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Pereyra RG, Sebastianelli P, Ávila EE. Homogeneous nucleation in supercooled liquid water. Determination of ice germ size and activation energy barrier in Molecular Dynamics simulations. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2068801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rodolfo G. Pereyra
- Fa.M.A.F., Universidad Nacional de Córdoba, Av. Medina Allende s/n, Ciudad Universitaria Córdoba, Argentina
- IFEG-CONICET, Av. Medina Allende s/n, Ciudad Universitaria Córdoba, Argentina
| | - Paolo Sebastianelli
- Fa.M.A.F., Universidad Nacional de Córdoba, Av. Medina Allende s/n, Ciudad Universitaria Córdoba, Argentina
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Eldo E. Ávila
- Fa.M.A.F., Universidad Nacional de Córdoba, Av. Medina Allende s/n, Ciudad Universitaria Córdoba, Argentina
- IFEG-CONICET, Av. Medina Allende s/n, Ciudad Universitaria Córdoba, Argentina
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Elbourne A, Besford QA, Meftahi N, Crawford RJ, Daeneke T, Greaves TL, McConville CF, Bryant G, Bryant SJ, Christofferson AJ. The Impact of Water on the Lateral Nanostructure of a Deep Eutectic Solvent–Solid Interface. Aust J Chem 2021. [DOI: 10.1071/ch21078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Deep eutectic solvents (DESs) are tuneable solvents with attractive properties for numerous applications. Their structure–property relationships are still under investigation, especially at the solid–liquid interface. Moreover, the influence of water on interfacial nanostructure must be understood for process optimization. Here, we employ a combination of atomic force microscopy and molecular dynamics simulations to determine the lateral and surface-normal nanostructure of the DES choline chloride:glycerol at the mica interface with different concentrations of water. For the neat DES system, the lateral nanostructure is driven by polar interactions. The surface adsorbed layer forms a distinct rhomboidal symmetry, with a repeat spacing of ~0.9 nm, comprising all DES species. The adsorbed nanostructure remains largely unchanged in 75 mol-% DES compared with pure DES, but at 50 mol-%, the structure is broken and there is a compromise between the native DES and pure water structure. By 25 mol-% DES, the water species dominates the adsorbed liquid layer, leaving very few DES species aggregates at the interface. In contrast, the near-surface surface-normal nanostructure, over a depth of ~3 nm from the surface, remains relatively unchanged down to 25 mol-% DES where the liquid arrangement changed. These results demonstrate not only the significant influence that water has on liquid nanostructure, but also show that there is an asymmetric effect whereby water disrupts the nanostructure to a greater degree closer to the surface. This work provides insight into the complex interactions between DES and water and may enhance their optimization for surface-based applications.
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Sandilya A, Natarajan U, Priya MH. Molecular View into the Cyclodextrin Cavity: Structure and Hydration. ACS OMEGA 2020; 5:25655-25667. [PMID: 33073091 PMCID: PMC7557249 DOI: 10.1021/acsomega.0c02760] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/14/2020] [Indexed: 05/21/2023]
Abstract
We find, through atomistic molecular dynamics simulation of native cyclodextrins (CDs) in water, that although the outer surface of a CD appears like a truncated cone, the inner cavity resembles a conical hourglass because of the inward protrusion of the glycosidic oxygens. Furthermore, the conformations of the constituent α-glucose molecules are found to differ significantly from a free monomeric α-glucose molecule. This is the first computational study that maps the conformational change to the preferential hydrogen bond donating capacity of one of the secondary hydroxyl groups of CD, in consensus with an NMR experiment. We have developed a simple and novel geometry-based technique to identify water molecules occupying the nonspherical CD cavity, and the computed water occupancies are in close agreement with the experimental and density functional theory studies. Our analysis reveals that a water molecule in CD cavity loses out about two hydrogen bonds and remains energetically frustrated but possesses higher orientational degree of freedom compared to bulk water. In the context of CD-drug complexation, these imply a nonclassical, that is, enthalpically driven hydrophobic association of a drug in CD cavity.
