1
|
Santos DS, De Nicola A, dos Santos VF, Milano G, Soares TA. Exploring the Molecular Dynamics of a Lipid-A Vesicle at the Atom Level: Morphology and Permeation Mechanism. J Phys Chem B 2023; 127:6694-6702. [PMID: 37467380 PMCID: PMC10405212 DOI: 10.1021/acs.jpcb.3c02848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/18/2023] [Indexed: 07/21/2023]
Abstract
Lipid-A was previously shown to spontaneously aggregate into a vesicle via the hybrid particle field approach. We assess the validity of the proposed vesiculation mechanism by simulating the resulting lipid-A vesicle at the atom level. The spatial confinement imposed by the vesicle geometry on the conformation and packing of lipid-A induces significant heterogeneity of physical properties in the inner and outer leaflets. It also induces tighter molecular packing and lower acyl chain order compared to the lamellar arrangement. Around 5% of water molecules passively permeates the vesicle membrane inward and outward. The permeation is facilitated by interactions with water molecules that are transported across the membrane by a network of electrostatic interactions with the hydrogen bond donors/acceptors in the N-acetylglucosamine ring and upper region of the acyl chains of lipid-A. The permeation process takes place at low rates but still at higher frequencies than observed for the lamellar arrangement of lipid-A. These findings not only substantiate the proposed lipid-A vesiculation mechanism but also reveal the complex structural dynamics of an important nonlamellar arrangement of lipid-A.
Collapse
Affiliation(s)
- Denys
E. S. Santos
- Departmento
de Química Fundamental, Universidade
Federal de Pernambuco, Recife 50740-560, Brazil
| | - Antonio De Nicola
- Scuola
Superiore Meridionale, Largo S. Marcellino 10, Napoli 80138, Italy
- Graduate
School of Organic Materials Science, Yamagata
University, Yonezawa 992-8510, Yamagata, Japan
| | - Vinicius F. dos Santos
- Departamento
de Química, Faculdade de Filosofia, Ciências e Letras
de Ribeirão Preto, Universidade de
São Paulo, Ribeirão
Preto 14040-901, Brazil
| | - Giuseppe Milano
- Department
of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, Napoli 80125, Italy
| | - Thereza A. Soares
- Departamento
de Química, Faculdade de Filosofia, Ciências e Letras
de Ribeirão Preto, Universidade de
São Paulo, Ribeirão
Preto 14040-901, Brazil
- Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, Norway
| |
Collapse
|
2
|
De Nicola A, Montis C, Donati G, Molinaro A, Silipo A, Balestri A, Berti D, Di Lorenzo F, Zhu YL, Milano G. Bacterial lipids drive compartmentalization on the nanoscale. NANOSCALE 2023; 15:8988-8995. [PMID: 37144495 PMCID: PMC10210972 DOI: 10.1039/d3nr00559c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/21/2023] [Indexed: 05/06/2023]
Abstract
The design of cellular functions in synthetic systems, inspired by the internal partitioning of living cells, is a constantly growing research field that is paving the way to a large number of new remarkable applications. Several hierarchies of internal compartments like polymersomes, liposomes, and membranes are used to control the transport, release, and chemistry of encapsulated species. However, the experimental characterization and the comprehension of glycolipid mesostructures are far from being fully addressed. Lipid A is indeed a glycolipid and the endotoxic part of Gram-negative bacterial lipopolysaccharide; it is the moiety that is recognized by the eukaryotic receptors giving rise to the modulation of innate immunity. Herein we propose, for the first time, a combined approach based on hybrid Particle-Field (hPF) Molecular Dynamics (MD) simulations and Small Angle X-Ray Scattering (SAXS) experiments to gain a molecular picture of the complex supramolecular structures of lipopolysaccharide (LPS) and lipid A at low hydration levels. The mutual support of data from simulations and experiments allowed the unprecedented discovery of the presence of a nano-compartmentalized phase composed of liposomes of variable size and shape which can be used in synthetic biological applications.
