Leveraging the anisotropic shape of DNA-functionalized nanoparticles holds potential for shape-directed crystallization of a wide collection of superlattice structures. Using coarse-grained molecular dynamics simulations, we study the self-assembly of a binary mixture of cubic gold nanoparticles, which are functionalized by complementary DNA strands. We observe the spontaneous self-assembly of simple cubic (SC), plastic body-centered tetragonal (pBCT), and compositionally disordered plastic body-centered tetragonal (d-pBCT) phases due to hybridization of the DNA strands. We systematically investigate the effect of length, grafting density, as well as rigidity of the DNA strands on the self-assembly behavior of cubic nanoparticles. We measure the potential of mean force between DNA-functionalized nanocubes for varying rigidity of the DNA strands and DNA lengths. Using free-energy calculations, we find that longer and flexible DNA strands can lead to a phase transformation from SC to the pBCT phase due to a gain in entropy arising from the orientational degrees of freedom of the nanocubes in the pBCT phase. Our results may serve as a guide for self-assembly experiments on DNA-functionalized cubic nanoparticles.
REFERENCES
1.
M.
Dijkstra
and E.
Luijten
, “From predictive modelling to machine learning and reverse engineering of colloidal self-assembly
,” Nat. Mater.
20
, 762
–773
(2021
).2.
L.
Adler-Abramovich
, N.
Kol
, I.
Yanai
, D.
Barlam
, R. Z.
Shneck
, E.
Gazit
, and I.
Rousso
, “Self-assembled organic nanostructures with metallic-like stiffness
,” Angew. Chem., Int. Ed.
122
, 10135
–10138
(2010
).3.
X.-B.
Li
, Y.-J.
Gao
, Y.
Wang
, F.
Zhan
, X.-Y.
Zhang
, Q.-Y.
Kong
, N.-J.
Zhao
, Q.
Guo
, H.-L.
Wu
, Z.-J.
Li
et al, “Self-assembled framework enhances electronic communication of ultrasmall-sized nanoparticles for exceptional solar hydrogen evolution
,” J. Am. Chem. Soc.
139
, 4789
–4796
(2017
).4.
J. F.
Shin
, W.
Xu
, M.
Zanella
, K.
Dawson
, S. N.
Savvin
, J. B.
Claridge
, and M. J.
Rosseinsky
, “Self-assembled dynamic perovskite composite cathodes for intermediate temperature solid oxide fuel cells
,” Nat. Energy
2
, 16214
(2017
).5.
Y. D.
Park
, A. T.
Hanbicki
, S. C.
Erwin
, C. S.
Hellberg
, J. M.
Sullivan
, J. E.
Mattson
, T. F.
Ambrose
, A.
Wilson
, G.
Spanos
, and B. T.
Jonker
, “A group-IV ferromagnetic semiconductor: MnxGe1−x
,” Science
295
, 651
–654
(2002
).6.
H.
Wu
, G.
Chan
, J. W.
Choi
, I.
Ryu
, Y.
Yao
, M. T.
McDowell
, S. W.
Lee
, A.
Jackson
, Y.
Yang
, L.
Hu
and Y.
Cui
, “Stable cycling of double-walled silicon nanotube battery anodes through solid–electrolyte interphase control
,” Nat. Nanotechnol.
7
, 310
–315
(2012
).7.
C. A.
Mirkin
, “The polyvalent gold nanoparticle conjugate—Materials synthesis, biodiagnostics, and intracellular gene regulation
,” MRS Bull.
35
, 532
–539
(2010
).8.
U.
Agarwal
and F. A.
Escobedo
, “Mesophase behaviour of polyhedral particles
,” Nat. Mater.
10
, 230
–235
(2011
).9.
P. F.
Damasceno
, M.
Engel
, and S. C.
Glotzer
, “Predictive self-assembly of polyhedra into complex structures
,” Science
337
, 453
–457
(2012
).10.
M.
Dijkstra
, “Entropy-driven phase transitions in colloids: From spheres to anisotropic particles
,” Adv. Chem. Phys.
156
, 35
(2014
).11.
M. A.
Boles
, M.
Engel
, and D. V.
Talapin
, “Self-assembly of colloidal nanocrystals: From intricate structures to functional materials
,” Chem. Rev.
116
, 11220
–11289
(2016
).12.
S.
Torquato
and Y.
Jiao
, “Dense packings of the platonic and archimedean solids
,” Nature
460
, 876
–879
(2009
).13.
J.
de Graaf
, R.
van Roij
, and M.
Dijkstra
, “Dense regular packings of irregular nonconvex particles
,” Phys. Rev. Lett.
107
, 155501
(2011
).14.
J.
de Graaf
, L.
Filion
, M.
