1
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Advincula XR, Backus EHG, Bonn M, Cox SJ, Diebold U, Fellows A, Finney AR, Goel G, Hedley J, Jiang Y, Jin D, Kapil V, Kavokine N, Klein J, Laage D, Mohandas N, Morgenstern K, Mukherjee T, Olvera de la Cruz M, Orlikowska-Rzeznik H, Perkin S, Piaggi PM, Rodellar CG, Ryan P, Sayer T, Seyffertitz M, Shepelenko M, Sosso GC, Thämer M, Vilangottunjalil A, Walker-Gibbons R, Wang Y, Willard AP, Zhang P. Electrified/charged aqueous interfaces: general discussion. Faraday Discuss 2024; 249:381-407. [PMID: 38170868 DOI: 10.1039/d3fd90065g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
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2
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Advincula XR, Blow KE, Bonn M, Bui AT, Cheng Y, Cox SJ, Della Pia F, Diebold U, Fumagalli L, Goel G, Hayton JA, Jiang Y, Kapil V, Kavokine N, Koga K, Laage D, Lahav M, Miao S, Michaelides A, Montero de Hijes P, Morgenstern K, Mukherjee T, O'Neill N, Pan D, Piaggi PM, Rempe SLB, Salvalaglio M, Salzmann CG, Sayer T, Shepelenko M, Sosso GC, Wang S, Webber B, Willard AP, Yao Y. Dynamics and nano-rheology of interfacial water: general discussion. Faraday Discuss 2024; 249:243-266. [PMID: 38174388 DOI: 10.1039/d3fd90064a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
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3
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Blow KE, Whale TF, Quigley D, Sosso GC. Understanding the impact of ammonium ion substitutions on heterogeneous ice nucleation. Faraday Discuss 2024; 249:114-132. [PMID: 37782066 DOI: 10.1039/d3fd00097d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Understanding the mechanisms underpinning heterogeneous ice nucleation in the presence of ionic inclusions is important for fields such as cryopreservation and for improved models of climate and weather prediction. Feldspar and ammonium are both present in significant quantities in the atmosphere, and experimental evidence has shown that feldspar can nucleate ice from ammonium-containing solutions at temperatures warmer than water alone. In recent work, Whale hypothesised that this increase in nucleation temperature is due to an increase in configurational entropy when an ammonium ion is included in the ice hydrogen bond network (T. F. Whale, J. Chem. Phys., 2022, 156, 144503). In this work, we investigate the impact of the inclusion of an ammonium ion on the hydrogen bond network by direct enumeration of the number of structures found using Rick's algorithm. We also determine the energy of these systems and thus compare the effects of enthalpy and entropy to test Whale's hypothesis. We find that the inclusion of an ammonium ion increases the total number of configurations under conditions consistent with a realistic surface charge. We also find that the enthalpic contribution is dominant in determining the location of the ammonium ion within the structure, although we note that this neglects other practicalities of ice nucleation.
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Affiliation(s)
- Katarina E Blow
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - Thomas F Whale
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - David Quigley
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
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4
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Advincula XR, Backus EHG, Bartels-Rausch T, Benaglia S, Ben Ari G, Blow KE, Bonn M, Bui AT, Cox SJ, Della Pia F, Diebold U, Finney AR, Franceschi G, Fumagalli L, Goel G, Hayton JA, Holdship C, Jiang Y, Jin D, Kapil V, Kavokine N, Koga K, Laage D, Lahav M, Miao S, Michaelides A, Mohandas N, Morgenstern K, Mukherjee T, Nagata Y, Olvera de la Cruz M, Pan D, Piaggi PM, Rempe SLB, Ryan P, Salzmann CG, Sayer T, Saykally RJ, Shepelenko M, Sosso GC, Whale TF, White JJ, Willard AP, Zhang P. Ice interfaces: general discussion. Faraday Discuss 2024; 249:133-161. [PMID: 38174608 DOI: 10.1039/d3fd90063k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
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5
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Barnard T, Sosso GC. Combining machine learning and molecular simulations to predict the stability of amorphous drugs. J Chem Phys 2023; 159:014503. [PMID: 37403861 DOI: 10.1063/5.0156222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/08/2023] [Indexed: 07/06/2023] Open
Abstract
Amorphous drugs represent an intriguing option to bypass the low solubility of many crystalline formulations of pharmaceuticals. The physical stability of the amorphous phase with respect to the crystal is crucial to bring amorphous formulations into the market-however, predicting the timescale involved with the onset of crystallization a priori is a formidably challenging task. Machine learning can help in this context by crafting models capable of predicting the physical stability of any given amorphous drug. In this work, we leverage the outcomes of molecular dynamics simulations to further the state-of-the-art. In particular, we devise, compute, and use "solid state" descriptors that capture the dynamical properties of the amorphous phases, thus complementing the picture offered by the "traditional," "one-molecule" descriptors used in most quantitative structure-activity relationship models. The results in terms of accuracy are very encouraging and demonstrate the added value of using molecular simulations as a tool to enrich the traditional machine learning paradigm for drug design and discovery.
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Affiliation(s)
- Trent Barnard
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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6
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Blow KE, Tribello GA, Sosso GC, Quigley D. Interplay of multiple clusters and initial interface positioning for forward flux sampling simulations of crystal nucleation. J Chem Phys 2023; 158:2895225. [PMID: 37290068 DOI: 10.1063/5.0152343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023] Open
Abstract
Forward flux sampling (FFS) is a path sampling technique widely used in computer simulations of crystal nucleation from the melt. In such studies, the order parameter underpinning the progress of the FFS algorithm is often the size of the largest crystalline nucleus. In this work, we investigate the effects of two computational aspects of FFS simulations, using the prototypical Lennard-Jones liquid as our computational test bed. First, we quantify the impact of the positioning of the liquid basin and first interface in the space of the order parameter. In particular, we demonstrate that these choices are key to ensuring the consistency of the FFS results. Second, we focus on the frequently encountered scenario where the population of crystalline nuclei is such that there are multiple clusters of size comparable to the largest one. We demonstrate the contribution of clusters other than the largest cluster to the initial flux; however, we also show that they can be safely ignored for the purposes of converging a full FFS calculation. We also investigate the impact of different clusters merging, a process that appears to be facilitated by substantial spatial correlations-at least at the supercooling considered here. Importantly, all of our results have been obtained as a function of system size, thus contributing to the ongoing discussion on the impact of finite size effects on simulations of crystal nucleation. Overall, this work either provides or justifies several practical guidelines for performing FFS simulations that can also be applied to more complex and/or computationally expensive models.