Collapse
Affiliation(s)
- Antonio De Nicola
- Scuola Superiore Meridionale, Via Largo San Marcellino 10, 80132 Napoli, Italy
- Graduate School of Organic Materials Science, Yamagata, University, Jonan 4-3-16, Yonezawa, Yamagata, 992-8510, Japan
| | - Costanza Montis
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze and CSGI, 50019 Firenze, Italy.
| | - Greta Donati
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Santangelo, Via Cintia 4, 80126 Napoli, Italy.
| | - Alba Silipo
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Santangelo, Via Cintia 4, 80126 Napoli, Italy.
| | - Arianna Balestri
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze and CSGI, 50019 Firenze, Italy.
| | - Debora Berti
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze and CSGI, 50019 Firenze, Italy.
| | - Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Santangelo, Via Cintia 4, 80126 Napoli, Italy.
| | - You-Liang Zhu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130021, China
| | - Giuseppe Milano
- University of Naples Federico II, Department of Chemical, Materials and Production Engineering, Piazzale V. Tecchio, 80, 80125 Napoli, Italy.
| |
Collapse
|
3
|
Ledum M, Sen S, Bore SL, Cascella M. On the equivalence of the hybrid particle-field and Gaussian core models. J Chem Phys 2023; 158:2890484. [PMID: 37184022 DOI: 10.1063/5.0145142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Hybrid particle-field molecular dynamics is a molecular simulation strategy, wherein particles couple to a density field instead of through ordinary pair potentials. Traditionally considered a mean-field theory, a momentum and energy-conserving hybrid particle-field formalism has recently been introduced, which was demonstrated to approach the Gaussian Core model potential in the grid-converged limit. Here, we expand on and generalize the correspondence between the Hamiltonian hybrid particle-field method and particle-particle pair potentials. Using the spectral procedure suggested by Bore and Cascella, we establish compatibility to any local soft pair potential in the limit of infinitesimal grid spacing. Furthermore, we document how the mean-field regime often observed in hybrid particle-field simulations is due to the systems under consideration, and not an inherent property of the model. Considering the Gaussian filter form, in particular, we demonstrate the ability of the Hamiltonian hybrid particle-field model to recover all structural and dynamical properties of the Gaussian Core model, including solid phases, a first-order phase transition, and anomalous transport properties. We quantify the impact of the grid spacing on the correspondence, as well as the effect of the particle-field filtering length scale on the emergent particle-particle correlations.
Collapse
Affiliation(s)
- Morten Ledum
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Samiran Sen
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| |
Collapse
|
4
|
Bjørnestad VA, Li X, Tribet C, Lund R, Cascella M. Micelle kinetics of photoswitchable surfactants: Self-assembly pathways and relaxation mechanisms. J Colloid Interface Sci 2023; 646:883-899. [PMID: 37235934 DOI: 10.1016/j.jcis.2023.05.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/19/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023]
Abstract
HYPOTHESIS A key question in the kinetics of surfactant self-assembly is whether exchange of unimers or fusion/fission of entire micelles is the dominant pathway. In this study, an isomerizable surfactant is used to explore fundamental out-of-equilibrium kinetics and mechanisms for growth and dissolution of micelles. EXPERIMENTS The kinetics of cationic surfactant 4-butyl-4'-(3-trimethylammoniumpropoxy)-phenylazobenzene was studied using molecular dynamics simulations. The fusion and exchange processes were investigated using umbrella sampling. Equilibrium states were validated by comparison with small-angle X-ray scattering data. The photo-isomerization event was simulated by modifying the torsion potential of the photo-responsive group to emulate the trans-to-cis transition. FINDINGS Micelle growth is dominated by unimer exchange processes, whereas, depending on the conditions, dissolution can occur both through fission and unimer expulsion. Fusion barriers increase steeply with the aggregation number making this an unlikely pathway to equilibrium for micelles of sizes that fit with the experimental data. The barriers for unimer expulsion remain constant and are much lower for unimer insertion, making exchange more likely at high aggregation. When simulating photo-conversion events, both fission and a large degree of unimer expulsion can occur depending on the extent of the out-of-equilibrium stress that is put on the system.
Collapse
Affiliation(s)
- Victoria Ariel Bjørnestad
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Sem Sælands vei 26, Oslo, 0371, Norway
| | - Xinmeng Li
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Sem Sælands vei 26, Oslo, 0371, Norway
| | - Christophe Tribet
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
| | - Reidar Lund
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Sem Sælands vei 26, Oslo, 0371, Norway.
| | - Michele Cascella
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Sem Sælands vei 26, Oslo, 0371, Norway.