Marechal
, R.
van Roij
, and M.
Dijkstra
, “Crystal-structure prediction via the floppy-box Monte Carlo algorithm: Method and application to hard (non) convex particles
,” J. Chem. Phys.
137
, 214101
(2012
).15.
C. A.
Mirkin
, R. L.
Letsinger
, R. C.
Mucic
, and J. J.
Storhoff
, “A DNA-based method for rationally assembling nanoparticles into macroscopic materials
,” Nature
382
, 607
–609
(1996
).16.
A. P.
Alivisatos
, K. P.
Johnsson
, X.
Peng
, T. E.
Wilson
, C. J.
Loweth
, M. P.
Bruchez
, and P. G.
Schultz
, “Organization of “nanocrystal molecules” using DNA
,” Nature
382
, 609
–611
(1996
).17.
D.
Nykypanchuk
, M. M.
Maye
, D.
van der Lelie
, and O.
Gang
, “DNA-guided crystallization of colloidal nanoparticles
,” Nature
451
, 549
–552
(2008
).18.
R. J.
Macfarlane
, B.
Lee
, M. R.
Jones
, N.
Harris
, G. C.
Schatz
, and C. A.
Mirkin
, “Nanoparticle superlattice engineering with DNA
,” Science
334
, 204
–208
(2011
).19.
M. R.
Jones
, R. J.
Macfarlane
, B.
Lee
, J.
Zhang
, K. L.
Young
, A. J.
Senesi
, and C. A.
Mirkin
, “DNA-nanoparticle superlattices formed from anisotropic building blocks
,” Nat. Mater.
9
, 913
–917
(2010
).20.
C. R.
Laramy
, M. N.
O’Brien
, and C. A.
Mirkin
, “Crystal engineering with DNA
,” Nat. Rev. Mater.
4
, 201
–224
(2019
).21.
W. B.
Rogers
, W. M.
Shih
, and V. N.
Manoharan
, “Using DNA to program the self-assembly of colloidal nanoparticles and microparticles
,” Nat. Rev. Mater.
1
, 16008
(2016
).22.
M.
Girard
, S.
Wang
, J. S.
Du
, A.
Das
, Z.
Huang
, V. P.
Dravid
, B.
Lee
, C. A.
Mirkin
, and M.
Olvera de la Cruz
, “Particle analogs of electrons in colloidal crystals
,” Science
364
, 1174
–1178
(2019
).23.
X.
Zhou
, D.
Yao
, W.
Hua
, N.
Huang
, X.
Chen
, L.
Li
, M.
He
, Y.
Zhang
, Y.
Guo
, S.
Xiao
et al, “Programming colloidal bonding using DNA strand-displacement circuitry
,” Proc. Natl. Acad. Sci. U. S. A.
117
, 5617
–5623
(2020
).24.
W. B.
Rogers
and V. N.
Manoharan
, “Programming colloidal phase transitions with DNA strand displacement
,” Science
347
, 639
–642
(2015
).25.
Q.
Yu
, X.
Zhang
, Y.
Hu
, Z.
Zhang
, and R.
Wang
, “Dynamic properties of DNA-programmable nanoparticle crystallization
,” ACS Nano
10
, 7485
–7492
(2016
).26.
C.
Knorowski
, S.
Burleigh
, and A.
Travesset
, “Dynamics and statics of DNA-programmable nanoparticle self-assembly and crystallization
,” Phys. Rev. Lett.
106
, 215501
(2011
).27.
T. I. N. G.
Li
, R.
Sknepnek
, and M.
Olvera de la Cruz
, “Thermally active hybridization drives the crystallization of DNA-functionalized nanoparticles
,” J. Am. Chem. Soc.
135
, 8535
–8541
(2013
).28.
T. I. N. G.
Li
, R.
Sknepnek
, R. J.
Macfarlane
, C. A.
Mirkin
, and M.
Olvera de la Cruz
, “Modeling the crystallization of spherical nucleic acid nanoparticle conjugates with molecular dynamics simulations
,” Nano Lett.
12
, 2509
–2514
(2012
).29.
G.
Zhu
, Z.
Xu
, Y.
Yang
, X.
Dai
, and L.-T.
Yan
, “Hierarchical crystals formed from DNA-functionalized Janus nanoparticles
,” ACS Nano
12
, 9467
–9475
(2018
).30.
M. N.
O’Brien
, M. R.
Jones
, B.
Lee
, and C. A.
Mirkin
, “Anisotropic nanoparticle complementarity in DNA-mediated co-crystallization
,” Nat. Mater.
14
, 833
–839
(2015
).31.
R. N.
Kress
and M. R.
Jones
, “Colloidal interactions get patchy and directional
,” Proc. Natl. Acad. Sci. U. S. A.