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Affiliation(s)
- Katarina E Blow
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Gareth A Tribello
- Centre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - David Quigley
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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7
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Abstract
Recent advances in machine learning methods have had a significant impact on protein structure prediction, but accurate generation and characterization of protein-folding pathways remains intractable. Here, we demonstrate how protein folding trajectories can be generated using a directed walk strategy operating in the space defined by the residue-level contact-map. This double-ended strategy views protein folding as a series of discrete transitions between connected minima on the potential energy surface. Subsequent reaction-path analysis for each transition enables thermodynamic and kinetic characterization of each protein-folding path. We validate the protein-folding paths generated by our discretized-walk strategy against direct molecular dynamics simulations for a series of model coarse-grained proteins constructed from hydrophobic and polar residues. This comparison demonstrates that ranking discretized paths based on the intermediate energy barriers provides a convenient route to identifying physically sensible folding ensembles. Importantly, by using directed walks in the protein contact-map space, we circumvent several of the traditional challenges associated with protein-folding studies, namely, long time scales required and the choice of a specific order parameter to drive the folding process. As such, our approach offers a useful new route for studying the protein-folding problem.
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Affiliation(s)
- Ziad Fakhoury
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Scott Habershon
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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8
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González-Jiménez M, Barnard T, Russell BA, Tukachev NV, Javornik U, Hayes LA, Farrell AJ, Guinane S, Senn HM, Smith AJ, Wilding M, Mali G, Nakano M, Miyazaki Y, McMillan P, Sosso GC, Wynne K. Author Correction: Understanding the emergence of the boson peak in molecular glasses. Nat Commun 2023; 14:884. [PMID: 36797270 PMCID: PMC9935499 DOI: 10.1038/s41467-023-36662-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Affiliation(s)
| | - Trent Barnard
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Warwick, UK
| | - Ben A. Russell
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Nikita V. Tukachev
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Uroš Javornik
- grid.454324.00000 0001 0661 0844Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Laure-Anne Hayes
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Andrew J. Farrell
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Sarah Guinane
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Hans M. Senn
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Andrew J. Smith
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Harwell, UK
| | - Martin Wilding
- grid.5600.30000 0001 0807 5670School of Chemistry, University of Cardiff, Cardiff, UK
| | - Gregor Mali
- grid.454324.00000 0001 0661 0844Department of Inorganic Chemistry and Technology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Motohiro Nakano
- grid.136593.b0000 0004 0373 3971Research Center for Thermal and Entropic Science, Osaka University, Osaka, Japan
| | - Yuji Miyazaki
- grid.136593.b0000 0004 0373 3971Research Center for Thermal and Entropic Science, Osaka University, Osaka, Japan
| | - Paul McMillan
- grid.83440.3b0000000121901201Department of Chemistry, University College London, London, UK
| | - Gabriele C. Sosso
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Warwick, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, UK.
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9
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González-Jiménez M, Barnard T, Russell BA, Tukachev NV, Javornik U, Hayes LA, Farrell AJ, Guinane S, Senn HM, Smith AJ, Wilding M, Mali G, Nakano M, Miyazaki Y, McMillan P, Sosso GC, Wynne K. Understanding the emergence of the boson peak in molecular glasses. Nat Commun 2023; 14:215. [PMID: 36639380 PMCID: PMC9839737 DOI: 10.1038/s41467-023-35878-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023] Open
Abstract
A common feature of glasses is the "boson peak", observed as an excess in the heat capacity over the crystal or as an additional peak in the terahertz vibrational spectrum. The microscopic origins of this peak are not well understood; the emergence of locally ordered structures has been put forward as a possible candidate. Here, we show that depolarised Raman scattering in liquids consisting of highly symmetric molecules can be used to isolate the boson peak, allowing its detailed observation from the liquid into the glass. The boson peak in the vibrational spectrum matches the excess heat capacity. As the boson peak intensifies on cooling, wide-angle x-ray scattering shows the simultaneous appearance of a pre-peak due to molecular clusters consisting of circa 20 molecules. Atomistic molecular dynamics simulations indicate that these are caused by over-coordinated molecules. These findings represent an essential step toward our understanding of the physics of vitrification.
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Affiliation(s)
| | - Trent Barnard
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Warwick, UK
| | - Ben A. Russell
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Nikita V. Tukachev
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Uroš Javornik
- grid.454324.00000 0001 0661 0844Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Laure-Anne Hayes
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Andrew J. Farrell
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Sarah Guinane
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Hans M. Senn
- grid.8756.c0000 0001 2193 314XSchool of Chemistry, University of Glasgow, Glasgow, UK
| | - Andrew J. Smith
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Harwell, UK
| | - Martin Wilding
- grid.5600.30000 0001 0807 5670School of Chemistry, University of Cardiff, Cardiff, UK
| | - Gregor Mali
- grid.454324.00000 0001 0661 0844Department of Inorganic Chemistry and Technology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Motohiro Nakano
- grid.136593.b0000 0004 0373 3971Research Center for Thermal and Entropic Science, Osaka University, Osaka, Japan
| | - Yuji Miyazaki
- grid.136593.b0000 0004 0373 3971Research Center for Thermal and Entropic Science, Osaka University, Osaka, Japan
| | - Paul McMillan
- grid.83440.3b0000000121901201Department of Chemistry, University College London, London, UK
| | - Gabriele C. Sosso
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Warwick, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, UK.