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Affiliation(s)
- Avilasha
A. Sandilya
- Department
of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Upendra Natarajan
- Department
of Chemical Engineering, Indian Institute
of Technology Madras, Chennai 600036, India
| | - M. Hamsa Priya
- Department
of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- . Phone: +91-44-22574132
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Horstmann R, Vogel M. Common behaviors associated with the glass transitions of water-like models. J Chem Phys 2017; 147:034505. [DOI: 10.1063/1.4993445] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- R. Horstmann
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - M. Vogel
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
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Khusnutdinoff RM. Structural and dynamic features of water and amorphous ice. COLLOID JOURNAL 2017. [DOI: 10.1134/s1061933x17010070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Schmitz R, Müller N, Ullmann S, Vogel M. A molecular dynamics simulations study on ethylene glycol-water mixtures in mesoporous silica. J Chem Phys 2016; 145:104703. [DOI: 10.1063/1.4962240] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Rebecca Schmitz
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Niels Müller
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Svenja Ullmann
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Michael Vogel
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
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Kar RK, Bhunia A. Will It Be Beneficial To Simulate the Antifreeze Proteins at Ice Freezing Condition or at Lower Temperature? J Phys Chem B 2015; 119:11485-95. [DOI: 10.1021/acs.jpcb.5b04919] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rajiv K. Kar
- Department
of Biophysics, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
| | - Anirban Bhunia
- Department
of Biophysics, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, India
- Biophysics
and Department of Chemistry, University of Michigan, 930 N. University
Avenue, Ann Arbor, Michigan 48109, United States
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Weiß RG, Heyden M, Dzubiella J. Curvature dependence of hydrophobic hydration dynamics. PHYSICAL REVIEW LETTERS 2015; 114:187802. [PMID: 26001018 DOI: 10.1103/physrevlett.114.187802] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Indexed: 06/04/2023]
Abstract
We investigate the solute curvature dependence of water dynamics in the vicinity of hydrophobic spherical solutes using molecular dynamics simulations. For both the lateral and perpendicular diffusivity, as well as for H-bond kinetics of water in the first hydration shell, we find a nonmonotonic solute-size dependence, exhibiting extrema close to the well-known structural crossover length scale for hydrophobic hydration. Additionally, we find an apparent anomalous diffusion for water moving parallel to the surface of small solutes, which, however, can be explained by topology effects. Our findings regarding the intimate connection between solute curvature and water dynamics has implications for our understanding of hydration dynamics at heterogeneous biomolecular surfaces.
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Affiliation(s)
- R Gregor Weiß
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstrasse 15, D-12489 Berlin, Germany
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, D-14109 Berlin, Germany
| | - Matthias Heyden
- Max-Planck-Insitut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Joachim Dzubiella
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstrasse 15, D-12489 Berlin, Germany
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, D-14109 Berlin, Germany
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Kreck CA, Mancera RL. Characterization of the Glass Transition of Water Predicted by Molecular Dynamics Simulations Using Nonpolarizable Intermolecular Potentials. J Phys Chem B 2014; 118:1867-80. [DOI: 10.1021/jp411716y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Cara A. Kreck
- School of Biomedical Sciences,
CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
| | - Ricardo L. Mancera
- School of Biomedical Sciences,
CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
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Picasso GC, Malaspina DC, Carignano MA, Szleifer I. Cooperative dynamic and diffusion behavior above and below the dynamical crossover of supercooled water. J Chem Phys 2013; 139:044509. [DOI: 10.1063/1.4816523] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Malaspina DC, di Lorenzo AJB, Pereyra RG, Szleifer I, Carignano MA. The water supercooled regime as described by four common water models. J Chem Phys 2013; 139:024506. [DOI: 10.1063/1.4812928] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Gladich I, Roeselová M. Comparison of selected polarizable and nonpolarizable water models in molecular dynamics simulations of ice Ih. Phys Chem Chem Phys 2012; 14:11371-85. [DOI: 10.1039/c2cp41497j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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