117
, 15382
–15384
(2020
).32.
F.
Smallenburg
, L.
Filion
, M.
Marechal
, and M.
Dijkstra
, “Vacancy-stabilized crystalline order in hard cubes
,” Proc. Natl. Acad. Sci. U. S. A.
109
, 17886
–17890
(2012
).33.
A. P.
Gantapara
, J.
de Graaf
, R.
van Roij
, and M.
Dijkstra
, “Phase diagram and structural diversity of a family of truncated cubes: Degenerate close-packed structures and vacancy-rich states
,” Phys. Rev. Lett.
111
, 015501
(2013
).34.
A. P.
Gantapara
, J.
de Graaf
, R.
van Roij
, and M.
Dijkstra
, “Phase behavior of a family of truncated hard cubes
,” J. Chem. Phys.
142
, 054904
(2015
).35.
R. D.
Batten
, F. H.
Stillinger
, and S.
Torquato
, “Phase behavior of colloidal superballs: Shape interpolation from spheres to cubes
,” Phys. Rev. E
81
, 061105
(2010
).36.
R.
Ni
, A. P.
Gantapara
, J.
Dde Graaf
, R.
van Roij
, and M.
Dijkstra
, “Phase diagram of colloidal hard superballs: From cubes via spheres to octahedra
,” Soft Matter
8
, 8826
–8834
(2012
).37.
L.
Rossi
, S.
Sacanna
, W. T. M.
Irvine
, P. M.
Chaikin
, D. J.
Pine
, and A. P.
Philipse
, “Cubic crystals from cubic colloids
,” Soft Matter
7
, 4139
–4142
(2011
).38.
J.-M.
Meijer
, A.
Pal
, S.
Ouhajji
, H. N.
Lekkerkerker
, A. P.
Philipse
, and A. V.
Petukhov
, “Observation of solid–solid transitions in 3D crystals of colloidal superballs
,” Nat. Commun.
8
, 14352
(2017
).39.
J.
Henzie
, M.
Grünwald
, A.
Widmer-Cooper
, P. L.
Geissler
, and P.
Yang
, “Self-assembly of uniform polyhedral silver nanocrystals into densest packings and exotic superlattices
,” Nat. Mater.
11
, 131
–137
(2012
).40.
C.
Avci
, I.
Imaz
, A.
Carné-Sánchez
, J. A.
Pariente
, N.
Tasios
, J.
Pérez-Carvajal
, M. I.
Alonso
, A.
Blanco
, M.
Dijkstra
, C.
López
and D.
Maspoch
, “Self-assembly of polyhedral metal–organic framework particles into three-dimensional ordered superstructures
,” Nat. Chem.
10
, 78
–84
(2018
).41.
A.
Klinkova
, H.
Thérien-Aubin
, A.
Ahmed
, D.
Nykypanchuk
, R. M.
Choueiri
, B.
Gagnon
, A.
Muntyanu
, O.
Gang
, G. C.
Walker
, and E.
Kumacheva
, “Structural and optical properties of self-assembled chains of plasmonic nanocubes
,” Nano Lett.
14
, 6314
–6321
(2014
).42.
B.
Gao
, G.
Arya
, and A. R.
Tao
, “Self-orienting nanocubes for the assembly of plasmonic nanojunctions
,” Nat. Nanotechnol.
7
, 433
–437
(2012
).43.
K. L.
Gurunatha
, S.
Marvi
, G.
Arya
, and A. R.
Tao
, “Computationally guided assembly of oriented nanocubes by modulating grafted polymer–surface interactions
,” Nano Lett.
15
, 7377
–7382
(2015
).44.
W. H.
Evers
, B.
Goris
, S.
Bals
, M.
Casavola
, J.
De Graaf
, R.
van Roij
, M.
Dijkstra
, and D.
Vanmaekelbergh
, “Low-dimensional semiconductor superlattices formed by geometric control over nanocrystal attachment
,” Nano Lett.
13
, 2317
–2323
(2013
).45.
J. J.
Geuchies
, C.
Van Overbeek
, W. H.
Evers
, B.
Goris
, A.
De Backer
, A. P.
Gantapara
, F. T.
Rabouw
, J.
Hilhorst
, J. L.
Peters
, O.
Konovalov
et al, “In situ study of the formation mechanism of two-dimensional superlattices from PbSe nanocrystals
,” Nat. Mater.
15
, 1248
–1254
(2016
).46.
C.
Anzivino
, G.
Soligno
, R.
van Roij
, and M.
Dijkstra
, “Chains of cubic colloids at fluid–fluid interfaces
,” Soft Matter
17
, 965
–975
(2021
).47.
G.
Soligno
and D.
