1
|
Iida Y, Hiratsuka T, Miyahara MT, Watanabe S. Mechanism of Nucleation Pathway Selection in Binary Lennard-Jones Solution: A Combined Study of Molecular Dynamics Simulation and Free Energy Analysis. J Phys Chem B 2023; 127:3524-3533. [PMID: 37027488 DOI: 10.1021/acs.jpcb.2c08893] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
The nucleation process, which is the initial step in particle synthesis, determines the properties of the resultant particles. Although recent studies have observed various nucleation pathways, the physical factors that determine these pathways have not been fully elucidated. Herein, we conducted molecular dynamics simulations in a binary Lennard-Jones system as a model solution and found that the nucleation pathway can be classified into four types depending on microscopic interactions. The key parameters are (1) the strength of the solute-solute interaction and (2) the difference between the strengths of the like-pair and unlike-pair interactions. The increment of the former alters the nucleation mechanism from a two-step to a one-step pathway, whereas that of the latter causes quick assembly of solutes. Moreover, we developed a thermodynamic model based on the formation of core-shell nuclei to calculate the free energy landscapes. Our model successfully described the pathway observed in the simulations and demonstrated that the two parameters, (1) and (2), define the degree of supercooling and supersaturation, respectively. Thus, our model interpreted the microscopic insights from a macroscopic point of view. Because the only inputs required for our model are the interaction parameters, our model can a priori predict the nucleation pathway.
Collapse
Affiliation(s)
- Yuya Iida
- Department of Chemical Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Tatsumasa Hiratsuka
- Department of Chemical Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Minoru T Miyahara
- Department of Chemical Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Satoshi Watanabe
- Department of Chemical Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510, Japan
| |
Collapse
|
2
|
Tang X, Han W. Multiscale Exploration of Concentration-Dependent Amyloid-β(16-21) Amyloid Nucleation. J Phys Chem Lett 2022; 13:5009-5016. [PMID: 35649244 DOI: 10.1021/acs.jpclett.2c00685] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Atomic descriptions of peptide aggregation nucleation remain lacking due to the difficulty of exploring complex configurational spaces on long time scales. To elucidate this process, we develop a multiscale approach combining a metadynamics-based method with cluster statistical mechanics to derive concentration-dependent free energy surfaces of nucleation at near-atomic resolution. A kinetic transition network of nucleation is then constructed and employed to systematically explore nucleation pathways and kinetics through stochastic simulations. This approach is applied to describe Aβ16-21 amyloid nucleation, revealing a two-step mechanism involving disordered aggregates at millimolar concentration, and an unexpected mechanism at submillimolar concentrations that exhibits kinetics reminiscent of classical nucleation but atypical pathways involving growing clusters with structured cores wrapped by disordered surface. When this atypical mechanism is operative, critical nucleus size can be reflected by the nucleation reaction order. Collectively, our approach paves the way for a more quantitative and detailed understanding of peptide aggregation nucleation.
Collapse
Affiliation(s)
- Xuan Tang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| |
Collapse
|
3
|
Bowles RK, Harrowell P. Influence on crystal nucleation of an order-disorder transition among the subcritical clusters. Phys Rev E 2022; 105:L062602. [PMID: 35854518 DOI: 10.1103/physreve.105.l062602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Studies of nucleation generally focus on the properties of the critical cluster, but the presence of defects within the crystal lattice means that the population of nuclei necessarily evolve through a distribution of precritical clusters with varying degrees of structural disorder on their way to forming a growing stable crystal. To investigate the role precritical clusters play in nucleation, we develop a simple thermodynamic model for crystal nucleation in terms of cluster size and the degree of cluster order that allows us to alter the work of forming the precritical clusters without affecting the properties of the critical cluster. The steady state and transient nucleation behavior of the system are then studied numerically, for different microscopic ordering kinetics. We find that the model exhibits a generic order-disorder transition in the precritical clusters. Independent of the types of ordering kinetics, increasing the accessibility of disordered precritical clusters decreases both the steady state nucleation rate and the nucleation lag time. Furthermore, the interplay between the free-energy surface and the microscopic ordering kinetics leads to three distinct nucleation pathways.
