1
|
Matamoros-Recio A, Alonso-Rueda E, Borrego E, Caballero A, Pérez PJ, Martín-Santamaría S. Molecular Dynamic Simulations of Aqueous Micellar Organometallic Catalysis: Methane Functionalization as a Case Study. Angew Chem Int Ed Engl 2024; 63:e202314773. [PMID: 38055325 DOI: 10.1002/anie.202314773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/07/2023]
Abstract
Molecular Dynamics (MD) simulations constitute a powerful tool that provides a 3D perspective of the dynamical behavior of chemical systems. Herein the first MD study of the dynamics of a catalytic organometallic system, in micellar media, is presented. The challenging methane catalytic functionalization into ethyl propionate through a silver-catalyzed process has been targeted as the case study. The intimate nature of the micelles formed with the surfactants sodium dodecylsulfate (SDS) and potassium perfluorooctane sulfonate (PFOS) has been ascertained, as well as the relative distribution of the main actors in this transformation, namely methane, the diazo reagent and the silver catalyst, the latter in two different forms: the initial compound and a silver-carbene intermediate. Catalyst deactivation occurs with halide containing surfactants dodecyltrimethylammonium chloride (DTAC) and Triton X-100. Computed simulations allow explaining the experimental results, indicating that micelles behave differently regarding the degree of accumulation and the local distribution of the reactants and their effect in the molecular collisions leading to net reaction.
Collapse
Affiliation(s)
- Alejandra Matamoros-Recio
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
| | - Elia Alonso-Rueda
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
| | - Elena Borrego
- Laboratorio de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química, Universidad de Huelva, 21007, Huelva, Spain
| | - Ana Caballero
- Laboratorio de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química, Universidad de Huelva, 21007, Huelva, Spain
| | - Pedro J Pérez
- Laboratorio de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química, Universidad de Huelva, 21007, Huelva, Spain
| | - Sonsoles Martín-Santamaría
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
| |
Collapse
|
2
|
Lanz C, Krysiak Y, Liu X, Hohgardt M, Walla PJ, Polarz S. Non-Classical Self-Assembly of Anisotropic Magneto-Organosilica Janus Particles Possessing Surfactant Properties and the Field-Triggered Breakdown of Surface Activity and Amphiphilic Properties. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2304380. [PMID: 37649193 DOI: 10.1002/smll.202304380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/26/2023] [Indexed: 09/01/2023]
Abstract
Using colloidal particles as models to understand processes on a smaller scale is a precious approach. Compared to molecules, particles are less defined, but their architecture can be more complex and so is their long-range interaction. One can observe phenomena that are unknown or much more difficult to realize on the molecular level. The current paper focuses on particle-based surfactants and reports on numerous unexpected properties. The main goal is creating an amphiphilic system with responsiveness in surface activity and associated self-organization phenomena depending on applying an external trigger, preferably a physical field. A key step is the creation of a Janus-type particle characterized by two types of dipoles (electric and magnetic) which geometrically stand orthogonal to each other. In a field, one can control which contribution and direction dominate the interparticle interactions. As a result, one can drastically change the system's properties. The features of ferrite-core organosilica-shell particles with grain-like morphology modified by click chemistry are studied in response to spatially isotropic and anisotropic triggers. A highly unusual aggregation-dissolution-reaggregation sequence w as discovered. Using a magnetic field, one can even switch off the amphiphilic properties and use this for the field-triggered breaking of multiphase systems such as emulsions.