Vanmaekelbergh
, “Understanding the formation of PbSe honeycomb superstructures by dynamics simulations
,” Phys. Rev. X
9
, 021015
(2019
).48.
G.
Soligno
, M.
Dijkstra
, and R.
van Roij
, “Self-assembly of cubic colloidal particles at fluid–fluid interfaces by hexapolar capillary interactions
,” Soft Matter
14
, 42
–60
(2018
).49.
G.
Soligno
, M.
Dijkstra
, and R.
van Roij
, “Self-assembly of cubes into 2D hexagonal and honeycomb lattices by hexapolar capillary interactions
,” Phys. Rev. Lett.
116
, 258001
(2016
).50.
M. N.
O’Brien
, M.
Girard
, H.-X.
Lin
, J. A.
Millan
, M.
Olvera de la Cruz
, B.
Lee
, and C. A.
Mirkin
, “Exploring the zone of anisotropy and broken symmetries in DNA-mediated nanoparticle crystallization
,” Proc. Natl. Acad. Sci. U. S. A.
113
, 10485
–10490
(2016
).51.
F.
Lu
, T.
Vo
, Y.
Zhang
, A.
Frenkel
, K. G.
Yager
, S.
Kumar
, and O.
Gang
, “Unusual packing of soft-shelled nanocubes
,” Sci. Adv.
5
, eaaw2399
(2019
).52.
J. A.
Anderson
, C. D.
Lorenz
, and A.
Travesset
, “General purpose molecular dynamics simulations fully implemented on graphics processing units
,” J. Chem. Phys.
227
, 5342–5359 (2008
).53.
T. D.
Nguyen
, C. L.
Phillips
, J. A.
Anderson
, and S. C.
Glotzer
, “Rigid body constraints realized in massively-parallel molecular dynamics on graphics processing units
,” Comput. Phys. Commun.
182
, 2307
–2313
(2011
).54.
J. A.
Anderson
, J.
Glaser
, and S. C.
Glotzer
, “HOOMD-blue: A python package for high-performance molecular dynamics and hard particle Monte Carlo simulations
,” Comput. Mater. Sci.
173
, 109363
(2020
).55.
P.
Bartlett
and A. I.
Campbell
, “Three-dimensional binary superlattices of oppositely charged colloids
,” Phys. Rev. Lett.
95
, 128302
(2005
).56.
R.
Mao
, J.
O’Leary
, A.
Mesbah
, and J.
Mittal
, “A deep learning framework discovers compositional order and self-assembly pathways in binary colloidal mixtures
,” JACS Au.
2
, 1818
–1828
(2022
).57.
G.
Hou
, X.
Xia
, J.
Liu
, W.
Wang
, M.
Dong
, and L.
Zhang
, “Designing superlattice structure via self-assembly of one-component polymer-grafted nanoparticles
,” J. Phys. Chem. B
123
, 2157
–2168
(2019
).58.
M. X.
Wang
, J. D.
Brodin
, J. A.
Millan
, S. E.
Seo
, M.
Girard
, M.
Olvera de la Cruz
, B.
Lee
, and C. A.
Mirkin
, “Altering DNA-programmable colloidal crystallization paths by modulating particle repulsion
,” Nano Lett.
17
, 5126
–5132
(2017
).59.
P. D.
Duncan
, M.
Dennison
, A. J.
Masters
, and M. R.
Wilson
, “Theory and computer simulation for the cubatic phase of cut spheres
,” Phys. Rev. E
79
, 031702
(2009
).60.
R. V.
Thaner
, Y.
Kim
, T. I. N. G.
Li
, R. J.
Macfarlane
, S. T.
Nguyen
, M.
Olvera de la Cruz
, and C. A.
Mirkin
, “Entropy-driven crystallization behavior in DNA-mediated nanoparticle assembly
,” Nano Lett.
15
, 5545
–5551
(2015
).61.
E. J.
Meijer
, D.
Frenkel
, R. A.
LeSar
, and A. J. C.
Ladd
, “Location of melting point at 300 K of nitrogen by Monte Carlo simulation
,” J. Chem. Phys.
92
, 7570
–7575
(1990
).62.
Z.
Fan
and M.
Grünwald
, “Orientational order in self-assembled nanocrystal superlattices
,” J. Am. Chem. Soc.
141
, 1980
–1988
(2019
).63.
M. P.
Howard
, A. Z.
Panagiotopoulos
, and A.
Nikoubashman
, “Efficient mesoscale hydrodynamics: Multiparticle collision dynamics with massively parallel GPU acceleration
,” Comput. Phys. Commun.
230
, 10
–20
(2018
).© 2023 Author(s). Published under an exclusive license by AIP Publishing.
2023
Author(s)
You do not currently have access to this content.