Collapse
Affiliation(s)
- Richard K Bowles
- Department of Chemistry, University of Saskatchewan, Saskatoon, SK, Canada S7H 0H1
- Centre for Quantum Topology and its Applications (quanTA), University of Saskatchewan, SK, Canada S7N 5E6
| | - Peter Harrowell
- School of Chemistry, University of Sydney, New South Wales 2006, Australia
| |
Collapse
|
4
|
Bulutoglu PS, Wang S, Boukerche M, Nere NK, Corti DS, Ramkrishna D. An investigation of the kinetics and thermodynamics of NaCl nucleation through composite clusters. PNAS NEXUS 2022; 1:pgac033. [PMID: 36713321 PMCID: PMC9802385 DOI: 10.1093/pnasnexus/pgac033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/04/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023]
Abstract
Having a good understanding of nucleation is critical for the control of many important processes, such as polymorph selection during crystallization. However, a complete picture of the molecular-level mechanisms of nucleation remains elusive. In this work, we take an in-depth look at the NaCl homogeneous nucleation mechanism through thermodynamics. Distinguished from the classical nucleation theory, we calculate the free energy of nucleation as a function of two nucleus size coordinates: crystalline and amorphous cluster sizes. The free energy surface reveals a thermodynamic preference for a nonclassical mechanism of nucleation through a composite cluster, where the crystalline nucleus is surrounded by an amorphous layer. The thickness of the amorphous layer increases with an increase in supersaturation. The computed free energy landscape agrees well with the composite cluster-free energy model, through which phase specific thermodynamic properties are evaluated. As the supersaturation increases, there is a change in stability of the amorphous phase relative to the solution phase, resulting in a change from one-step to two-step mechanism, seen clearly from the free energy profile along the minimum free energy path crossing the transition curve. By obtaining phase-specific diffusion coefficients, we construct the full mesoscopic model and present a clear roadmap for NaCl nucleation.
Collapse
Affiliation(s)
- Pelin S Bulutoglu
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907-2100, USA
| | - Shiyan Wang
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907-2100, USA
| | - Moussa Boukerche
- Process Research and Development , AbbVie Inc, North Chicago, IL 60064, USA
| | - Nandkishor K Nere
- Process Research and Development , AbbVie Inc, North Chicago, IL 60064, USA
| | - David S Corti
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907-2100, USA
| | | |
Collapse
|
5
|
Holder J, Schmid R, Nielaba P. Two-step nucleation in confined geometry: Phase diagram of finite particles on a lattice gas model. J Chem Phys 2022; 156:124504. [DOI: 10.1063/5.0073043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We use a degenerated Ising model to describe nucleation and crystallization from solution in a confined two-component system. The free energy is calculated using metadynamics simulation with coordination numbers as the reaction coordinates. We deploy nudged elastic band simulation to determine the minimum energy path and give properties of the crystallization path. In this confined system, depletion effects, which could also be caused by slow material transport in the solution, prevent the post-critical cluster from further growth, and the crystalline state would only be stable at larger cluster sizes. Fluctuation of the higher coupling strength of the crystalline state enables further growth until the crystalline cluster is in equilibrium with the solvent, and this way, a second barrier is crossed. From the parameters and setup, we find necessary conditions for the occurrence of two-step nucleation in our system. These findings can be adapted to real systems as biomineralization, colloidal crystallization, and the solidification of metals.
Collapse
Affiliation(s)
- Jacob Holder
- Department of Physics, University of Konstanz, 78464 Konstanz, Germany
| | - Ralf Schmid
- Department of Physics, University of Konstanz, 78464 Konstanz, Germany
| | - Peter Nielaba
- Department of Physics, University of Konstanz, 78464 Konstanz, Germany
| |
Collapse
|
6
|
Condensation and Crystal Nucleation in a Lattice Gas with a Realistic Phase Diagram. ENTROPY 2022; 24:e24030419. [PMID: 35327929 PMCID: PMC8953323 DOI: 10.3390/e24030419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 11/17/2022]
Abstract
We reconsider model II of Orban et al. (J. Chem. Phys. 1968, 49, 1778−1783), a two-dimensional lattice-gas system featuring a crystalline phase and two distinct fluid phases (liquid and vapor). In this system, a particle prevents other particles from occupying sites up to third neighbors on the square lattice, while attracting (with decreasing strength) particles sitting at fourth- or fifth-neighbor sites. To make the model more realistic, we assume a finite repulsion at third-neighbor distance, with the result that a second crystalline phase appears at higher pressures. However, the similarity with real-world substances is only partial: Upon closer inspection, the alleged liquid−vapor transition turns out to be a continuous (albeit sharp) crossover, even near the putative triple point. Closer to the standard picture is instead the freezing transition, as we show by computing the free-energy barrier relative to crystal nucleation from the “liquid”.