Collapse
Affiliation(s)
- Cornelia Lanz
- Institute of Inorganic Chemistry, Leibniz Universität Hannover, Callinstrasse 9, D-30167, Hannover, Germany
| | - Yaşar Krysiak
- Institute of Inorganic Chemistry, Leibniz Universität Hannover, Callinstrasse 9, D-30167, Hannover, Germany
| | - Xu Liu
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Manuel Hohgardt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Peter Jomo Walla
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Sebastian Polarz
- Institute of Inorganic Chemistry, Leibniz Universität Hannover, Callinstrasse 9, D-30167, Hannover, Germany
| |
Collapse
|
3
|
King M, Avaro JT, Peter C, Hauser K, Gebauer D. Solvent-mediated isotope effects strongly influence the early stages of calcium carbonate formation: exploring D 2O vs. H 2O in a combined computational and experimental approach. Faraday Discuss 2022; 235:36-55. [PMID: 35388817 DOI: 10.1039/d1fd00078k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In experimental studies, heavy water (D2O) is employed, e.g., so as to shift the spectroscopic solvent background, but any potential effects of this solvent exchange on reaction pathways are often neglected. While the important role of light water (H2O) during the early stages of calcium carbonate formation has been realized, studies into the actual effects of aqueous solvent exchanges are scarce. Here, we present a combined computational and experimental approach to start to fill this gap. We extended a suitable force field for molecular dynamics (MD) simulations. Experimentally, we utilised advanced titration assays and time-resolved attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. We find distinct effects in various mixtures of the two aqueous solvents, and in pure H2O or D2O. Disagreements between the computational results and experimental data regarding the stabilities of ion associates might be due to the unexplored role of HDO, or an unprobed complex phase behaviour of the solvent mixtures in the simulations. Altogether, however, our data suggest that calcium carbonate formation might proceed "more classically" in D2O. Also, there are indications for the formation of new structures in amorphous and crystalline calcium carbonates. There is huge potential towards further improving the understanding of mineralization mechanisms by studying solvent-mediated isotope effects, also beyond calcium carbonate. Last, it must be appreciated that H2O and D2O have significant, distinct effects on mineralization mechanisms, and that care has to be taken when experimental data from D2O studies are used, e.g., for the development of H2O-based computer models.
Collapse
Affiliation(s)
- Michael King
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Jonathan T Avaro
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany.,Empa, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Denis Gebauer
- Institute of Inorganic Chemistry, Leibniz University of Hannover, Callinstr. 9, 30167 Hannover, Germany.
| |
Collapse
|
4
|
Rai DK, Gillilan RE, Huang Q, Miller R, Ting E, Lazarev A, Tate MW, Gruner SM. High-pressure small-angle X-ray scattering cell for biological solutions and soft materials. J Appl Crystallogr 2021; 54:111-122. [PMID: 33841059 PMCID: PMC7941318 DOI: 10.1107/s1600576720014752] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/06/2020] [Indexed: 11/10/2022] Open
Abstract
Pressure is a fundamental thermodynamic parameter controlling the behavior of biological macromolecules. Pressure affects protein denaturation, kinetic parameters of enzymes, ligand binding, membrane permeability, ion trans-duction, expression of genetic information, viral infectivity, protein association and aggregation, and chemical processes. In many cases pressure alters the molecular shape. Small-angle X-ray scattering (SAXS) is a primary method to determine the shape and size of macromolecules. However, relatively few SAXS cells described in the literature are suitable for use at high pressures and with biological materials. Described here is a novel high-pressure SAXS sample cell that is suitable for general facility use by prioritization of ease of sample loading, temperature control, mechanical stability and X-ray background minimization. Cell operation at 14 keV is described, providing a q range of 0.01 < q < 0.7 Å-1, pressures of 0-400 MPa and an achievable temperature range of 0-80°C. The high-pressure SAXS cell has recently been commissioned on the ID7A beamline at the Cornell High Energy Synchrotron Source and is available to users on a peer-reviewed proposal basis.
