar
- Department of Chemical and Petroleum Engineering, The University of Kansas, 1530 W 15(th) Street, Lawrence, Kansas 66045, USA; Bioengineering Program, School of Engineering, The University of Kansas, 1530 W 15(th) Street, Lawrence, Kansas 66045, USA.
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Sanches-Neto FO, Dias-Silva JR, Keng Queiroz Junior LH, Carvalho-Silva VH. " pySiRC": Machine Learning Combined with Molecular Fingerprints to Predict the Reaction Rate Constant of the Radical-Based Oxidation Processes of Aqueous Organic Contaminants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:12437-12448. [PMID: 34473479 DOI: 10.1021/acs.est.1c04326] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We developed a web application structured in a machine learning and molecular fingerprint algorithm for the automatic calculation of the reaction rate constant of the oxidative processes of organic pollutants by •OH and SO4•- radicals in the aqueous phase-the pySiRC platform. The model development followed the OECD principles: internal and external validation, applicability domain, and mechanistic interpretation. Three machine learning algorithms combined with molecular fingerprints were evaluated, and all the models resulted in high goodness-of-fit for the training set with R2 > 0.931 for the •OH radical and R2 > 0.916 for the SO4•- radical and good predictive capacity for the test set with Rext2 = Qext2 values in the range of 0.639-0.823 and 0.767-0.824 for the •OH and SO4•- radicals. The model was interpreted using the SHAP (SHapley Additive exPlanations) method: the results showed that the model developed made the prediction based on a reasonable understanding of how electron-withdrawing and -donating groups interfere with the reactivity of the •OH and SO4•- radicals. We hope that our models and web interface can stimulate and expand the application and interpretation of kinetic research on contaminants in water treatment units based on advanced oxidative technologies.
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Affiliation(s)
| | | | | | - Valter Henrique Carvalho-Silva
- Instituto de Química, Universidade de Brasília, Caixa Postal 4478, Brasília 70904-970, Brazil
- Modeling of Physical and Chemical Transformations Division, Theoretical and Structural Chemistry Group, Goiás State University, Anápolis 75132-903, Brazil
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Habibi Khorassani SM, Ghodsi F, Arezomandan H, Shahraki M, Omidikia N, Hashemzaei M, Heidari Majd M. In Vitro Apoptosis Evaluation and Kinetic Modeling onto Cyclodextrin-Based Host–Guest Magnetic Nanoparticles Containing Methotrexate and Tamoxifen. BIONANOSCIENCE 2021. [DOI: 10.1007/s12668-021-00877-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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Abstract
Hysteresis is ubiquitous in nature and biology. It appears in ferromagnetism, ferroelectrism, traffic congestion, river sedimentation, electronics, thermoresponses, cell division, differentiation, and apoptosis. Hysteresis phenomena are beyond equilibrium and involve nonlinear, bistable, time delay, and memory events, which are described in input/output profiles by different outputs during continuous decreases and increases in input intensity. Although hysteresis profiles in these phenomena appear similar, the mechanisms underlying them are complex, and their basic understanding is desired. In this Account, I describe thermal hysteresis caused by molecules dispersed in dilute solutions containing optically active helicene oligomers, which form homo- and heterodouble helices, the cooling and heating processes of which cause different structural changes with regard to their relative concentrations. Reversible self-catalytic reactions are involved in the formation of a double helix, which catalyzes its own formation. The reactions accelerate as they progress, in contrast to ordinary reactions, which exhibit monotonic retardation as they progress. Thermal hysteresis involving reversible self-catalytic reactions exhibits notable phenomena, when various cooling/heating inputs are applied during the reaction; these phenomena are shown herein with profiles of experimental results of Δε outputs obtained by circular dichroism (CD) plotted against temperature inputs. Thermal hysteresis is discussed in terms of (1) two states of the homodouble helix and a random coil involving one reversible self-catalytic reaction and (2) three states of enantiomeric heterodouble helices and a random coil involving two reversible self-catalytic reactions. Repeated cooling and heating processes provide the same stable thermal hysteresis loops, when the initial and final high-temperature states are under equilibrium, and nonloop and unstable thermal hysteresis appears when whole the systems are beyond equilibrium. Diverse thermal hysteresis loops are obtained under different temperature change conditions for different oligomers. The mechanism of thermal hysteresis involves different macroscopic mechanisms at a fixed temperature, when the relative concentrations of substrates/products and the reaction direction differ. Microscopic mechanisms, which are shown by energy diagrams, are fixed at a temperature irrespective of cooling or heating. A comparison of thermal hysteresis loops and equilibrium curves provides distances to the metastable states on the loops from equilibrium, and reactions occur from the metastable states toward equilibrium. Notable phenomena described herein include bistability, high sensitivity to small concentration changes, equilibrium crossing, three-state one-directional structural change caused by a single heating procedure, reaction shortcuts, the memory effect on thermal history, figure-eight thermal hysteresis, chemical oscillation, stable and unstable thermal hysteresis, double-helix formation only under heating, and chiral symmetry breaking.