Collapse
|
7
|
Mandal D, Quigley D. Nucleation rate in the two dimensional Ising model in the presence of random impurities. SOFT MATTER 2021; 17:8642-8650. [PMID: 34533176 DOI: 10.1039/d1sm01172c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nucleation phenomena are ubiquitous in nature and the presence of impurities in every real and experimental system is unavoidable. Yet numerical studies of nucleation are nearly always conducted for entirely pure systems. We have studied the behaviour of the droplet free energy in two dimensional Ising model in the presence of randomly positioned static and dynamic impurities. We have shown that both the free energy barrier height and critical nucleus size monotonically decreases with increasing the impurity density for the static case. We have compared the nucleation rates obtained from the Classical Nucleation Theory and the Forward Flux Sampling method for different densities of the static impurities. The results show good agreement. In the case of dynamic impurities, we observe preferential occupancy of the impurities at the boundary positions of the nucleus when the temperature is low. This further boosts enhancement of the nucleation rate due to lowering of the effective interfacial free energy.
Collapse
Affiliation(s)
- Dipanjan Mandal
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK.
| | - David Quigley
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK.
| |
Collapse
|
8
|
Eaton D, Saika-Voivod I, Bowles RK, Poole PH. Free energy surface of two-step nucleation. J Chem Phys 2021; 154:234507. [PMID: 34241260 DOI: 10.1063/5.0055877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We test the theoretical free energy surface (FES) for two-step nucleation (TSN) proposed by Iwamatsu [J. Chem. Phys. 134, 164508 (2011)] by comparing the predictions of the theory to numerical results for the FES recently reported from Monte Carlo simulations of TSN in a simple lattice system [James et al., J. Chem. Phys. 150, 074501 (2019)]. No adjustable parameters are used to make this comparison. That is, all the parameters of the theory are evaluated directly for the model system, yielding a predicted FES, which we then compare to the FES obtained from simulations. We find that the theoretical FES successfully predicts the numerically evaluated FES over a range of thermodynamic conditions that spans distinct regimes of behavior associated with TSN. All the qualitative features of the FES are captured by the theory, and the quantitative comparison is also very good. Our results demonstrate that Iwamatsu's extension of classical nucleation theory provides an excellent framework for understanding the thermodynamics of TSN.
Collapse
Affiliation(s)
- Dean Eaton
- Department of Physics, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| | - Ivan Saika-Voivod
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X7, Canada
| | - Richard K Bowles
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan 57N 5C9, Canada
| | - Peter H Poole
- Department of Physics, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| |
Collapse
|
9
|
Metya AK, Molinero V. Is Ice Nucleation by Organic Crystals Nonclassical? An Assessment of the Monolayer Hypothesis of Ice Nucleation. J Am Chem Soc 2021; 143:4607-4624. [PMID: 33729789 DOI: 10.1021/jacs.0c12012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Potent ice nucleating organic crystals display an increase in nucleation efficiency with pressure and memory effect after pressurization that set them apart from inorganic nucleants. These characteristics were proposed to arise from an ordered water monolayer at the organic-water interface. It was interpreted that ordering of the monolayer is the limiting step for ice nucleation on organic crystals, rendering their mechanism of nucleation nonclassical. Despite the importance of organics in atmospheric ice nucleation, that explanation has never been investigated. Here we elucidate the structure of interfacial water and its role in ice nucleation at ambient pressure on phloroglucinol dihydrate, the paradigmatic example of outstanding ice nucleating organic crystal, using molecular simulations. The simulations confirm the existence of an interfacial monolayer that orders on cooling and becomes fully ordered upon ice formation. The monolayer does not resemble any ice face but seamlessly connects the distinct hydrogen-bonding orders of ice and the organic surface. Although large ordered patches develop in the monolayer before ice nucleates, we find that the critical step is the formation of the ice crystallite, indicating that the mechanism is classical. We predict that the fully ordered, crystalline monolayer nucleates ice above -2 °C and could be responsible for the exceptional ice nucleation by the organic crystal at high pressures. The lifetime of the fully ordered monolayer around 0 °C, however, is too short to account for the memory effect reported in the experiments. The latter could arise from an increase in the melting temperature of ice confined by strongly ice-binding surfaces.