Collapse
Affiliation(s)
- Durgesh K. Rai
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Richard E. Gillilan
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Robert Miller
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Department of Chemistry, Cornell University, Ithaca, NY 14853, USA
| | - Edmund Ting
- Pressure BioSciences Inc., South Easton, MA 02375, USA
| | | | - Mark W. Tate
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - Sol M. Gruner
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
5
|
Espinosa YR, Grigera RJ, Ferrara CG. Mechanisms associated with the effects of urea on the micellar structure of sodium dodecyl sulphate in aqueous solutions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 140:117-123. [PMID: 29758250 DOI: 10.1016/j.pbiomolbio.2018.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/10/2018] [Accepted: 05/08/2018] [Indexed: 10/14/2022]
Abstract
We used simulations by Molecular Dynamics to characterize the mechanism whereby the variations in the urea concentration modifies the micellar structure of sodium dodecyl sulfate monomers in water. From a self-assembled micellar system, we observed that increasing urea concentration leads to a decrease in aggregation number. Likewise, when increasing urea concentration, the micelles increase their nonpolar surface exposed to solvent, while the polar surface exposed to solvent decreases. This rearrangement process of SDS micelles in presence of urea is mainly due to the fact that the ions of Na+ that stabilize the micellar structure increase its interaction with urea. In this process, the SDS hydrophilic head and Na+ ions increases its solvation by urea, destabilizing micellar structure and exponing the hydrophobic core to the solvent.
Collapse
Affiliation(s)
- Yanis R Espinosa
- Institute of Physics of Liquids and Biological Systems (IFLYSIB), CONICET and National University of La Plata, Argentina
| | - Raúl J Grigera
- CEQUINOR, National University of La Plata and Conicet, Argentina
| | - C Gastón Ferrara
- Institute of Engineering and Agronomy, National University Arturo Jauretche, Av Calchaqui no. 6200, B1888BTE, Florencio Varela, Argentina; Institute of Physics of Liquids and Biological Systems (IFLYSIB), CONICET and National University of La Plata, Argentina.
| |
Collapse
|
6
|
Espinosa YR, Caffarena ER, Martínez YB, Grigera JR. Pressure effect on micellization of non-ionic surfactant Triton X-100. J Chem Phys 2018; 148:074901. [DOI: 10.1063/1.5003358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Yanis R. Espinosa
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), Calle 59 Nro 789, B1900BTE La Plata, Argentina
| | - Ernesto R. Caffarena
- Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz. Manguinhos, CEP 21040-360 Rio de Janeiro, Brazil
| | | | - J. Raúl Grigera
- CEQUINOR, Universidad de La Plata and CONICET, 47 y 115, B1900 La Plata, Argentina
| |
Collapse
|
7
|
Espinosa YR, Grigera JR, Caffarena ER. Essential dynamics of the cold denaturation: pressure and temperature effects in yeast frataxin. Proteins 2017; 85:125-136. [PMID: 27802581 DOI: 10.1002/prot.25205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/19/2016] [Accepted: 10/25/2016] [Indexed: 11/09/2022]
Abstract
The cold denaturation of globular proteins is a process that can be caused by increasing pressure or decreasing the temperature. Currently, the action mechanism of this process has not been clearly understood, raising an interesting debate on the matter. We have studied the process of cold denaturation using molecular dynamics simulations of the frataxin system Yfh1, which has a dynamic experimental characterization of unfolding at low and high temperatures. The frataxin model here studied allows a comparative analysis using experimental data. Furthermore, we monitored the cold denaturation process of frataxin and also investigated the effect under the high-pressure regime. For a better understanding of the dynamics and structural properties of the cold denaturation, we also analyzed the MD trajectories using essentials dynamic. The results indicate that changes in the structure of water by the effect of pressure and low temperatures destabilize the hydrophobic interaction modifying the solvation and the system volume leading to protein denaturation. Proteins 2016; 85:125-136. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Yanis R Espinosa
- CEQUINOR (CONICET-UNLP), 120 e/61 y 62, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - J Raúl Grigera
- CEQUINOR (CONICET-UNLP), 120 e/61 y 62, Universidad Nacional de La Plata, La Plata, 1900, Argentina
- Departmento de Biología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Ernesto R Caffarena
- Fundação Oswaldo Cruz., Rio de Janeiro, Programa de Computação Científica (PROCC), CEP, 21040-360, Rio de Janeiro, Brazil
| |
Collapse
|