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Afify N, Ferreiro-Rangel CA, Sweatman MB. Molecular Dynamics Investigation of Giant Clustering in Small-Molecule Solutions: The Case of Aqueous PEHA. J Phys Chem B 2022; 126:8882-8891. [PMID: 36282173 PMCID: PMC9639140 DOI: 10.1021/acs.jpcb.2c04489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/27/2022] [Indexed: 01/11/2023]
Abstract
The importance of the formation of giant clusters in solution, in nature and industry, is increasingly recognized. However, relatively little attention has been paid to the formation of giant clusters in solutions of small, relatively soluble but nonamphiphilic molecules. In this work, we present a general methodology based on molecular dynamics that can be used to investigate such systems. As a case study, we focus on the formation of apparently stable clusters of pentaethylenehexamine (PEHA) in water. These clusters have been used as templates for the construction of bioinspired silica nanoparticles. To better understand clustering in this system, we study the effect of PEHA protonation state (neutral, +1, and +2) and counterion type (chloride or acetate) on PEHA clustering in dilute aqueous solutions (200 and 400 mM) using large-scale classical molecular dynamics. We find that large stable clusters are formed by singly charged PEHA with chloride or acetate as the counterion, although it is not clear for the case with acetate whether bulk phase separation, that might lead to precipitation, would eventually occur. Large clusters also appear to be stable for doubly charged PEHA with acetate, the less soluble counterion. We attribute this behavior to a form of complex coacervation, observed here for relatively small and highly soluble molecules (PEHA + counterion) rather than the large polyions usually found to form such coacervates. We discuss whether this behavior might also be described by an effective SALR (short-range attraction, long-range repulsion) interaction. This work might help future studies of additives for the design of novel bioinspired templated nanomaterials and of giant clustering in small-molecule solutions more generally.
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Affiliation(s)
- Nasser
D. Afify
- School of Engineering, The University of Edinburgh, The King’s Buildings, Sanderson Building,
Mayfield Road, Edinburgh EH9 3JL, United Kingdom
| | - Carlos A. Ferreiro-Rangel
- School of Engineering, The University of Edinburgh, The King’s Buildings, Sanderson Building,
Mayfield Road, Edinburgh EH9 3JL, United Kingdom
| | - Martin B. Sweatman
- School of Engineering, The University of Edinburgh, The King’s Buildings, Sanderson Building,
Mayfield Road, Edinburgh EH9 3JL, United Kingdom
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2
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Sweatman MB, Afify ND, Ferreiro-Rangel CA, Jorge M, Sefcik J. Molecular Dynamics Investigation of Clustering in Aqueous Glycine Solutions. J Phys Chem B 2022; 126:4711-4722. [PMID: 35729500 PMCID: PMC9251761 DOI: 10.1021/acs.jpcb.2c01975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/30/2022] [Indexed: 12/23/2022]
Abstract
Recent experiments with undersaturated aqueous glycine solutions have repeatedly exhibited the presence of giant liquid-like clusters or nanodroplets around 100 nm in diameter. These nanodroplets re-appear even after careful efforts for their removal and purification of the glycine solution. The composition of these clusters is not clear, although it has been suggested that they are mainly composed of glycine, a small and very soluble amino acid. To gain insights into this phenomenon, we study the aggregation of glycine in aqueous solutions at concentrations below the experimental solubility limit using large-scale molecular dynamics simulations under ambient conditions. Three protonation states of glycine (zwitterion = GLZ, anion = GLA, and cation = GLC) are simulated using molecular force fields based on the 1.14*CM1A partial charge scheme, which incorporates the OPLS all-atom force field and TIP3P water. When initiated from dispersed states, we find that giant clusters do not form in our simulations unless salt impurities are present. Moreover, if simulations are initiated from giant cluster states, we find that they tend to dissolve in the absence of salt impurities. Therefore, the simulation results provide little support for the possibility that the giant clusters seen in experiments are composed purely of glycine (and water). Considering that strenuous efforts are made in experiments to remove impurities such as salt, we propose that the giant clusters observed might instead result from the aggregation of reaction products of aqueous glycine, such as diketopiperazine or other oligoglycines which may be difficult to separate from glycine using conventional methods, or their co-aggregation with glycine.