Collapse
Affiliation(s)
- Atanu K Metya
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| |
Collapse
|
10
|
Zhang TH, Zhang ZC, Cao JS, Liu XY. Can the pathway of stepwise nucleation be predicted and controlled? Phys Chem Chem Phys 2019; 21:7398-7405. [PMID: 30912550 DOI: 10.1039/c9cp00822e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Predicting the critical nucleus size and the nucleation barrier is of central importance in controlling the dynamics of nucleation. However, as the nucleation of a crystal involves intermediate states, the prediction becomes inaccessible with currently available models. Here, we show that based on single-particle level observations, the properties of crystal nuclei in a microscopic stepwise nucleation (MSN) can be well-quantified by incorporating the size and structure order parameter into the formula of free energy without prior knowledge of interfacial tension. The quantified free energy reveals that the intermediate structures arise from thermodynamics rather than kinetics. Precritical and postcritical nuclei are distinct not only in structure but also in the mechanism of crystalline ordering. The relative stability of intermediate structures and the pathway of nucleation can be well-controlled by supercooling. Our studies offer a successful approach to quantify MSN and shed new light on resolving the long-standing discrepancies between simulations and experiments.
Collapse
Affiliation(s)
- Tian Hui Zhang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, P. R. China.
| | | | | | | |
Collapse
|
11
|
James D, Beairsto S, Hartt C, Zavalov O, Saika-Voivod I, Bowles RK, Poole PH. Phase transitions in fluctuations and their role in two-step nucleation. J Chem Phys 2019; 150:074501. [DOI: 10.1063/1.5057429] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniella James
- Department of Physics, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| | - Seamus Beairsto
- Department of Physics, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| | - Carmen Hartt
- Department of Physics, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| | - Oleksandr Zavalov
- Department of Physics, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| | - Ivan Saika-Voivod
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X7, Canada
| | - Richard K. Bowles
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan 57N 5C9, Canada
| | - Peter H. Poole
- Department of Physics, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| |
Collapse
|
12
|
Schmid R, Nielaba P. Stability of nanoparticles in solution: A statistical description of crystallization as a finite particle size effect in a lattice-gas model. J Chem Phys 2019; 150:054504. [DOI: 10.1063/1.5063665] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ralf Schmid
- Department of Physics, University of Konstanz, D-78457 Konstanz, Germany
| | - Peter Nielaba
- Department of Physics, University of Konstanz, D-78457 Konstanz, Germany
| |
Collapse
|
13
|
Kumar A, Molinero V. Two-Step to One-Step Nucleation of a Zeolite through a Metastable Gyroid Mesophase. J Phys Chem Lett 2018; 9:5692-5697. [PMID: 30196700 DOI: 10.1021/acs.jpclett.8b02413] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The importance of nonclassical nucleation pathways in the formation of complex crystals has become apparent in recent years. Nonclassical pathways were unraveled for, among others, the crystallization of proteins, colloids, and clathrates. In those cases, the formation of a metastable fluid with density close to the crystal decreases the crystallization barrier. Recent simulations indicate that mesophases can facilitate the nucleation of zeolites. Here, we use molecular simulations to investigate the role of a gyroid mesophase on the crystallization of a model zeolite from liquid. The nucleation pathway is always nonclassical. At warmer temperatures, the mechanism proceeds in two well-defined steps: nucleation of a metastable gyroid followed by its crystallization into a zeolite. At colder temperatures, the second barrier becomes negligible, and the crystallization occurs in one step. This second scenario is also nonclassical, as the critical nucleus for the crystallization has the structure of the gyroid and seamlessly transforms into a zeolite as it grows past its critical size. To our knowledge, this is the first report of a nonclassical mechanism of crystallization mediated by a mesophase.