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10
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Warren MT, Galpin I, Bachtiger F, Gibson MI, Sosso GC. Correction to "Ice Recrystallization Inhibition by Amino Acids: The Curious Case of Alpha- and Beta-Alanine". J Phys Chem Lett 2022; 13:6994. [PMID: 35882052 PMCID: PMC9358702 DOI: 10.1021/acs.jpclett.2c02044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Indexed: 06/15/2023]
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11
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Warren MT, Galpin I, Hasan M, Hindmarsh SA, Padrnos JD, Edwards-Gayle C, Mathers RT, Adams DJ, Sosso GC, Gibson MI. Minimalistic ice recrystallisation inhibitors based on phenylalanine. Chem Commun (Camb) 2022; 58:7658-7661. [PMID: 35723608 PMCID: PMC9260883 DOI: 10.1039/d2cc02531k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Ice recrystallisation inhibition (IRI) is typically associated with ice binding proteins, but polymers and other mimetics are emerging. Here we identify phenylalanine as a minimalistic, yet potent, small-molecule IRI capable of inhibiting ice growth at just 1 mg mL-1. Facial amphiphilicity is shown to be a crucial structural feature, with para-substituents enhancing (hydrophobic) or decreasing (hydrophilic) IRI activity. Both amino and acid groups were found to be essential. Solution-phase self-assembly of Phenylalanine was not observed, but the role of self-assembly at the ice/water interface could not be ruled out as a contributing factor.
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Affiliation(s)
- Matthew T Warren
- Department of Chemistry, University of Warwick, CV5 6NP, UK. .,Warwick Medical School, University of Warwick, CV5 6NP, UK
| | - Iain Galpin
- Department of Chemistry, University of Warwick, CV5 6NP, UK.
| | - Muhammad Hasan
- Department of Chemistry, University of Warwick, CV5 6NP, UK. .,Warwick Medical School, University of Warwick, CV5 6NP, UK
| | | | - John D Padrnos
- Department of Chemistry, Penn State University, New Kensington, PA, 15068, USA
| | | | - Robert T Mathers
- Department of Chemistry, Penn State University, New Kensington, PA, 15068, USA
| | - Dave J Adams
- School of Chemistry, University of Glasgow, G12 8QQ, UK
| | | | - Matthew I Gibson
- Department of Chemistry, University of Warwick, CV5 6NP, UK. .,Warwick Medical School, University of Warwick, CV5 6NP, UK
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12
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Sosso GC, Sudera P, Backes AT, Whale TF, Fröhlich-Nowoisky J, Bonn M, Michaelides A, Backus EHG. The role of structural order in heterogeneous ice nucleation. Chem Sci 2022; 13:5014-5026. [PMID: 35655890 PMCID: PMC9067566 DOI: 10.1039/d1sc06338c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/07/2022] [Indexed: 01/10/2023] Open
Abstract
The freezing of water into ice is a key process that is still not fully understood. It generally requires an impurity of some description to initiate the heterogeneous nucleation of the ice crystals. The molecular structure, as well as the extent of structural order within the impurity in question, both play an essential role in determining its effectiveness. However, disentangling these two contributions is a challenge for both experiments and simulations. In this work, we have systematically investigated the ice-nucleating ability of the very same compound, cholesterol, from the crystalline (and thus ordered) form to disordered self-assembled monolayers. Leveraging a combination of experiments and simulations, we identify a “sweet spot” in terms of the surface coverage of the monolayers, whereby cholesterol maximises its ability to nucleate ice (which remains inferior to that of crystalline cholesterol) by enhancing the structural order of the interfacial water molecules. These findings have practical implications for the rational design of synthetic ice-nucleating agents. The freezing of water into ice is still not fully understood. Here, we investigate the role of structural disorder within the biologically relevant impurities that facilitate this fundamental phase transition.![]()
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Affiliation(s)
- Gabriele C Sosso
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Prerna Sudera
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
| | - Anna T Backes
- Max Planck Institute for Chemistry Hahn-Meitner-Weg 1 55128 Mainz Germany
| | - Thomas F Whale
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | | | - Mischa Bonn
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Ellen H G Backus
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany.,Department of Physical Chemistry, University of Vienna Währingerstrasse 42 1090 Wien Austria
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13
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Miles CM, Hsu PC, Dixon AM, Khalid S, Sosso GC. Lipid bilayers as potential ice nucleating agents. Phys Chem Chem Phys 2022; 24:6476-6491. [PMID: 35254357 DOI: 10.1039/d1cp05465a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cellular damage is a key issue in the context of cryopreservation. Much of this damage is believed to be caused by extracellular ice formation at temperatures well above the homogeneous freezing point of pure water. Hence the question: what initiates ice nucleation during cryopreservation? In this paper, we assess whether cellular membranes could be responsible for facilitating the ice nucleation process, and what characteristics would make them good or bad ice nucleating agents. By means of molecular dynamics simulations, we investigate a number of phospholipids and lipopolysaccharide bilayers at the interface with supercooled liquid water. While these systems certainly appear to act as ice nucleating agents, it is likely that other impurities might also play a role in initiating extracellular ice nucleation. Furthermore, we elucidate the factors which affect a bilayer's ability to act as an ice nucleating agent; these are complex, with specific reference to both chemical and structural factors. These findings represent a first attempt to pinpoint the origin of extracellular ice nucleation, with important implications for the cryopreservation process.
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Affiliation(s)
| | - Pin-Chia Hsu
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK.,Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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14
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Warren M, Galpin I, Bachtiger F, Gibson MI, Sosso GC. Ice Recrystallization Inhibition by Amino Acids: The Curious Case of Alpha- and Beta-Alanine. J Phys Chem Lett 2022; 13:2237-2244. [PMID: 35238571 PMCID: PMC9007522 DOI: 10.1021/acs.jpclett.1c04080] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Extremophiles produce macromolecules which inhibit ice recrystallization, but there is increasing interest in discovering and developing small molecules that can modulate ice growth. Realizing their potential requires an understanding of how these molecules function at the atomistic level. Here, we report the discovery that the amino acid l-α-alanine demonstrates ice recrystallization inhibition (IRI) activity, functioning at 100 mM (∼10 mg/mL). We combined experimental assays with molecular simulations to investigate this IRI agent, drawing comparison to β-alanine, an isomer of l-α-alanine which displays no IRI activity. We found that the difference in the IRI activity of these molecules does not originate from their ice binding affinity, but from their capacity to (not) become overgrown, dictated by the degree of structural (in)compatibility within the growing ice lattice. These findings shed new light on the microscopic mechanisms of small molecule cryoprotectants, particularly in terms of their molecular structure and overgrowth by ice.