| |
Collapse
|
5
|
Ledum M, Sen S, Li X, Carrer M, Feng Y, Cascella M, Bore SL. HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multiscale Simulations of Soft Matter. J Chem Theory Comput 2023; 19:2939-2952. [PMID: 37130290 DOI: 10.1021/acs.jctc.3c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We present HylleraasMD (HyMD), a comprehensive implementation of the recently proposed Hamiltonian formulation of hybrid particle-field molecular dynamics. The methodology is based on a tunable, grid-independent length-scale of coarse graining, obtained by filtering particle densities in reciprocal space. This enables systematic convergence of energies and forces by grid refinement, also eliminating nonphysical force aliasing. Separating the time integration of fast modes associated with internal molecular motion from slow modes associated with their density fields, we enable the first time-reversible, energy-conserving hybrid particle-field simulations. HyMD comprises the optional use of explicit electrostatics, which, in this formalism, corresponds to the long-range potential in particle-mesh Ewald. We demonstrate the ability of HyMD to perform simulations in the microcanonical and canonical ensembles with a series of test cases, comprising lipid bilayers and vesicles, surfactant micelles, and polypeptide chains, comparing our results to established literature. An on-the-fly increase of the characteristic coarse-grain length significantly speeds up dynamics, accelerating self-diffusion and leading to expedited aggregation. Exploiting this acceleration, we find that the time scales involved in the self-assembly of polymeric structures can lie in the tens to hundreds of picoseconds instead of the multimicrosecond regime observed with comparable coarse-grained models.
Collapse
Affiliation(s)
- Morten Ledum
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Samiran Sen
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Xinmeng Li
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Manuel Carrer
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Yu Feng
- Berkeley Center for Cosmological Physics and Department of Physics, University of California, Berkeley, California 94720, United States
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| |
Collapse
|
6
|
Sen S, Ledum M, Bore SL, Cascella M. Soft Matter under Pressure: Pushing Particle–Field Molecular Dynamics to the Isobaric Ensemble. J Chem Inf Model 2023; 63:2207-2217. [PMID: 36976890 PMCID: PMC10091448 DOI: 10.1021/acs.jcim.3c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Hamiltonian hybrid particle-field molecular dynamics is a computationally efficient method to study large soft matter systems. In this work, we extend this approach to constant-pressure (NPT) simulations. We reformulate the calculation of internal pressure from the density field by taking into account the intrinsic spread of the particles in space, which naturally leads to a direct anisotropy in the pressure tensor. The anisotropic contribution is crucial for reliably describing the physics of systems under pressure, as demonstrated by a series of tests on analytical and monatomic model systems as well as realistic water/lipid biphasic systems. Using Bayesian optimization, we parametrize the field interactions of phospholipids to reproduce the structural properties of their lamellar phases, including area per lipid, and local density profiles. The resulting model excels in providing pressure profiles in qualitative agreement with all-atom modeling, and surface tension and area compressibility in quantitative agreement with experimental values, indicating the correct description of long-wavelength undulations in large membranes. Finally, we demonstrate that the model is capable of reproducing the formation of lipid droplets inside a lipid bilayer.
Collapse
|
7
|
Schmid F. Understanding and Modeling Polymers: The Challenge of Multiple Scales. ACS POLYMERS AU 2022. [DOI: 10.1021/acspolymersau.2c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128Mainz, Germany
| |
Collapse
|
8
|
Gao H, Shi R, Zhu Y, Qian H, Lu Z. Coarse-grained Dynamics Simulation in Polymer Systems: from Structures to Material Properties. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-022-2080-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
9
|
Lavagnini E, Cook JL, Warren PB, Hunter CA. Systematic Parameterization of Ion-Surfactant Interactions in Dissipative Particle Dynamics Using Setschenow Coefficients. J Phys Chem B 2022; 126:2308-2315. [PMID: 35290050 PMCID: PMC9098171 DOI: 10.1021/acs.jpcb.2c00101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Dissipative
particle dynamics (DPD) simulations of nonionic surfactants
with an added salt show that the Setschenow relationship is reproduced;
that is, the critical micelle concentration is log-linearly dependent
on the added salt concentration. The simulated Setschenow coefficients
depend on the DPD bead–bead repulsion amplitudes, and matching
to the experimentally determined values provides a systematic method
to parameterize the interactions between salt ion beads and surfactant
beads. The optimized ion-specific interaction parameters appear to
be transferrable and follow the same trends as the empirical Hofmeister
series.