Collapse
Affiliation(s)
- Abhinaw Kumar
- Department of Chemistry , The University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Valeria Molinero
- Department of Chemistry , The University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| |
Collapse
|
14
|
Patel LA, Kindt JT. Simulations of NaCl Aggregation from Solution: Solvent Determines Topography of Free Energy Landscape. J Comput Chem 2018; 40:135-147. [DOI: 10.1002/jcc.25554] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Lara A. Patel
- Department of Chemistry; Emory University; 1515 Dickey Drive, Atlanta Georgia 30322
| | - James T. Kindt
- Department of Chemistry; Emory University; 1515 Dickey Drive, Atlanta Georgia 30322
| |
Collapse
|
15
|
Zimmermann NER, Vorselaars B, Espinosa JR, Quigley D, Smith WR, Sanz E, Vega C, Peters B. NaCl nucleation from brine in seeded simulations: Sources of uncertainty in rate estimates. J Chem Phys 2018; 148:222838. [DOI: 10.1063/1.5024009] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Nils. E. R. Zimmermann
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Bart Vorselaars
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom
| | - Jorge R. Espinosa
- Departmento de Quimica-Fisica I, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - David Quigley
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - William R. Smith
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario N1G2W1, Canada
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Eduardo Sanz
- Departmento de Quimica-Fisica I, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Carlos Vega
- Departmento de Quimica-Fisica I, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Baron Peters
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| |
Collapse
|
16
|
Poon GG, Lemke T, Peter C, Molinero V, Peters B. Soluble Oligomeric Nucleants: Simulations of Chain Length, Binding Strength, and Volume Fraction Effects. J Phys Chem Lett 2017; 8:5815-5820. [PMID: 29116791 DOI: 10.1021/acs.jpclett.7b02651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent theories and simulations suggest that molecular additives can bind to the surfaces of nuclei, lower the surface energy, and accelerate nucleation. Experiments have shown that oligomeric and polymeric additives can also modify nucleation rates of proteins, ice, and minerals; however, general design principles for oligomeric or polymeric promoters do not yet exist. Here we investigate oligomeric additives for which each segment of the oligomer can bind to surfaces of nuclei. We use semigrand canonical Monte Carlo simulations in a Potts lattice gas model to study the effects of oligomer chain length, volume fraction, and binding strength. We find that increasing each of those parameters lowers the nucleation barrier. At extremely low oligomer concentrations, the nucleation kinetics can be modeled as though each oligomer is a heterogeneous nucleation site in solution.
Collapse
Affiliation(s)
- Geoffrey G Poon
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| | - Tobias Lemke
- Department of Chemistry, University of Konstanz , Konstanz 78457, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz , Konstanz 78457, Germany
| | - Valeria Molinero
- Department of Chemistry, The University of Utah , Salt Lake City, Utah 84112, United States
| | - Baron Peters
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| |
Collapse
|
17
|
Lifanov Y, Vorselaars B, Quigley D. Nucleation barrier reconstruction via the seeding method in a lattice model with competing nucleation pathways. J Chem Phys 2016; 145:211912. [DOI: 10.1063/1.4962216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Yuri Lifanov
- Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Bart Vorselaars
- School of Mathematics and Physics, University of Lincoln, Lincolnshire LN6 7TS, United Kingdom
| | - David Quigley
- Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
18
|
Sosso G, Chen J, Cox SJ, Fitzner M, Pedevilla P, Zen A, Michaelides A. Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations. Chem Rev 2016; 116:7078-116. [PMID: 27228560 PMCID: PMC4919765 DOI: 10.1021/acs.chemrev.5b00744] [Citation(s) in RCA: 379] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 11/28/2022]
Abstract
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments.
Collapse
Affiliation(s)
- Gabriele
C. Sosso
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
| | - Ji Chen
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
| | | | - Martin Fitzner
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
| | - Philipp Pedevilla
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
| | - Andrea Zen
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
| | - Angelos Michaelides
- Thomas Young Centre, London
Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street WC1E
6BT London, U.K.
| |
Collapse
|
19
|
Poon GG, Peters B. Accelerated Nucleation Due to Trace Additives: A Fluctuating Coverage Model. J Phys Chem B 2015; 120:1679-84. [DOI: 10.1021/acs.jpcb.5b08510] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Geoffrey G. Poon
- Department of Chemical Engineering, University of California, Santa
Barbara, California 93106, United States
| | - Baron Peters
- Department of Chemical Engineering, University of California, Santa
Barbara, California 93106, United States
| |
Collapse
|
20
|
Popov AV, Craven GT, Hernandez R. Nonequilibrium structure in sequential assembly. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:052108. [PMID: 26651648 DOI: 10.1103/physreve.92.052108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Indexed: 06/05/2023]
Abstract
The assembly of monomeric constituents into molecular superstructures through sequential-arrival processes has been simulated and theoretically characterized. When the energetic interactions allow for complete overlap of the particles, the model is equivalent to that of the sequential absorption of soft particles on a surface. In the present work, we consider more general cases by including arbitrary aggregating geometries and varying prescriptions of the connectivity network. The resulting theory accounts for the evolution and final-state configurations through a system of equations governing structural generation. We find that particle geometries differ significantly from those in equilibrium. In particular, variations of structural rigidity and morphology tune particle energetics and result in significant variation in the nonequilibrium distributions of the assembly in comparison to the corresponding equilibrium case.