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Affiliation(s)
- Matthew
T. Warren
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
- Warwick
Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Iain Galpin
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Fabienne Bachtiger
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Matthew I. Gibson
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
- Warwick
Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Gabriele C. Sosso
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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15
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Herlihy A, Geddes HS, Sosso GC, Bull CL, Ridley CJ, Goodwin AL, Senn MS, Funnell NP. Recovering local structure information from high-pressure total scattering experiments. J Appl Crystallogr 2021; 54:1546-1554. [PMID: 34963760 PMCID: PMC8662973 DOI: 10.1107/s1600576721009420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/09/2021] [Indexed: 11/10/2022] Open
Abstract
High pressure is a powerful thermodynamic tool for exploring the structure and the phase behaviour of the crystalline state, and is now widely used in conventional crystallographic measurements. High-pressure local structure measurements using neutron diffraction have, thus far, been limited by the presence of a strongly scattering, perdeuterated, pressure-transmitting medium (PTM), the signal from which contaminates the resulting pair distribution functions (PDFs). Here, a method is reported for subtracting the pairwise correlations of the commonly used 4:1 methanol:ethanol PTM from neutron PDFs obtained under hydro-static compression. The method applies a molecular-dynamics-informed empirical correction and a non-negative matrix factorization algorithm to recover the PDF of the pure sample. Proof of principle is demonstrated, producing corrected high-pressure PDFs of simple crystalline materials, Ni and MgO, and benchmarking these against simulated data from the average structure. Finally, the first local structure determination of α-quartz under hydro-static pressure is presented, extracting compression behaviour of the real-space structure.
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Affiliation(s)
- Anna Herlihy
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, United Kingdom
- ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | - Harry S. Geddes
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Gabriele C. Sosso
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - Craig L. Bull
- ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | - Christopher J. Ridley
- ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | - Andrew L. Goodwin
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Mark S. Senn
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - Nicholas P. Funnell
- ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
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16
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Abstract
The formation of crystals has proven to be one of the most challenging phase transformations to quantitatively model-let alone to actually understand-be it by means of the latest experimental technique or the full arsenal of enhanced sampling approaches at our disposal. One of the most crucial quantities involved with the crystallization process is the nucleation rate, a single elusive number that is supposed to quantify the average probability for a nucleus of critical size to occur within a certain volume and time span. A substantial amount of effort has been devoted to attempt a connection between the crystal nucleation rates computed by means of atomistic simulations and their experimentally measured counterparts. Sadly, this endeavor almost invariably fails to some extent, with the venerable classical nucleation theory typically blamed as the main culprit. Here, we review some of the recent advances in the field, focusing on a number of perhaps more subtle details that are sometimes overlooked when computing nucleation rates. We believe it is important for the community to be aware of the full impact of aspects, such as finite size effects and slow dynamics, that often introduce inconspicuous and yet non-negligible sources of uncertainty into our simulations. In fact, it is key to obtain robust and reproducible trends to be leveraged so as to shed new light on the kinetics of a process, that of crystal nucleation, which is involved into countless practical applications, from the formulation of pharmaceutical drugs to the manufacturing of nano-electronic devices.
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Affiliation(s)
- Katarina E Blow
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David Quigley
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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17
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Stevens CA, Bachtiger F, Kong XD, Abriata LA, Sosso GC, Gibson MI, Klok HA. A minimalistic cyclic ice-binding peptide from phage display. Nat Commun 2021; 12:2675. [PMID: 33976148 PMCID: PMC8113477 DOI: 10.1038/s41467-021-22883-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 04/01/2021] [Indexed: 11/09/2022] Open
Abstract
Developing molecules that emulate the properties of naturally occurring ice-binding proteins (IBPs) is a daunting challenge. Rather than relying on the (limited) existing structure-property relationships that have been established for IBPs, here we report the use of phage display for the identification of short peptide mimics of IBPs. To this end, an ice-affinity selection protocol is developed, which enables the selection of a cyclic ice-binding peptide containing just 14 amino acids. Mutational analysis identifies three residues, Asp8, Thr10 and Thr14, which are found to be essential for ice binding. Molecular dynamics simulations reveal that the side chain of Thr10 hydrophobically binds to ice revealing a potential mechanism. To demonstrate the biotechnological potential of this peptide, it is expressed as a fusion ('Ice-Tag') with mCherry and used to purify proteins directly from cell lysate.
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Affiliation(s)
- Corey A Stevens
- Laboratoire des Polymères, Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Fabienne Bachtiger
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
| | - Xu-Dong Kong
- Laboratory of Therapeutic Proteins and Peptides, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Luciano A Abriata
- Protein Production and Structure Core Facility and Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
| | - Matthew I Gibson
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK.,Warwick Medical School, University of Warwick, Coventry, UK
| | - Harm-Anton Klok
- Laboratoire des Polymères, Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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18
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Wang L, Chen J, Cox SJ, Liu L, Sosso GC, Li N, Gao P, Michaelides A, Wang E, Bai X. Microscopic Kinetics Pathway of Salt Crystallization in Graphene Nanocapillaries. Phys Rev Lett 2021; 126:136001. [PMID: 33861106 DOI: 10.1103/physrevlett.126.136001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/08/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
The fundamental understanding of crystallization, in terms of microscopic kinetic and thermodynamic details, remains a key challenge in the physical sciences. Here, by using in situ graphene liquid cell transmission electron microscopy, we reveal the atomistic mechanism of NaCl crystallization from solutions confined within graphene cells. We find that rock salt NaCl forms with a peculiar hexagonal morphology. We also see the emergence of a transitory graphitelike phase, which may act as an intermediate in a two-step pathway. With the aid of density functional theory calculations, we propose that these observations result from a delicate balance between the substrate-solute interaction and thermodynamics under confinement. Our results highlight the impact of confinement on both the kinetics and thermodynamics of crystallization, offering new insights into heterogeneous crystallization theory and a potential avenue for materials design.