Collapse
Affiliation(s)
- Ennio Lavagnini
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Joanne L Cook
- Unilever R&D Port Sunlight, Quarry Road East, Bebington CH63 3JW, U.K
| | - Patrick B Warren
- Unilever R&D Port Sunlight, Quarry Road East, Bebington CH63 3JW, U.K.,STFC Hartree Centre, Sci-Tech Daresbury, Warrington WA4 4AD, U.K
| | - Christopher A Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| |
Collapse
|
10
|
Wu Z, Alberti SAN, Schneider J, Müller-Plathe F. Knotting behaviour of polymer chains in the melt state for soft-core models with and without slip-springs. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:244001. [PMID: 33725671 DOI: 10.1088/1361-648x/abef25] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
We analyse the knotting behaviour of linear polymer melts in two types of soft-core models, namely dissipative-particle dynamics and hybrid-particle-field models, as well as their variants with slip-springs which are added to recover entangled polymer dynamics. The probability to form knots is found drastically higher in the hybrid-particle-field model compared to its parent hard-core molecular dynamics model. By comparing the knottedness in dissipative-particle dynamics and hybrid-particle-field models with and without slip-springs, we find the impact of slip-springs on the knotting properties to be negligible. As a dynamic property, we measure the characteristic time of knot formation and destruction, and find it to be (i) of the same order as single-monomer motion and (ii) independent of the chain length in all soft-core models. Knots are therefore formed and destroyed predominantly by the unphysical chain crossing. This work demonstrates that the addition of slip-springs does not alter the knotting behaviour, and it provides a general understanding of knotted structures in these two soft-core models of polymer melts.
Collapse
Affiliation(s)
- Zhenghao Wu
- Technical University of Darmstadt, Eduard-Zintl-Institute for Inorganic and Physical Chemistry and Profile Area Thermofluids and Interfaces, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
| | - Simon A N Alberti
- Technical University of Darmstadt, Eduard-Zintl-Institute for Inorganic and Physical Chemistry and Profile Area Thermofluids and Interfaces, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
| | - Jurek Schneider
- Technical University of Darmstadt, Eduard-Zintl-Institute for Inorganic and Physical Chemistry and Profile Area Thermofluids and Interfaces, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Technical University of Darmstadt, Eduard-Zintl-Institute for Inorganic and Physical Chemistry and Profile Area Thermofluids and Interfaces, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
| |
Collapse
|
11
|
Schäfer K, Kolli HB, Killingmoe Christensen M, Bore SL, Diezemann G, Gauss J, Milano G, Lund R, Cascella M. Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles. Angew Chem Int Ed Engl 2020; 59:18591-18598. [PMID: 32543728 PMCID: PMC7589243 DOI: 10.1002/anie.202004522] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/29/2020] [Indexed: 12/16/2022]
Abstract
The shape and size of self-assembled structures upon local organization of their molecular building blocks are hard to predict in the presence of long-range interactions. Combining small-angle X-ray/neutron scattering data, theoretical modelling, and computer simulations, sodium dodecyl sulfate (SDS), over a broad range of concentrations and ionic strengths, was investigated. Computer simulations indicate that micellar shape changes are associated with different binding of the counterions. By employing a toy model based on point charges on a surface, and comparing it to experiments and simulations, it is demonstrated that the observed morphological changes are caused by symmetry breaking of the irreducible building blocks, with the formation of transient surfactant dimers mediated by the counterions that promote the stabilization of cylindrical instead of spherical micelles. The present model is of general applicability and can be extended to all systems controlled by the presence of mobile charges.