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Affiliation(s)
- Martin B. Sweatman
- School
of Engineering, The University of Edinburgh, The King’s Buildings, Sanderson
Building, Mayfield Road, Edinburgh EH9 3JL, U.K.
| | - Nasser D. Afify
- School
of Engineering, The University of Edinburgh, The King’s Buildings, Sanderson
Building, Mayfield Road, Edinburgh EH9 3JL, U.K.
| | - Carlos A. Ferreiro-Rangel
- School
of Engineering, The University of Edinburgh, The King’s Buildings, Sanderson
Building, Mayfield Road, Edinburgh EH9 3JL, U.K.
| | - Miguel Jorge
- Department
of Chemical and Process Engineering, Faculty of Engineering, University of Strathclyde, James Weir Building, Montrose Street, Glasgow G1 1XJ, U.K.
| | - Jan Sefcik
- Department
of Chemical and Process Engineering, Faculty of Engineering, University of Strathclyde, James Weir Building, Montrose Street, Glasgow G1 1XJ, U.K.
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Hagan MF, Grason GM. Equilibrium mechanisms of self-limiting assembly. REVIEWS OF MODERN PHYSICS 2021; 93:025008. [PMID: 35221384 PMCID: PMC8880259 DOI: 10.1103/revmodphys.93.025008] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of equilibrium assembly processes give rise to two states: one consisting of dispersed disassociated subunits, and the other, a bulk-condensed state of unlimited size. This review focuses on the more specialized class of self-limiting assembly, which describes equilibrium assembly processes resulting in finite-size structures. These systems pose a generic and basic question, how do thermodynamic processes involving non-covalent interactions between identical subunits "measure" and select the size of assembled structures? In this review, we begin with an introduction to the basic statistical mechanical framework for assembly thermodynamics, and use this to highlight the key physical ingredients that ensure equilibrium assembly will terminate at finite dimensions. Then, we introduce examples of self-limiting assembly systems, and classify them within this framework based on two broad categories: self-closing assemblies and open-boundary assemblies. These include well-known cases in biology and synthetic soft matter - micellization of amphiphiles and shell/tubule formation of tapered subunits - as well as less widely known classes of assemblies, such as short-range attractive/long-range repulsive systems and geometrically-frustrated assemblies. For each of these self-limiting mechanisms, we describe the physical mechanisms that select equilibrium assembly size, as well as potential limitations of finite-size selection. Finally, we discuss alternative mechanisms for finite-size assemblies, and draw contrasts with the size-control that these can achieve relative to self-limitation in equilibrium, single-species assemblies.
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Affiliation(s)
- Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
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4
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Haw MD. Structure and kinetics in colloidal films with competing interactions. Phys Rev E 2019; 99:012603. [PMID: 30780380 DOI: 10.1103/physreve.99.012603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Indexed: 11/07/2022]
Abstract
Using computer simulation we explore how two-dimensional systems of colloids with a combination of short-range attractive and long-range repulsive interactions generate complex structures and kinetics. Cooperative effects mean the attractive potential, despite being very short-ranged compared to the repulsion, can have significant effects on large-scale structure. By considering the number of particles occupying a notional "repulsion zone" defined by the repulsion length scale, we classify different characteristic structural regimes in which the combination of attraction and repulsion leads to different structural and kinetic outcomes, such as compact clustering, chain labyrinths, and coexisting clusters and chains. In some regimes small changes in repulsion range and/or area fraction can change timescales of structural evolution by many orders of magnitude.
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Affiliation(s)
- Mark D Haw
- Department of Chemical and Process Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
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Beck C, Grimaldo M, Roosen-Runge F, Braun MK, Zhang F, Schreiber F, Seydel T. Nanosecond Tracer Diffusion as a Probe of the Solution Structure and Molecular Mobility of Protein Assemblies: The Case of Ovalbumin. J Phys Chem B 2018; 122:8343-8350. [PMID: 30106587 DOI: 10.1021/acs.jpcb.8b04349] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein diffusion is not only an important process ensuring biological function but can also be used as a probe to obtain information on structural properties of protein assemblies in liquid solutions. Here, we explore the oligomerization state of ovalbumin at high protein concentrations by means of its short-time self-diffusion. We employ high-resolution incoherent quasielastic neutron scattering to access the self-diffusion on nanosecond timescales, on which interparticle contacts are not altered. Our results indicate that ovalbumin in aqueous (D2O) solutions occurs in increasingly large assemblies of its monomeric subunits with rising protein concentration. It changes from nearly monomeric toward dimeric and ultimately larger than tetrameric complexes. Simultaneously, we access information on the internal molecular mobility of ovalbumin on the nanometer length scale and compare it with results obtained for bovine serum albumin, immunoglobulin, and β-lactoglobulin.
