Explicit all-atom modeling of realistically sized ligand-capped nanocrystals

Handle URI:
http://hdl.handle.net/10754/598286
Title:
Explicit all-atom modeling of realistically sized ligand-capped nanocrystals
Authors:
Kaushik, Ananth P.; Clancy, Paulette
Abstract:
We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes. © 2012 American Institute of Physics.
Citation:
Kaushik AP, Clancy P (2012) Explicit all-atom modeling of realistically sized ligand-capped nanocrystals. J Chem Phys 136: 114702. Available: http://dx.doi.org/10.1063/1.3689973.
Publisher:
AIP Publishing
Journal:
The Journal of Chemical Physics
KAUST Grant Number:
KUS-C1-018-02
Issue Date:
2012
DOI:
10.1063/1.3689973
PubMed ID:
22443785
Type:
Article
ISSN:
0021-9606
Sponsors:
This publication was based on work supported by the Award No. KUS-C1-018-02, made by the King Abdullah University of Science and Technology (KAUST). The Hanrath research group at Cornell is thanked for access to their experimental data in advance of publication. Intel Corporation is thanked for the donation of computing resources crucial to the studies performed here.
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Full metadata record

DC FieldValue Language
dc.contributor.authorKaushik, Ananth P.en
dc.contributor.authorClancy, Pauletteen
dc.date.accessioned2016-02-25T13:18:00Zen
dc.date.available2016-02-25T13:18:00Zen
dc.date.issued2012en
dc.identifier.citationKaushik AP, Clancy P (2012) Explicit all-atom modeling of realistically sized ligand-capped nanocrystals. J Chem Phys 136: 114702. Available: http://dx.doi.org/10.1063/1.3689973.en
dc.identifier.issn0021-9606en
dc.identifier.pmid22443785en
dc.identifier.doi10.1063/1.3689973en
dc.identifier.urihttp://hdl.handle.net/10754/598286en
dc.description.abstractWe present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes. © 2012 American Institute of Physics.en
dc.description.sponsorshipThis publication was based on work supported by the Award No. KUS-C1-018-02, made by the King Abdullah University of Science and Technology (KAUST). The Hanrath research group at Cornell is thanked for access to their experimental data in advance of publication. Intel Corporation is thanked for the donation of computing resources crucial to the studies performed here.en
dc.publisherAIP Publishingen
dc.titleExplicit all-atom modeling of realistically sized ligand-capped nanocrystalsen
dc.typeArticleen
dc.identifier.journalThe Journal of Chemical Physicsen
dc.contributor.institutionCornell University, Ithaca, United Statesen
kaust.grant.numberKUS-C1-018-02en

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