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Affiliation(s)
- Lifen Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Laboratory for Materials Science, Dongguan 523000, China
| | - Ji Chen
- School of Physics and the Collaborative Innovation Center of Quantum Matters, Peking University, Beijing 100871, China
| | - Stephen J Cox
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Lei Liu
- School of Materials Science and Engineering, Peking University, Beijing 100871, China
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Ning Li
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, China
- Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, China
| | - Peng Gao
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, China
- Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, China
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Physics and Astronomy, and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, United Kingdom
| | - Enge Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Laboratory for Materials Science, Dongguan 523000, China
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, China
- School of Physics, Liaoning University, Shenyang 110036, China
- Interdisciplinary Institute of Light-Element Quantum Materials and Research Center for Light-Element Advanced Materials, Peking University, Beijing 100871, China
| | - Xuedong Bai
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Laboratory for Materials Science, Dongguan 523000, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
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19
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Lawrence J, Sosso GC, Đorđević L, Pinfold H, Bonifazi D, Costantini G. Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding. Nat Commun 2020; 11:2103. [PMID: 32355173 PMCID: PMC7192931 DOI: 10.1038/s41467-020-15898-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/24/2020] [Indexed: 12/02/2022] Open
Abstract
Scanning tunnelling microscopy (STM) is commonly used to identify on-surface molecular self-assembled structures. However, its limited ability to reveal only the overall shape of molecules and their relative positions is not always enough to fully solve a supramolecular structure. Here, we analyse the assembly of a brominated polycyclic aromatic molecule on Au(111) and demonstrate that standard STM measurements cannot conclusively establish the nature of the intermolecular interactions. By performing high-resolution STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, determining that halogen bonding governs the assemblies. This is supported by density functional theory calculations that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron density topology analysis that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramolecular structures, and we predict its increasing use in molecular nanoscience at surfaces.
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Affiliation(s)
- James Lawrence
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
- Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
| | - Luka Đorđević
- School of Chemistry, Cardiff University, Park Place Main Building, Cardiff, CF10 3AT, UK
| | - Harry Pinfold
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Davide Bonifazi
- School of Chemistry, Cardiff University, Park Place Main Building, Cardiff, CF10 3AT, UK.
| | - Giovanni Costantini
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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20
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Abstract
The structural evolution of supercooled liquid water as we approach the glass transition temperature continues to be an active area of research. Here, we use molecular dynamics simulations of TIP4P/ice water to study the changes in the connected regions of empty space within the liquid, which we investigate using the Voronoi-voids network. We observe two important features: supercooling enhances the fraction of nonspherical voids and different sizes of voids tend to cluster forming a percolating network. By examining order parameters such as the local structure index (LSI), tetrahedrality and topological defects, we show that water molecules near large void clusters tend to be slightly more tetrahedral than those near small voids, with a lower population of under- and overcoordinated defects. We show further that the distribution of closed rings of water molecules around small and large void clusters maintain a balance between 6 and 7 membered rings. Our results highlight the changes of the dual voids and water network as a structural hallmark of supercooling and provide insights into the molecular origins of cooperative effects underlying density fluctuations on the subnanometer and nanometer length scale. In addition, the percolation of the voids and the hydrogen bond network around the voids may serve as useful order parameters to investigate density fluctuations in supercooled water.
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Affiliation(s)
- Narjes Ansari
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Berk Onat
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom.,School of Engineering, University of Warwick, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Ali Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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21
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Ishibe T, Congdon T, Stubbs C, Hasan M, Sosso GC, Gibson MI. Enhancement of Macromolecular Ice Recrystallization Inhibition Activity by Exploiting Depletion Forces. ACS Macro Lett 2019; 8:1063-1067. [PMID: 31475076 PMCID: PMC6711362 DOI: 10.1021/acsmacrolett.9b00386] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/07/2019] [Indexed: 11/29/2022]
Abstract
![]()
Antifreeze
(glyco) proteins (AF(G)Ps) are potent inhibitors of
ice recrystallization and may have biotechnological applications.
The most potent AF(G)Ps function at concentrations a thousand times
lower than synthetic mimics such as poly(vinyl alcohol), PVA. Here,
we demonstrate that PVA’s ice recrystallization activity can
be rescued at concentrations where it does not normally function,
by the addition of noninteracting polymeric depletants, due to PVA
forming colloids in the concentrated saline environment present between
ice crystals. These depletants shift the equilibrium toward ice binding
and, hence, enable PVA to inhibit ice growth at lower concentrations.
Using theory and experiments, we show this effect requires polymeric
depletants, not small molecules, to enhance activity. These results
increase our understanding of how to design new ice growth inhibitors,
but also offer opportunities to enhance activity by exploiting depletion
forces, without re-engineering ice-binding materials. It also shows
that when screening for IRI activity that polymer contaminants in
buffers may give rise to false positive results.
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22
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Abstract
We present insights into the nature of structural heterogeneities in liquid water by characterizing the empty space within the hydrogen bond network. Using molecular dynamics simulations, we show that density fluctuations create regions of empty space characterized by a diverse morphology - from spherical to fractal-like voids. These voids allow for the identification of low and high density patches of the liquid, encompassing short (0.3-0.5 nm) as well as long (1-2 nm) length-scales. In addition, we show that the formation of these patches is coupled to collective fluctuations involving the topology of hydrogen-bonded rings of water molecules. In particular, water molecules in the high density patches tend to be slightly more tetrahedral - which is consistent with the predictions of the hydrophobic effect.
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Affiliation(s)
- N Ansari
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - R Dandekar
- The Institute of Mathematical Sciences-HBNI, 4th Cross Street, CIT Campus, Tharamani, Chennai, India
| | - S Caravati
- Department of Chemistry, University of Zurich, Winterhurerstrasse 190, Zurich CH-8057, Switzerland
| | - G C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - A Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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23
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Sosso GC, Whale TF, Holden MA, Pedevilla P, Murray BJ, Michaelides A. Unravelling the origins of ice nucleation on organic crystals. Chem Sci 2018; 9:8077-8088. [PMID: 30542556 PMCID: PMC6238755 DOI: 10.1039/c8sc02753f] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/27/2018] [Indexed: 12/01/2022] Open
Abstract
Organic molecules such as steroids or amino acids form crystals that can facilitate the formation of ice - arguably the most important phase transition on earth. However, the origin of the ice nucleating ability of organic crystals is still largely unknown. Here, we combine experiments and simulations to unravel the microscopic details of ice formation on cholesterol, a prototypical organic crystal widely used in cryopreservation. We find that cholesterol - which is also a substantial component of cell membranes - is an ice nucleating agent more potent than many inorganic substrates, including the mineral feldspar (one of the most active ice nucleating materials in the atmosphere). Scanning electron microscopy measurements reveal a variety of morphological features on the surfaces of cholesterol crystals: this suggests that the topography of the surface is key to the broad range of ice nucleating activity observed (from -4 to -20 °C). In addition, we show via molecular simulations that cholesterol crystals aid the formation of ice nuclei in a unconventional fashion. Rather than providing a template for a flat ice-like contact layer (as found in the case of many inorganic substrates), the flexibility of the cholesterol surface and its low density of hydrophilic functional groups leads to the formation of molecular cages involving both water molecules and terminal hydroxyl groups of the cholesterol surface. These cages are made of 6- and, surprisingly, 5-membered hydrogen bonded rings of water and hydroxyl groups that favour the nucleation of hexagonal as well as cubic ice (a rare occurrence). We argue that the phenomenal ice nucleating activity of steroids such as cholesterol (and potentially of many other organic crystals) is due to (i) the ability of flexible hydrophilic surfaces to form unconventional ice-templating structures and (ii) the different nucleation sites offered by the diverse topography of the crystalline surfaces. These findings clarify how exactly organic crystals promote the formation of ice, thus paving the way toward deeper understanding of ice formation in soft and biological matter - with obvious reverberations on atmospheric science and cryobiology.