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Affiliation(s)
- Christian Beck
- Institut Max von Laue-Paul Langevin (ILL) , B.P.156, F-38042 Grenoble , France.,Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Marco Grimaldo
- Institut Max von Laue-Paul Langevin (ILL) , B.P.156, F-38042 Grenoble , France
| | - Felix Roosen-Runge
- Division of Physical Chemistry, Department of Chemistry , Lund University , Naturvetarvägen 16 , SE-22100 Lund , Sweden
| | - Michal K Braun
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Fajun Zhang
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Frank Schreiber
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Tilo Seydel
- Institut Max von Laue-Paul Langevin (ILL) , B.P.156, F-38042 Grenoble , France
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van Gruijthuijsen K, Obiols-Rabasa M, Schurtenberger P, Bouwman WG, Stradner A. The extended law of corresponding states when attractions meet repulsions. SOFT MATTER 2018; 14:3704-3715. [PMID: 29557476 DOI: 10.1039/c8sm00160j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Short-range attractive colloids show well-defined phase behaviour in the absence of repulsions, and highly intriguing equilibrium gelation in the presence of long-range repulsions. We present the state diagram of short-range attractive colloids with repulsions that range from fully screened to intermediately ranged, i.e. longer-ranged than the attractions, but shorter ranged than the colloid size. We demonstrate that although the macroscopic phase behaviour does not change perceptibly, there is a dramatic increase of inhomogeneities once the repulsions become longer-ranged than the attractions. The interaction potentials are characterized with small angle neutron scattering, and used to renormalize the state diagram with the minimum in the interaction potential, min[U(r)], and with the reduced second virial coefficient, B2*. We find that the extended law of corresponding states captures the onset of phase separation for shorter ranged repulsions, but fails for longer ranged repulsions. Instead, for a given model of U(r), the transition from visually homogeneous fluid to phase separation and/or gelation can be rescaled with min[U(r)] over the full range of repulsions. Finally, we suggest a generic state diagram to describe the effect of repulsions on short-range attractive systems.
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Affiliation(s)
- K van Gruijthuijsen
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland.
| | - M Obiols-Rabasa
- Division of Physical Chemistry, Department of Chemistry, Lund University, Naturvetarvägen 16, SE-223 62 Lund, Sweden
| | - P Schurtenberger
- Division of Physical Chemistry, Department of Chemistry, Lund University, Naturvetarvägen 16, SE-223 62 Lund, Sweden
| | - W G Bouwman
- Delft University of Technology, Mekelweg 15, 2629 JB Delft, The Netherlands
| | - A Stradner
- Division of Physical Chemistry, Department of Chemistry, Lund University, Naturvetarvägen 16, SE-223 62 Lund, Sweden
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7
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Braun MK, Grimaldo M, Roosen-Runge F, Hoffmann I, Czakkel O, Sztucki M, Zhang F, Schreiber F, Seydel T. Crowding-Controlled Cluster Size in Concentrated Aqueous Protein Solutions: Structure, Self- and Collective Diffusion. J Phys Chem Lett 2017; 8:2590-2596. [PMID: 28525282 DOI: 10.1021/acs.jpclett.7b00658] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigate the concentration-controlled formation of clusters in β-lactoglobulin (BLG) protein solutions combining structural and dynamical scattering techniques. The static structure factor from small-angle X-ray scattering as well as de-Gennes narrowing in the nanosecond diffusion function D(q) from neutron spin echo spectroscopy support a picture of cluster formation. Using neutron backscattering spectroscopy, a monotonous increase of the average hydrodynamic cluster radius is monitored over a broad protein concentration range, corresponding to oligomeric structures of BLG ranging from the native dimers up to roughly four dimers. The results suggest that BLG forms compact clusters that are static on the observation time scale of several nanoseconds. The presented analysis provides a general framework to access the structure and dynamics of macromolecular assemblies in solution.