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Affiliation(s)
- Masahiko Yamaguchi
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
- Department of Organic Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan
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22
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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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Loumprinis N, Maier E, Belli R, Petschelt A, Eliades G, Lohbauer U. Viscosity and stickiness of dental resin composites at elevated temperatures. Dent Mater 2021; 37:413-422. [DOI: 10.1016/j.dental.2020.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 01/01/2023]
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Uspenskaya EV, Pleteneva TV, Kazimova IV, Syroeshkin AV. Evaluation of Poorly Soluble Drugs' Dissolution Rate by Laser Scattering in Different Water Isotopologues. Molecules 2021; 26:601. [PMID: 33498881 PMCID: PMC7866158 DOI: 10.3390/molecules26030601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 11/24/2022] Open
Abstract
The most important task in the design of dosage forms is to modify the pharmaceutical substances structure in order to increase solubilization, targeted delivery, controlled rate of drug administration, and its bioavailability. Screening-laboratory (in vitro) or computer (in silico)-as a procedure for selecting a prototype for the design of a drug molecule, involves several years of research and significant costs. Among a large number of solvents and diluents (alcohol, ether, oils, glycerol, Vaseline) used in the pharmaceutical industry for the manufacture of drugs water finds the greatest application. This is because all biological reactions (reactions in living systems) take place in water and distribution of the fluid in the body and the substances found within is critical for the maintenance of intracellular and extracellular functions. Modern studies in the field of the stable isotopic compositions of natural water and its structure and properties make it possible to use isotopic transformations of the water to improve the pharmacokinetic properties of medicinal substances without previous structural modification. It is known that by replacing any of the atoms in the reacting substance molecule with its isotope, it is possible to record changes in the reactivity, which are expressed as a change in the reaction rate constant, i.e., in the manifestation of the kinetic isotope effect (KIE). The article presents the results of studies on the effect of the kinetic isotope effect of a solvent-water-on increasing the solubility and dissolution rate constants of poorly soluble drugs using laser diffraction spectroscopy. The results of the studies can be successfully implemented in pharmaceutical practice to overcome the poor solubility of medicinal substances of classes II and IV, according to the biopharmaceutical classification system (BCS), in water for pharmaceutical purposes by performing its preliminary and safe isotopic modification.
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Affiliation(s)
- Elena V. Uspenskaya
- Department of Pharmaceutical and Toxicological Chemistry, Medical Institute, RUDN University, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia; (T.V.P.); (I.V.K.); (A.V.S.)
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25
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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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26
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Preparation of Asphalt Concretes by Gyratory Compactor: A Case of Study with Rheological and Mechanical Aspects. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10238567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
For asphalt concrete preparation in laboratory mix-design operations, bitumens are usually mixed with micrometer-sized particles (filler), sand and centimeter-sized crushed stones in a gyratory press at a temperature of about 140–155 °C depending on the bitumen viscosity, until adequate homogenization and compaction take place (air voids optimum). This requires energy consumption. To minimize it, the process needs to be optimized and is usually made empirically. The aim of this manuscript is to gain a comprehension of the physico-chemical mechanisms involved in the process by exploring: (i) the rheological properties (viscosity, activation energy) of a neat and RTFOT-aged bitumen, in presence and in absence of a filler, (ii) the volumetric and resistance behavior under the compaction in a standard Gyratory Compactor (GC) of their blends with aggregates and (iii) the mechanical properties (Indirect Tensile Strength, compression and tensile deformation) of the final products. Correlations between activation energy and pre-exponential factor of the viscosity on a side, and between viscosity, workability and final mechanical properties on the other side allowed to provide a rational interpretation of the physico-chemical processes involved in the framework of the physics of complex fluids. The scientific clues will be of help in optimizing the workability in asphalt concretes productions with obvious repercussions in terms of energy savings, useful for economic and environmental issues.