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Affiliation(s)
- Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , UK .
| | - Thomas F Whale
- School of Earth and Environment , University of Leeds , Leeds LS2 9JT , UK
| | - Mark A Holden
- School of Earth and Environment , University of Leeds , Leeds LS2 9JT , UK
- Chemistry , University of Leeds , Leeds LS2 9JT , UK
| | - Philipp Pedevilla
- Thomas Young Centre , London Centre for Nanotechnology and Department of Physics and Astronomy , University College London , London WC1E 6BT , UK
| | - Benjamin J Murray
- School of Earth and Environment , University of Leeds , Leeds LS2 9JT , UK
| | - Angelos Michaelides
- Thomas Young Centre , London Centre for Nanotechnology and Department of Physics and Astronomy , University College London , London WC1E 6BT , UK
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24
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Pedevilla P, Fitzner M, Sosso GC, Michaelides A. Heterogeneous seeded molecular dynamics as a tool to probe the ice nucleating ability of crystalline surfaces. J Chem Phys 2018; 149:072327. [PMID: 30134662 DOI: 10.1063/1.5029336] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ice nucleation plays a significant role in a large number of natural and technological processes, but it is challenging to investigate experimentally because of the small time scales (ns) and short length scales (nm) involved. On the other hand, conventional molecular simulations struggle to cope with the relatively long time scale required for critical ice nuclei to form. One way to tackle this issue is to take advantage of free energy or path sampling techniques. Unfortunately, these are computationally costly. Seeded molecular dynamics is a much less demanding alternative that has been successfully applied already to study the homogeneous freezing of water. However, in the case of heterogeneous ice nucleation, nature's favourite route to form ice, an array of suitable interfaces between the ice seeds and the substrate of interest has to be built, and this is no trivial task. In this paper, we present a Heterogeneous SEEDing (HSEED) approach which harnesses a random structure search framework to tackle the ice-substrate challenge, thus enabling seeded molecular dynamics simulations of heterogeneous ice nucleation on crystalline surfaces. We validate the HSEED framework by investigating the nucleation of ice on (i) model crystalline surfaces, using the coarse-grained mW model, and (ii) cholesterol crystals, employing the fully atomistic TIP4P/ice water model. We show that the HSEED technique yields results in excellent agreement with both metadynamics and forward flux sampling simulations. Because of its computational efficiency, the HSEED method allows one to rapidly assess the ice nucleation ability of whole libraries of crystalline substrates-a long-awaited computational development in, e.g., atmospheric science.
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Affiliation(s)
- Philipp Pedevilla
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Martin Fitzner
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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25
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Sosso GC, Tribello GA, Zen A, Pedevilla P, Michaelides A. Ice formation on kaolinite: Insights from molecular dynamics simulations. J Chem Phys 2018; 145:211927. [PMID: 28799377 DOI: 10.1063/1.4968796] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral.
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Affiliation(s)
- Gabriele C Sosso
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Gareth A Tribello
- Atomistic Simulation Centre, Department of Physics and Astronomy, Queen's University Belfast, University Road, Belfast BT7 1NN, United Kingdom
| | - Andrea Zen
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Philipp Pedevilla
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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26
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Sosso GC, Deringer VL, Elliott SR, Csányi G. Understanding the thermal properties of amorphous solids using machine-learning-based interatomic potentials. Molecular Simulation 2018. [DOI: 10.1080/08927022.2018.1447107] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gabriele C. Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick , Coventry, UK
| | - Volker L. Deringer
- Department of Engineering, University of Cambridge , Cambridge, UK
- Department of Chemistry, University of Cambridge , Cambridge, UK
| | | | - Gábor Csányi
- Department of Engineering, University of Cambridge , Cambridge, UK
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27
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Fitzner M, Sosso GC, Pietrucci F, Pipolo S, Michaelides A. Pre-critical fluctuations and what they disclose about heterogeneous crystal nucleation. Nat Commun 2017; 8:2257. [PMID: 29273707 PMCID: PMC5741629 DOI: 10.1038/s41467-017-02300-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/17/2017] [Indexed: 11/29/2022] Open
Abstract
Heterogeneous crystal nucleation is ubiquitous in nature and at the heart of many industrial applications. At the molecular scale, however, major gaps in understanding this phenomenon persist. Here we investigate through molecular dynamics simulations how the formation of precritical crystalline clusters is connected to the kinetics of nucleation. Considering heterogeneous water freezing as a prototypical scenario of practical relevance, we find that precritical fluctuations connote which crystalline polymorph will form. The emergence of metastable phases can thus be promoted by templating crystal faces characteristic of specific polymorphs. As a consequence, heterogeneous classical nucleation theory cannot describe our simulation results, because the different substrates lead to the formation of different ice polytypes. We discuss how the issue of polymorphism needs to be incorporated into analysis and comparison of heterogeneous and homogeneous nucleation. Our results will help to interpret and analyze the growing number of experiments and simulations dealing with crystal polymorph selection.
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Affiliation(s)
- Martin Fitzner
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street London, London, WC1E 6BT, UK
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Fabio Pietrucci
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS UMR 7590, IRD UMR 206, MNHN, Sorbonne Universités-Université Pierre et Marie Curie Paris 6, F-75005, Paris, France
| | - Silvio Pipolo
- Université de Lille, CNRS, Centrale Lille, ENSCL, Université d' Artois UMR 8181- UCCS Unité de Catalyse et Chimie du Solide, F-59000, Lille, France
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street London, London, WC1E 6BT, UK.