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Affiliation(s)
- Michal K Braun
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Marco Grimaldo
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Felix Roosen-Runge
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
- Division of Physical Chemistry, Department of Chemistry, Lund University , Naturvetarvägen 14, 221 00 Lund, Sweden
| | - Ingo Hoffmann
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Orsolya Czakkel
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Sztucki
- ESRF - The European Synchrotron , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
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McDermott D, Olson Reichhardt CJ, Reichhardt C. Structural transitions and hysteresis in clump- and stripe-forming systems under dynamic compression. SOFT MATTER 2016; 12:9549-9560. [PMID: 27834430 DOI: 10.1039/c6sm01939k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Using numerical simulations, we study the dynamical evolution of particles interacting via competing long-range repulsion and short-range attraction in two dimensions. The particles are compressed using a time-dependent quasi-one dimensional trough potential that controls the local density, causing the system to undergo a series of structural phase transitions from a low density clump lattice to stripes, voids, and a high density uniform state. The compression proceeds via slow elastic motion that is interrupted with avalanche-like bursts of activity as the system collapses to progressively higher densities via plastic rearrangements. The plastic events vary in magnitude from small rearrangements of particles, including the formation of quadrupole-like defects, to large-scale vorticity and structural phase transitions. In the dense uniform phase, the system compresses through row reduction transitions mediated by a disorder-order process. We characterize the rearrangement events by measuring changes in the potential energy, the fraction of sixfold coordinated particles, the local density, and the velocity distribution. At high confinements, we find power law scaling of the velocity distribution during row reduction transitions. We observe hysteresis under a reversal of the compression when relatively few plastic rearrangements occur. The decompressing system exhibits distinct phase morphologies, and the phase transitions occur at lower compression forces as the system expands compared to when it is compressed.
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Affiliation(s)
- Danielle McDermott
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA. and Department of Physics, Wabash College, Crawfordsville, Indiana 47933, USA.
| | | | - Charles Reichhardt
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
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Cigala G, Costa D, Bomont JM, Caccamo C. Aggregate formation in a model fluid with microscopic piecewise-continuous competing interactions. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1078006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- G. Cigala
- Dipartimento di Fisica e di Scienze della Terra, Università degli Studi di Messina Viale , Messina, Italy
| | - D. Costa
- Dipartimento di Fisica e di Scienze della Terra, Università degli Studi di Messina Viale , Messina, Italy
| | | | - C. Caccamo
- Dipartimento di Fisica e di Scienze della Terra, Università degli Studi di Messina Viale , Messina, Italy
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10
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Role of clusters in nonclassical nucleation and growth of protein crystals. Proc Natl Acad Sci U S A 2014; 111:E546-53. [PMID: 24449867 DOI: 10.1073/pnas.1309320111] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The development of multistep nucleation theory has spurred on experimentalists to find intermediate metastable states that are relevant to the solidification pathway of the molecule under interest. A great deal of studies focused on characterizing the so-called "precritical clusters" that may arise in the precipitation process. However, in macromolecular systems, the role that these clusters might play in the nucleation process and in the second stage of the precipitation process, i.e., growth, remains to a great extent unknown. Therefore, using biological macromolecules as a model system, we have studied the mesoscopic intermediate, the solid end state, and the relationship that exists between them. We present experimental evidence that these clusters are liquid-like and stable with respect to the parent liquid and metastable compared with the emerging crystalline phase. The presence of these clusters in the bulk liquid is associated with a nonclassical mechanism of crystal growth and can trigger a self-purifying cascade of impurity-poisoned crystal surfaces. These observations demonstrate that there exists a nontrivial connection between the growth of the macroscopic crystalline phase and the mesoscopic intermediate which should not be ignored. On the other hand, our experimental data also show that clusters existing in protein solutions can significantly increase the nucleation rate and therefore play a relevant role in the nucleation process.
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