Collapse
Affiliation(s)
- Ken Schäfer
- Department ChemieJohannes Gutenberg-Universität MainzDuesbergweg 10–1455128MainzGermany
| | - Hima Bindu Kolli
- Department of Physics and AstronomyThe University of SheffieldWestern BankSheffieldS10 2TNUK
| | - Mikkel Killingmoe Christensen
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
| | - Gregor Diezemann
- Department ChemieJohannes Gutenberg-Universität MainzDuesbergweg 10–1455128MainzGermany
| | - Jürgen Gauss
- Department ChemieJohannes Gutenberg-Universität MainzDuesbergweg 10–1455128MainzGermany
| | - Giuseppe Milano
- Department of Organic Materials ScienceYamagata University4-3-16 JonanYonezawaYamagata-ken992-8510Japan
| | - Reidar Lund
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
| |
Collapse
|
12
|
Wu Z, Kalogirou A, De Nicola A, Milano G, Müller‐Plathe F. Atomistic hybrid
particle‐field
molecular dynamics combined with
slip‐springs
: Restoring entangled dynamics to simulations of polymer melts. J Comput Chem 2020; 42:6-18. [DOI: 10.1002/jcc.26428] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/07/2020] [Accepted: 09/11/2020] [Indexed: 02/03/2023]
Affiliation(s)
- Zhenghao Wu
- Eduard‐Zintl‐Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt Darmstadt Germany
| | - Andreas Kalogirou
- Eduard‐Zintl‐Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt Darmstadt Germany
| | - Antonio De Nicola
- Department of Organic Materials Science Yamagata University Yamagata‐ken Japan
| | - Giuseppe Milano
- Department of Organic Materials Science Yamagata University Yamagata‐ken Japan
| | - Florian Müller‐Plathe
- Eduard‐Zintl‐Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt Darmstadt Germany
| |
Collapse
|
13
|
Bore SL, Cascella M. Hamiltonian and alias-free hybrid particle–field molecular dynamics. J Chem Phys 2020; 153:094106. [DOI: 10.1063/5.0020733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern 0315, Oslo, Norway
| | - Michele Cascella
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern 0315, Oslo, Norway
| |
Collapse
|
14
|
Schäfer K, Kolli HB, Killingmoe Christensen M, Bore SL, Diezemann G, Gauss J, Milano G, Lund R, Cascella M. Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004522] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ken Schäfer
- Department Chemie Johannes Gutenberg-Universität Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Hima Bindu Kolli
- Department of Physics and Astronomy The University of Sheffield Western Bank Sheffield S10 2TN UK
| | - Mikkel Killingmoe Christensen
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
| | - Gregor Diezemann
- Department Chemie Johannes Gutenberg-Universität Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Jürgen Gauss
- Department Chemie Johannes Gutenberg-Universität Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Giuseppe Milano
- Department of Organic Materials Science Yamagata University 4-3-16 Jonan Yonezawa Yamagata-ken 992-8510 Japan
| | - Reidar Lund
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
| |
Collapse
|
15
|
Carrer M, Škrbić T, Bore SL, Milano G, Cascella M, Giacometti A. Can Polarity-Inverted Surfactants Self-Assemble in Nonpolar Solvents? J Phys Chem B 2020; 124:6448-6458. [PMID: 32618191 PMCID: PMC8009519 DOI: 10.1021/acs.jpcb.0c04842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
We investigate the
self-assembly process of a surfactant with inverted
polarity in water and cyclohexane using both all-atom and coarse-grained
hybrid particle-field molecular dynamics simulations. Unlike conventional
surfactants, the molecule under study, proposed in a recent experiment,
is formed by a rigid and compact hydrophobic adamantane moiety, and
a long and floppy triethylene glycol tail. In water, we report the
formation of stable inverted micelles with the adamantane heads grouping
together into a hydrophobic core and the tails forming hydrogen bonds
with water. By contrast, microsecond simulations do not provide evidence
of stable micelle formation in cyclohexane. Validating the computational
results by comparison with experimental diffusion constant and small-angle
X-ray scattering intensity, we show that at laboratory thermodynamic
conditions the mixture resides in the supercritical region of the
phase diagram, where aggregated and free surfactant states coexist
in solution. Our simulations also provide indications as to how to
escape this region to produce thermodynamically stable micellar aggregates.
Collapse
Affiliation(s)
- Manuel Carrer
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Tatjana Škrbić
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, United States.,Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia,Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, 992-8510 Yamagata-ken, Japan.,Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia,Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy.,European Centre for Living Technology (ECLT) Ca' Bottacin, 3911 Dorsoduro, Calle Crosera, 30123 Venice, Italy
| |
Collapse
|
16
|
Ledum M, Løland Bore S, Cascella M. Automated determination of hybrid particle-field parameters by machine learning. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1785571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Morten Ledum
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| |
Collapse
|
17
|
Bore SL, Kolli HB, De Nicola A, Byshkin M, Kawakatsu T, Milano G, Cascella M. Hybrid particle-field molecular dynamics under constant pressure. J Chem Phys 2020; 152:184908. [PMID: 32414244 DOI: 10.1063/5.0007445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hybrid particle-field methods are computationally efficient approaches for modeling soft matter systems. So far, applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field interactions to represent systems coupled to constant external pressure. First, we show that the commonly used particle-field energy functional can be modified to model and parameterize the isotropic contributions to the pressure tensor without interfering with the microscopic forces on the particles. Second, we employ a square gradient particle-field interaction term to model non-isotropic contributions to the pressure tensor, such as in surface tension phenomena. This formulation is implemented within the hybrid particle-field molecular dynamics approach and is tested on a series of model systems. Simulations of a homogeneous water box demonstrate that it is possible to parameterize the equation of state to reproduce any target density for a given external pressure. Moreover, the same parameterization is transferable to systems of similar coarse-grained mapping resolution. Finally, we evaluate the feasibility of the proposed approach on coarse-grained models of phospholipids, finding that the term between water and the lipid hydrocarbon tails is alone sufficient to reproduce the experimental area per lipid in constant-pressure simulations and to produce a qualitatively correct lateral pressure profile.