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28
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Fitzner M, Joly L, Ma M, Sosso GC, Zen A, Michaelides A. Communication: Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces. J Chem Phys 2017; 147:121102. [DOI: 10.1063/1.4997698] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Martin Fitzner
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Laurent Joly
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne,
France
| | - Ming Ma
- Department of Mechanical Engineering, State Key Laboratory of Tribology and Center for Nano and Micro Mechanics, Tsinghua University, Beijing 100084, China
| | - Gabriele C. Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL,
United Kingdom
| | - Andrea Zen
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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29
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Shephard JJ, Ling S, Sosso GC, Michaelides A, Slater B, Salzmann CG. Is High-Density Amorphous Ice Simply a "Derailed" State along the Ice I to Ice IV Pathway? J Phys Chem Lett 2017; 8:1645-1650. [PMID: 28323429 DOI: 10.1021/acs.jpclett.7b00492] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The structural nature of high-density amorphous ice (HDA), which forms through low-temperature pressure-induced amorphization of the "ordinary" ice I, is heavily debated. Clarifying this question is important for understanding not only the complex condensed states of H2O but also in the wider context of pressure-induced amorphization processes, which are encountered across the entire materials spectrum. We first show that ammonium fluoride (NH4F), which has a similar hydrogen-bonded network to ice I, also undergoes a pressure collapse upon compression at 77 K. However, the product material is not amorphous but NH4F II, a high-pressure phase isostructural with ice IV. This collapse can be rationalized in terms of a highly effective mechanism. In the case of ice I, the orientational disorder of the water molecules leads to a deviation from this mechanism, and we therefore classify HDA as a "derailed" state along the ice I to ice IV pathway.
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Affiliation(s)
- Jacob J Shephard
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Sanliang Ling
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Gabriele C Sosso
- Thomas Young Centre, Department of Physics and Astronomy, and London Centre for Nanotechnology, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre, Department of Physics and Astronomy, and London Centre for Nanotechnology, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Ben Slater
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Christoph G Salzmann
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
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Tribello GA, Giberti F, Sosso GC, Salvalaglio M, Parrinello M. Analyzing and Driving Cluster Formation in Atomistic Simulations. J Chem Theory Comput 2017; 13:1317-1327. [DOI: 10.1021/acs.jctc.6b01073] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gareth A. Tribello
- Atomistic
Simulation Centre, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Federico Giberti
- Computational
Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland
| | - Gabriele C. Sosso
- Thomas
Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Matteo Salvalaglio
- Department
of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom
| | - Michele Parrinello
- Computational
Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland
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Sosso GC, Li T, Donadio D, Tribello G, Michaelides A. Microscopic Mechanism and Kinetics of Ice Formation at Complex Interfaces: Zooming in on Kaolinite. J Phys Chem Lett 2016; 7:2350-5. [PMID: 27269363 PMCID: PMC4939469 DOI: 10.1021/acs.jpclett.6b01013] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/06/2016] [Indexed: 05/20/2023]
Abstract
Most ice in nature forms because of impurities which boost the exceedingly low nucleation rate of pure supercooled water. However, the microscopic details of ice nucleation on these substances remain largely unknown. Here, we have unraveled the molecular mechanism and the kinetics of ice formation on kaolinite, a clay mineral playing a key role in climate science. We find that the formation of ice at strong supercooling in the presence of this clay is about 20 orders of magnitude faster than homogeneous freezing. The critical nucleus is substantially smaller than that found for homogeneous nucleation and, in contrast to the predictions of classical nucleation theory (CNT), it has a strong two-dimensional character. Nonetheless, we show that CNT describes correctly the formation of ice at this complex interface. Kaolinite also promotes the exclusive nucleation of hexagonal ice, as opposed to homogeneous freezing where a mixture of cubic and hexagonal polytypes is observed.
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Affiliation(s)
- Gabriele C. Sosso
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E
6BT, United Kingdom
- E-mail:
| | - Tianshu Li
- Department
of Civil and Environmental Engineering, George Washington University, Washington, D.C. 20052, United States
| | - Davide Donadio
- Department
of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Gareth
A. Tribello
- Atomistic Simulation Centre, Department of Physics and Astronomy, Queen’s
University Belfast, University
Road Belfast BT7 1NN, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E
6BT, United Kingdom
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Fitzner M, Sosso GC, Cox SJ, Michaelides A. The Many Faces of Heterogeneous Ice Nucleation: Interplay Between Surface Morphology and Hydrophobicity. J Am Chem Soc 2015; 137:13658-69. [PMID: 26434775 DOI: 10.1021/jacs.5b08748] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
What makes a material a good ice nucleating agent? Despite the importance of heterogeneous ice nucleation to a variety of fields, from cloud science to microbiology, major gaps in our understanding of this ubiquitous process still prevent us from answering this question. In this work, we have examined the ability of generic crystalline substrates to promote ice nucleation as a function of the hydrophobicity and the morphology of the surface. Nucleation rates have been obtained by brute-force molecular dynamics simulations of coarse-grained water on top of different surfaces of a model fcc crystal, varying the water-surface interaction and the surface lattice parameter. It turns out that the lattice mismatch of the surface with respect to ice, customarily regarded as the most important requirement for a good ice nucleating agent, is at most desirable but not a requirement. On the other hand, the balance between the morphology of the surface and its hydrophobicity can significantly alter the ice nucleation rate and can also lead to the formation of up to three different faces of ice on the same substrate. We have pinpointed three circumstances where heterogeneous ice nucleation can be promoted by the crystalline surface: (i) the formation of a water overlayer that acts as an in-plane template; (ii) the emergence of a contact layer buckled in an ice-like manner; and (iii) nucleation on compact surfaces with very high interaction strength. We hope that this extensive systematic study will foster future experimental work aimed at testing the physiochemical understanding presented herein.