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Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins. PLoS Comput Biol 2020; 16:e1008323. [PMID: 33196646 PMCID: PMC7704049 DOI: 10.1371/journal.pcbi.1008323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/30/2020] [Accepted: 10/17/2020] [Indexed: 11/19/2022] Open
Abstract
Atomistic simulations can provide valuable, experimentally-verifiable insights into protein folding mechanisms, but existing ab initio simulation methods are restricted to only the smallest proteins due to severe computational speed limits. The folding of larger proteins has been studied using native-centric potential functions, but such models omit the potentially crucial role of non-native interactions. Here, we present an algorithm, entitled DBFOLD, which can predict folding pathways for a wide range of proteins while accounting for the effects of non-native contacts. In addition, DBFOLD can predict the relative rates of different transitions within a protein’s folding pathway. To accomplish this, rather than directly simulating folding, our method combines equilibrium Monte-Carlo simulations, which deploy enhanced sampling, with unfolding simulations at high temperatures. We show that under certain conditions, trajectories from these two types of simulations can be jointly analyzed to compute unknown folding rates from detailed balance. This requires inferring free energies from the equilibrium simulations, and extrapolating transition rates from the unfolding simulations to lower, physiologically-reasonable temperatures at which the native state is marginally stable. As a proof of principle, we show that our method can accurately predict folding pathways and Monte-Carlo rates for the well-characterized Streptococcal protein G. We then show that our method significantly reduces the amount of computation time required to compute the folding pathways of large, misfolding-prone proteins that lie beyond the reach of existing direct simulation. Our algorithm, which is available online, can generate detailed atomistic models of protein folding mechanisms while shedding light on the role of non-native intermediates which may crucially affect organismal fitness and are frequently implicated in disease. Many proteins must adopt a specific structure in order to function. Computational simulations have been used to shed light on the mechanisms of protein folding, but unfortunately, realistic simulations can typically only be run for small proteins, due to severe limits in computational speed. Here, we present a method to solve this problem, whereby instead of directly simulating folding from an unfolded state, we run simulations that allow for computation of equilibrium folding free energies, alongside high temperature simulations to compute unfolding rates. From these quantities, folding rates can be computed using detailed balance. Importantly, our method can account for the effects of nonnative contacts which transiently form during folding and must be broken prior to adoption of the native state. Such contacts, which are often excluded from simple models of folding, may crucially affect real protein folding pathways and are often observed in folding intermediates implicated in disease.
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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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Role of stable hydrogen isotope variations in water for drug dissolution managing. CURRENT ISSUES IN PHARMACY AND MEDICAL SCIENCES 2020. [DOI: 10.2478/cipms-2020-0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Abstract
In the present work, we provide the results of defining by utilizing Laser diffraction spectroscopy, the kinetic isotopic effect of solvent and constant of dissolution rate κ, s−1 of аn active pharmaceutical ingredient (API) in water with a different content of a stable
2
1
H
_2^1{\rm{H}}
isotope on the basis of the laws of first-order kinetics. This approach is based on the analysis of the light scattering profile that occurs when the particles of the dispersion phase in the aquatic environment are covered with a collimated laser beam. For the first time, the dependence of the rate of dissolution is demonstrated not only on the properties of the pharmaceutical substance itself (water solubility mg/ml, octanol–water partition coefficient log P oct/water, topological polar surface area, Abraham solvation parameters, the lattice type), but also on the properties of the solvent, depending on the content of stable hydrogen isotope. We show that the rate constant of dissolution of a sparingly hydrophobic substance moxifloxacin hydrochloride (MF · HCl) in the Mili-Q water is: k=1.20±0.14∙10−2 s−1 at 293.15 K, while in deuterium depleted water, it is k=4.24±0.4∙10−2 s−1. Consequently, we have established the development of the normal kinetic isotopic effect (kH/kD >1) of the solvent. This effect can be explained both by the positions of the difference in the vibrational energy of zero levels in the initial and transition states, and from the position of water clusters giving volumetric effects of salvation, depending on the ratio D/H. The study of kinetic isotopic effects is a method that gives an indication of the mechanism of reactions and the nature of the transition state. The effect of increasing the dissolution of the API, as a function of the D/H ratio, we have discovered, can be used in the chemical and pharmaceutical industries in the study of API properties and in the drug production through improvement in soluble and pharmacokinetic characteristics.