Collapse
Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Hima Bindu Kolli
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Antonio De Nicola
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata-ken 992-8510, Japan
| | - Maksym Byshkin
- Institute of Computational Science, Università Della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata-ken 992-8510, Japan
| | - Michele Cascella
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| |
Collapse
|
18
|
Jiang J, Chen X, Yang S, Chen EQ. The size and affinity effect of counterions on self-assembly of charged block copolymers. J Chem Phys 2020; 152:124901. [PMID: 32241155 DOI: 10.1063/5.0002896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The effect of counterions' size and affinity on the microphase separated morphologies of neutral-charged diblock copolymers is investigated systematically using a random phase approximation (RPA) and self-consistent field theory (SCFT). The phase diagrams as a function of χAB and fA at different counterion sizes and different affinities to neutral blocks are constructed, respectively. Stability limits calculated using the RPA are in good agreement with the disorder-body-centered cubic phase boundaries from SCFT calculations. It was found that increasing the size of counterions causes the phase diagram to shift upward and leftward, which is attributed to electrostatic interactions and the intrinsic volume of counterions. The domain size of the ordered phase shows an unexpected tendency that it decreases with increasing counterions' size. The counterions' distributions in H and G phases demonstrate that it is electrostatic interaction, instead of packing frustration, that plays a leading role in such systems. For finite size counterions, with the increase in affinity between counterions and neutral blocks, the phase diagram shifts upward, indicating the improved compatibility between different blocks. Furthermore, the affinity effect between counterions and neutral blocks can be mapped into an effective Flory parameter χAB ' = χAB + 0.27χBC.
Collapse
Affiliation(s)
- Jiadi Jiang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| | - Xu Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| | - Shuang Yang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| | - Er-Qiang Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| |
Collapse
|
19
|
Aggregation of Lipid A Variants: A Hybrid Particle-Field Model. Biochim Biophys Acta Gen Subj 2020; 1865:129570. [PMID: 32105775 DOI: 10.1016/j.bbagen.2020.129570] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/10/2020] [Accepted: 02/19/2020] [Indexed: 12/23/2022]
Abstract
Lipid A is one of the three components of bacterial lipopolysaccharides constituting the outer membrane of Gram-negative bacteria, and is recognized to have an important biological role in the inflammatory response of mammalians. Its biological activity is modulated by the number of acyl-chains that are present in the lipid and by the dielectric medium, i.e., the type of counter-ions, through electrostatic interactions. In this paper, we report on a coarse-grained model of chemical variants of Lipid A based on the hybrid particle-field/molecular dynamics approach (hPF-MD). In particular, we investigate the stability of Lipid A bilayers for two different hexa- and tetra-acylated structures. Comparing particle density profiles along bilayer cross-sections, we find good agreement between the hPF-MD model and reference all-atom simulation for both chemical variants of Lipid A. hPF-MD models of constituted bilayers composed by hexa-acylated Lipid A in water are stable within the simulation time. We further validate our model by verifying that the phase behavior of Lipid A/counterion/water mixtures is correctly reproduced. In particular, hPF-MD simulations predict the correct self-assembly of different lamellar and micellar phases from an initially random distribution of Lipid A molecules with counterions in water. Finally, it is possible to observe the spontaneous formation and stability of Lipid A vesicles by fusion of micellar aggregates.
Collapse
|
20
|
Bore SL, Kolli HB, Kawakatsu T, Milano G, Cascella M. Mesoscale Electrostatics Driving Particle Dynamics in Nonhomogeneous Dielectrics. J Chem Theory Comput 2019; 15:2033-2041. [DOI: 10.1021/acs.jctc.8b01201] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Hima Bindu Kolli
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Miyagi, Japan
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan ,Yonezawa, Yamagata-ken 992-8510, Japan
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| |
Collapse
|