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Affiliation(s)
- Martin Fitzner
- London Centre for Nanotechnology, Department of Chemistry and Thomas Young Centre, University College London , 17-19 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Gabriele C Sosso
- London Centre for Nanotechnology, Department of Chemistry and Thomas Young Centre, University College London , 17-19 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Stephen J Cox
- London Centre for Nanotechnology, Department of Chemistry and Thomas Young Centre, University College London , 17-19 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Angelos Michaelides
- London Centre for Nanotechnology, Department of Chemistry and Thomas Young Centre, University College London , 17-19 Gordon Street, London WC1H 0AJ, United Kingdom
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Campi D, Baldi E, Graceffa G, Sosso GC, Bernasconi M. Electron-phonon interaction and thermal boundary resistance at the interfaces of Ge2Sb2Te5 with metals and dielectrics. J Phys Condens Matter 2015; 27:175009. [PMID: 25873568 DOI: 10.1088/0953-8984/27/17/175009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The Ge2Sb2Te5 compound is of interest for applications in phase change non-volatile memories. First-principles calculations of phonon dispersion relations and electron-phonon coupling constant provide an estimate of the electron-phonon contribution to the thermal boundary resistance at the interfaces of Ge2Sb2Te5 with dielectrics (silica) and metal electrodes (Al and TiN). The diffuse mismatch model including full phononic dispersion has been used to compute the phononic contribution to the thermal boundary resistance. The calculated value of the electron-phonon contribution to the TBR at 300 K of about 14 m(2)K GW(-1) would dominate the TBR at the interfaces of hexagonal Ge2Sb2Te5 with the surrounding dielectrics and metals considered here once interdiffusion at the boundaries could be minimized.
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Affiliation(s)
- D Campi
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, Via R. Cozzi 55, I-20125 Milano, Italy
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Sosso GC, Colombo J, Behler J, Del Gado E, Bernasconi M. Dynamical Heterogeneity in the Supercooled Liquid State of the Phase Change Material GeTe. J Phys Chem B 2014; 118:13621-8. [DOI: 10.1021/jp507361f] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriele C. Sosso
- Department
of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg
1-5 CH-8093 Zurich, Switzerland
- Faculty
of Informatics, Università della Svizzera Italiana, Via
G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Jader Colombo
- Department
of Civil, Environmental and Geomatic Engineering, ETH Zurich, CH-8903 Zurich, Switzerland
| | - Jörg Behler
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität Bochum, Universitätsstrasse
150, D-44780 Bochum, Germany, and
| | - Emanuela Del Gado
- Department
of Civil, Environmental and Geomatic Engineering, ETH Zurich, CH-8903 Zurich, Switzerland
| | - Marco Bernasconi
- Dipartimento
di Scienza dei Materiali, Università di Milano-Bicocca, Via
R. Cozzi 53, I-20125 Milano, Italy
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Sosso GC, Miceli G, Caravati S, Giberti F, Behler J, Bernasconi M. Fast Crystallization of the Phase Change Compound GeTe by Large-Scale Molecular Dynamics Simulations. J Phys Chem Lett 2013; 4:4241-4246. [PMID: 26296172 DOI: 10.1021/jz402268v] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Phase change materials are of great interest as active layers in rewritable optical disks and novel electronic nonvolatile memories. These applications rest on a fast and reversible transformation between the amorphous and crystalline phases upon heating, taking place on the nanosecond time scale. In this work, we investigate the microscopic origin of the fast crystallization process by means of large-scale molecular dynamics simulations of the phase change compound GeTe. To this end, we use an interatomic potential generated from a Neural Network fitting of a large database of ab initio energies. We demonstrate that in the temperature range of the programming protocols of the electronic memories (500-700 K), nucleation of the crystal in the supercooled liquid is not rate-limiting. In this temperature range, the growth of supercritical nuclei is very fast because of a large atomic mobility, which is, in turn, the consequence of the high fragility of the supercooled liquid and the associated breakdown of the Stokes-Einstein relation between viscosity and diffusivity.
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Affiliation(s)
- Gabriele C Sosso
- †Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, Via R. Cozzi 53, I-20125 Milano, Italy
- ‡Department of Chemistry and Applied Biosciences and Facoltà di Informatica, ETH Zurich and Università della Svizzera Italiana, Istituto di Scienze Computazionali, Via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Giacomo Miceli
- ¶Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fèdèrale de Lausanne (EPFL), PH H2 482 Station 3, CH-1015 Lausanne, Switzerland
| | - Sebastiano Caravati
- †Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, Via R. Cozzi 53, I-20125 Milano, Italy
| | - Federico Giberti
- ‡Department of Chemistry and Applied Biosciences and Facoltà di Informatica, ETH Zurich and Università della Svizzera Italiana, Istituto di Scienze Computazionali, Via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Jörg Behler
- §Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Universitätstrasse 150, D-44780 Bochum, Germany
| | - Marco Bernasconi
- †Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, Via R. Cozzi 53, I-20125 Milano, Italy
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Sosso GC, Caravati S, Gatti C, Assoni S, Bernasconi M. Vibrational properties of hexagonal Ge(2)Sb(2)Te(5) from first principles. J Phys Condens Matter 2009; 21:245401. [PMID: 21693943 DOI: 10.1088/0953-8984/21/24/245401] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Phonons at the Γ point and the Raman spectrum of the hexagonal Ge(2)Sb(2)Te(5) were computed within density functional perturbation theory. The three different stackings of the Ge/Sb planes proposed in the experimental literature were considered. The theoretical Raman spectrum is similar for the three stackings with a marginally better agreement with experiments for the structure proposed by Matsunaga et al (2004 Acta Crystallogr. B 60 685) which assumes a disorder in Ge/Sb site occupation. Although the large broadening of the experimental Raman peaks prevents discriminating among the different stackings, the assignment of the Raman peaks to specific phonons is possible because the main features of the spectrum are rather insensitive to the actual distribution of atoms in the Sb/Ge sublattices. On the basis of the energetics (including configurational entropy) two stackings seem plausible candidates for GST, but only the mixed stacking by Matsunaga et al reproduces the spread of Ge/Sb-Te bond lengths measured experimentally.
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Affiliation(s)
- G C Sosso
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, Via R Cozzi 53, I-20125, Milano, Italy
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Abstract
Phonon dispersion relations and infrared and Raman spectra of crystalline Sb(2)Te(3) were computed within density functional perturbation theory. Overall good agreement with experiments is obtained, which allows us to assign the Raman and IR peaks to specific phonons.
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Affiliation(s)
- G C Sosso
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, Via R Cozzi 53, I-20125 Milano, Italy
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