Collapse
Affiliation(s)
- Alexander V Popov
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Galen T Craven
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Rigoberto Hernandez
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| |
Collapse
|
21
|
Zimmermann NER, Vorselaars B, Quigley D, Peters B. Nucleation of NaCl from Aqueous Solution: Critical Sizes, Ion-Attachment Kinetics, and Rates. J Am Chem Soc 2015; 137:13352-61. [DOI: 10.1021/jacs.5b08098] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Bart Vorselaars
- Department
of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, U.K
| | - David Quigley
- Department
of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, U.K
| | | |
Collapse
|
22
|
Okamoto A, Kuwatani T, Omori T, Hukushima K. Free-energy landscape and nucleation pathway of polymorphic minerals from solution in a Potts lattice-gas model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042130. [PMID: 26565191 DOI: 10.1103/physreve.92.042130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 06/05/2023]
Abstract
Metastable minerals commonly form during reactions between water and rock. The nucleation mechanism of polymorphic phases from solution are explored here using a two-dimensional Potts model. The model system is composed of a solvent and three polymorphic solid phases. The local state and position of the solid phase are updated by Metropolis dynamics. Below the critical temperature, a large cluster of the least stable solid phase initially forms in the solution before transitioning into more-stable phases following the Ostwald step rule. The free-energy landscape as a function of the modal abundance of each solid phase clearly reveals that before cluster formation, the least stable phase has an energetic advantage because of its low interfacial energy with the solution, and after cluster formation, phase transformation occurs along the valley of the free-energy landscape, which contains several minima for the regions of three phases. Our results indicate that the solid-solid and solid-liquid interfacial energy contribute to the formation of the complex free-energy landscape and nucleation pathways following the Ostwald step rule.
Collapse
Affiliation(s)
- Atsushi Okamoto
- Graduate School of Environmental Studies, Tohoku University, 6-6-20 Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Tatsu Kuwatani
- Department of Solid Earth Geochemistry, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Toshiaki Omori
- Department of Electrical and Electronic Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Koji Hukushima
- Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| |
Collapse
|
23
|
Affiliation(s)
- Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| | - Robert L. Jack
- Department of Physics, University of Bath, Bath BA2 7AY, United Kingdom;
| |
Collapse
|
24
|
Poon GG, Seritan S, Peters B. A design equation for low dosage additives that accelerate nucleation. Faraday Discuss 2015; 179:329-41. [DOI: 10.1039/c4fd00226a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Additives are used to control nucleation in many natural and industrial environments. However, the mechanisms by which additives inhibit or accelerate solute precipitate nucleation are not well understood. We propose an equation that predicts changes in nucleation barriers based on the adsorption properties and concentrations of trace additives. The equation shows that nucleant efficacy depends on the product of an adsorption equilibrium constant and the reduction in interfacial tension. Moreover, the two factors that determine the potency of additives are related to each other, suggesting that assays of just one property might facilitate additive design. We test the design equation for a Potts lattice gas model with surfactant-like additives in addition to solutes and solvents.
Collapse
Affiliation(s)
- Geoffrey G. Poon
- Department of Chemical Engineering
- University of California
- Santa Barbara
- USA
| | - Stefan Seritan
- Department of Chemical Engineering
- University of California
- Santa Barbara
- USA
| | - Baron Peters
- Department of Chemical Engineering
- University of California
- Santa Barbara
- USA
- Department of Chemistry
| |
Collapse
|
25
|
Duff N, Dahal YR, Schmit JD, Peters B. Salting out the polar polymorph: analysis by alchemical solvent transformation. J Chem Phys 2014; 140:014501. [PMID: 24410227 DOI: 10.1063/1.4853775] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We computationally examine how adding NaCl to an aqueous solution with α- and γ-glycine nuclei alters the structure and interfacial energy of the nuclei. The polar γ-glycine nucleus in pure aqueous solution develops a melted layer of amorphous glycine around the nucleus. When NaCl is added, a double layer is formed that stabilizes the polar glycine polymorph and eliminates the surface melted layer. In contrast, the non-polar α-glycine nucleus is largely unaffected by the addition of NaCl. To quantify the stabilizing effect of NaCl on γ-glycine nuclei, we alchemically transform the aqueous glycine solution into a brine solution of glycine. The alchemical transformation is performed both with and without a nucleus in solution and for nuclei of α-glycine and γ-glycine polymorphs. The calculations show that adding 80 mg/ml NaCl reduces the interfacial free energy of a γ-glycine nucleus by 7.7 mJ/m(2) and increases the interfacial free energy of an α-glycine nucleus by 3.1 mJ/m(2). Both results are consistent with experimental reports on nucleation rates which suggest: J(α, brine) < J(γ, brine) < J(α, water). For γ-glycine nuclei, Debye-Hückel theory qualitatively, but not quantitatively, captures the effect of salt addition. Only the alchemical solvent transformation approach can predict the results for both polar and non-polar polymorphs. The results suggest a general "salting out" strategy for obtaining polar polymorphs and also a general approach to computationally estimate the effects of solvent additives on interfacial free energies for nucleation.