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Reaction kinetics: scientific passion or applicative tool? RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2020. [DOI: 10.1007/s12210-020-00884-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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Román-Ramírez LA, McKeown P, Jones MD, Wood J. Kinetics of Methyl Lactate Formation from the Transesterification of Polylactic Acid Catalyzed by Zn(II) Complexes. ACS OMEGA 2020; 5:5556-5564. [PMID: 32201849 PMCID: PMC7081642 DOI: 10.1021/acsomega.0c00291] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 02/20/2020] [Indexed: 05/21/2023]
Abstract
The kinetics of the transesterification of polylactic acid (PLA) with methanol to form methyl lactate catalyzed by Zn(II) complexes was studied experimentally and numerically. The complexes, Zn(1 Et )2 and Zn(2 Pr )2, were synthesized from ethylenediamine and propylenediamine Schiff bases, respectively. The temperature range covered was 313.2-383.2 K. An increase in the reaction rate with the increase in temperature was observed for the Zn(1 Et )2-catalyzed reaction. The temperature relationship of the rate coefficients can be explained by a linear Arrhenius dependency with constant activation energy. The kinetics of Zn(2 Pr )2, on the other hand, is only explained by non-Arrhenius kinetics with convex variable activation energy, resulting in faster methyl lactate production rates at 323.2 and 343.2 K. The formation of a new catalyst species, likely through reaction with protic reagents, appears to promote the formation of intermediate complexes, resulting in the nonlinear behavior. Stirring speed induced the stability of the intermediate complexes. Contrary to Zn(1 Et )2, Zn(2 Pr )2 was susceptible to the presence of air/moisture in solution. The kinetic parameters were obtained by fitting the experimental data to the mass and energy balance of a consecutive second step reversible reaction taking place in a jacketed stirred batch reactor. For the case of Zn(2 Pr )2, the activation energy was fitted to a four-parameter equation. The kinetic parameters presented in this work are valuable for the design of processes involving the chemical recycling of PLA into green solvents.
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Affiliation(s)
- Luis A. Román-Ramírez
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Paul McKeown
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2
7AY, U.K.
| | - Matthew D. Jones
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2
7AY, U.K.
- E-mail: . Phone: +44 (0)1225 384908. Fax: +44 (0)1225
386231 (M.D.J.)
| | - Joseph Wood
- School
of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
- E-mail: . Phone: +44 (0) 121
414 5295. Fax: +44 (0) 121
414 5324 (J.W.)
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Polysaccharides-Reinforced Bitumens: Specificities and Universality of Rheological Behavior. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9245564] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The rheological properties of bitumens can be modified by the addition of specific chemical additives. Taking into account the molecular complex aggregation pattern, we hypothesized that macromolecules characterized by long, flexible, and hydrophilic chains can establish soft bridges connecting the different polar aggregates of asphaltenes, strengthening their overall hierarchical supra-structures, and consequently increasing rheological performance at higher temperatures. Here, we propose the use of low cost and high availability polysaccharides as chemical additives to improve the rheological characteristics of a bitumen and to strengthen its thermal resistance. Fourteen different low-cost and high-availability polysaccharides, (flours, gums, and extracts from vegetable products) have been tested. While alghae euchemae have proved to be the most effective additive, corn and 00 flours are the least effective. Attempts to explain their differences have been made considering their chemical interactions with the polar molecules of asphaltenes within the complex framework of their supramolecular hierarchical structures. Through Arrhenius analysis, a correlation between activation energy and preexponential factor has been found, which can be useful for practical purposes, together with an unexpected consistency with the behavior of simple liquids, despite the striking differences in structure. Furthermore, a qualitative model has been suggested. The added value of this work is the focus on polysaccharides constituting low-cost, high availability materials which are sometimes even found as waste in industrial processes, all factors which, together with the environmental issues connected with their use, can be considered for large-scale applications.
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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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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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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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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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