Collapse
Affiliation(s)
- Nathan Duff
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Yuba Raj Dahal
- Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA
| | - Baron Peters
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| |
Collapse
|
26
|
Craven GT, Popov AV, Hernandez R. Effective Surface Coverage of Coarse-Grained Soft Matter. J Phys Chem B 2014; 118:14092-102. [DOI: 10.1021/jp505207h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Galen T. Craven
- Center for Computational
Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Alexander V. Popov
- Center for Computational
Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Rigoberto Hernandez
- Center for Computational
Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| |
Collapse
|
27
|
Agarwal V, Peters B. Solute Precipitate Nucleation: A Review of Theory and Simulation Advances. ADVANCES IN CHEMICAL PHYSICS 2014. [DOI: 10.1002/9781118755815.ch03] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
28
|
Agarwal V, Peters B. Nucleation near the eutectic point in a Potts-lattice gas model. J Chem Phys 2014; 140:084111. [DOI: 10.1063/1.4865338] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
|
29
|
Peters B, Bolhuis PG, Mullen RG, Shea JE. Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency. J Chem Phys 2013; 138:054106. [PMID: 23406097 DOI: 10.1063/1.4775807] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We propose a method for identifying accurate reaction coordinates among a set of trial coordinates. The method applies to special cases where motion along the reaction coordinate follows a one-dimensional Smoluchowski equation. In these cases the reaction coordinate can predict its own short-time dynamical evolution, i.e., the dynamics projected from multiple dimensions onto the reaction coordinate depend only on the reaction coordinate itself. To test whether this property holds, we project an ensemble of short trajectory swarms onto trial coordinates and compare projections of individual swarms to projections of the ensemble of swarms. The comparison, quantified by the Kullback-Leibler divergence, is numerically performed for each isosurface of each trial coordinate. The ensemble of short dynamical trajectories is generated only once by sampling along an initial order parameter. The initial order parameter should separate the reactants and products with a free energy barrier, and distributions on isosurfaces of the initial parameter should be unimodal. The method is illustrated for three model free energy landscapes with anisotropic diffusion. Where exact coordinates can be obtained from Kramers-Langer-Berezhkovskii-Szabo theory, results from the new method agree with the exact results. We also examine characteristics of systems where the proposed method fails. We show how dynamical self-consistency is related (through the Chapman-Kolmogorov equation) to the earlier isocommittor criterion, which is based on longer paths.
Collapse
Affiliation(s)
- Baron Peters
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | | | | | | |
Collapse
|
30
|
Cabriolu R, Kashchiev D, Auer S. Breakdown of nucleation theory for crystals with strongly anisotropic interactions between molecules. J Chem Phys 2012. [DOI: 10.1063/1.4767531] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
31
|
Duff N, Peters B. Polymorph specific RMSD local order parameters for molecular crystals and nuclei: α-, β-, and γ-glycine. J Chem Phys 2012; 135:134101. [PMID: 21992276 DOI: 10.1063/1.3638268] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Crystal nucleation is important for many processes including pharmaceutical crystallization, biomineralization, and material synthesis. The progression of structural changes which occur during crystal nucleation are often described using order parameters. Polymorph specific order parameters have been developed for crystallization of spherically symmetric particles; however, polymorph specific order parameters for molecular crystals remain a challenge. We introduce template based polymorph specific order parameters for molecular crystals. For each molecule in a simulation, we compute the root mean squared deviation (RMSD) between the local environment around the molecule and a template of the perfect crystal structure for each polymorph. The RMSD order parameters can clearly distinguish the α-, β-, and γ-glycine polymorph crystal structures in the bulk crystal and also in solvated crystallites. Surface melting of glycine crystallites in supersaturated aqueous solution is explored using the newly developed order parameters. The solvated α-glycine crystallite has a thinner surface melted layer than the γ-glycine crystallite. α-glycine forms first out of aqueous solution, so surface melted layer thickness may provide insight into interfacial energy and polymorph selection.
Collapse
Affiliation(s)
- Nathan Duff
- Department of Chemical Engineering, University of California, Santa Barbara 93106-5080, USA
| | | |
Collapse
|
32
|
Hedges LO, Whitelam S. Limit of validity of Ostwald's rule of stages in a statistical mechanical model of crystallization. J Chem Phys 2011; 135:164902. [DOI: 10.1063/1.3655358] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
33
|
Shah M, Santiso EE, Trout BL. Computer Simulations of Homogeneous Nucleation of Benzene from the Melt. J Phys Chem B 2011; 115:10400-12. [DOI: 10.1021/jp203550t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Manas Shah
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Erik E. Santiso
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Bernhardt L. Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
34
|
Peters B. On the coupling between slow diffusion transport and barrier crossing in nucleation. J Chem Phys 2011; 135:044107. [DOI: 10.1063/1.3613674] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
|
35
|
Knott BC, Doherty MF, Peters B. A simulation test of the optical Kerr mechanism for laser-induced nucleation. J Chem Phys 2011; 134:154501. [DOI: 10.1063/1.3574010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
36
|
Jacobson LC, Molinero V. Can Amorphous Nuclei Grow Crystalline Clathrates? The Size and Crystallinity of Critical Clathrate Nuclei. J Am Chem Soc 2011; 133:6458-63. [DOI: 10.1021/ja201403q] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Liam C. Jacobson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Valeria Molinero
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| |
Collapse
|
37
|
Jacobson LC, Hujo W, Molinero V. Nucleation pathways of clathrate hydrates: effect of guest size and solubility. J Phys Chem B 2011; 114:13796-807. [PMID: 20931990 DOI: 10.1021/jp107269q] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the microscopic mechanism of nucleation of clathrate hydrates is important for their use in hydrogen storage, CO(2) sequestration, storage and transport of natural gas, and the prevention of the formation of hydrate plugs in oil and gas pipelines. These applications involve hydrate guests of varied sizes and solubility in water that form different hydrate crystal structures. Nevertheless, molecular studies of the mechanism of nucleation of hydrates have focused on the single class of small hydrophobic guests that stabilize the sI crystal. In this work, we use molecular dynamics simulations with a very efficient coarse-grained model to elucidate the mechanisms of nucleation of clathrate hydrates of four model guests that span a 2 orders of magnitude range in solubility in water and that encompass sizes which stabilize each one a different hydrate structure (sI and sII, with and without occupancy of the dodecahedral cages). We find that the overall mechanism of clathrate nucleation is similar for all guests and involves a first step of formation of blobs, dense clusters of solvent-separated guest molecules that are the birthplace of the clathrate cages. Blobs of hydrophobic guests are rarer and longer-lived than those for soluble guests. For each guest, we find multiple competing channels to form the critical nuclei, filled dodecahedral (5(12)) cages, empty 5(12) cages, and a variety of filled large (5(12)6(n) with n = 2, 3, and 4) clathrate cages. Formation of empty dodecahedra is an important nucleation channel for all but the smallest guest. The empty 5(12) cages are stabilized by the presence of guests from the blob in their first solvation shell. Under conditions of high supercooling, the structure of the critical and subcritical nuclei is mainly determined by the size of the guest and does not reflect the cage composition or ordering of the stable or metastable clathrate crystals.
Collapse
Affiliation(s)
- Liam C Jacobson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
| | | | | |
Collapse
|
38
|
López LG, Linares DH, Ramirez-Pastor AJ, Cannas SA. Phase diagram of self-assembled rigid rods on two-dimensional lattices: Theory and Monte Carlo simulations. J Chem Phys 2010; 133:134706. [DOI: 10.1063/1.3496482] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
39
|
Duff N, Peters B. Mitosis method for directly calculating the interfacial free energy of nuclei. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927022.2010.483684] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
40
|
|
41
|
Duff N, Peters B. Erratum: “Nucleation in a Potts lattice gas model of crystallization from solution” [J. Chem. Phys. 131, 184101 (2009)]. J Chem Phys 2010; 132:129901. [DOI: 10.1063/1.3360145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
42
|
Peters B. Competing nucleation pathways in a mixture of oppositely charged colloids: Out-of-equilibrium nucleation revisited. J Chem Phys 2009; 131:244103. [DOI: 10.1063/1.3271024] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
43
|
Knott BC, Duff N, Doherty MF, Peters B. Estimating diffusivity along a reaction coordinate in the high friction limit: Insights on pulse times in laser-induced nucleation. J Chem Phys 2009; 131:224112. [DOI: 10.1063/1.3268704] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|