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Clathrate colloidal crystals

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Science  03 Mar 2017:
Vol. 355, Issue 6328, pp. 931-935
DOI: 10.1126/science.aal3919
  • Fig. 1 Self-assembly into clathrate colloidal crystals.

    (A) Geometry and scanning electron microscopy (SEM) image of gold TBPs with {110} facets and 109.5° large-edge angle. (B) When placing TBPs at the middle of network edges and rotating them appropriately, all triangular TBP facets align nearly parallel. In the resulting tetrahedral network, polar tips join at network nodes, and equatorial tips join in the center of network cages. (C) Illustration of the DNA linker design. The linker binds to the surface of Au bipyramid through a 28-base hexylthiol-anchor strand (red), which can recognize a linker strand (blue). Duplexer strands (green) hybridize the linker strand to form double-strand segments, except for specific single-base sites (black) and the four-base self-complementary sticky end. DNA length can be tuned by varying the number of duplexed block segments. (D) The TBP tetramer with its DNA shell has rounded edges and vertices. (E) Whole-view SEM image of the self-assembled TBP superlattice. (F and G) TEM images of the superlattice zoomed in on single-domain and multidomain regions, respectively, from a sectioned sample.

  • Fig. 2 Effect of DNA length on TBP assembly and presence of cavities.

    (A to F) SEM images of samples by using TBP particles with DNA bonding elements that contain (A) zero-, (B) one-, (C) two-, (D) three-, (E) four-, and (F) five-block segments paired with duplexer strands. An improvement of the assembly quality with the increase of the block segment number is apparent. (G) Cavities are observed in the middle of the clusters representing clathrate cages. Shown in this TEM image is a thin sectioned sample that contains the middle portion of clusters showing the empty spaces (center of the image) and off-center sectioned clusters, including the upper part of the clusters (top left) (fig. S13H). The particles in this sample have DNA ligands with five block segments. (H) Illustration of a single cluster (identified as cluster C) (Fig. 3D) before and after removing the top and bottom TBPs.

  • Fig. 3 Model and simulation of DNA-tethered nanocrystals.

    (A) The nanocrystal core (TBP) is surrounded by a wide shell of double-stranded DNA (ds-DNA) that terminates in a narrow shell of single-stranded DNA (ss-DNA). The interaction of PAEs is captured by an effective pair potential consisting of a Weeks-Chandler-Anderson (WCA) repulsion upon shell overlap plus a double-Gaussian model (DGM) attraction representing DNA hybridization of the ss-DNA. (B) Nanocrystals with DNA ligands containing five-block segments (68.7 nm length) cluster together in a simulation snapshot and spontaneously order. Without the DNA shell, local motifs of clathrates II and IV structure are identified. (C) Simulations by using DNA ligands containing eight-block segments (103.2 nm length) show exclusively clathrate II. (D) Clathrates are built by four types of clusters. Particles in sixfold rings are colored in red. (E) Relation of geometric frameworks derived from PAE cluster A. The tips of the cluster form a great dodecahedron. The cluster can be mapped onto the (pentagonal) dodecahedron by connecting polar tips. It can also be mapped onto the icosahedron, which is the dual of the dodecahedron and the Frank-Kasper polyhedron with coordination number 12, by connecting equatorial tips. Connecting PAE centers defines an icosidodecahedron. The same principles can be applied to other PAE cluster types (fig. S5).

  • Fig. 4 Identification of the three basic clathrate crystal structures.

    In the experimental data, we observe crystals analogous to (A to C) clathrate I oriented along [100], (D to F) clathrate IV oriented along [0001], and (G to I) clathrate II oriented along [110]. Each row shows the construction of a unit cell. [(A), (D), and (G)] Nonrounded TBPs highlight the local geometry. [(B), (E), and (H)] Connecting TBP polar tips reveals the clathrate cage representation. [(C), (F), and (I)] Comparison of electron microscopy images (left), zoom-ins of the red areas (middle), and TBP cores in the structure model (right). Pentagonal rings and hexagonal rings are indicated as white overlays. Characteristic structural features seen in projection along high-symmetry axis are outlined as orange overlays.

Supplementary Materials

  • Clathrate colloidal crystals

    Haixin Lin, Sangmin Lee, Lin Sun, Matthew Spellings, Michael Engel, Sharon C. Glotzer, Chad A. Mirkin

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S14
    • Tables S1 to S4
    • References

    Images, Video, and Other Media

    Movie S1
    A system of 2147 PAEs with n = 8 DNA shell (103.2 nm length) self-assembled over 20 million time steps. Visualized using (left) DNA-tethered nanoparticles, (middle) TBP cores, and (right) the clathrate network. Temperature is varied from T* = 2.7 to T* = 2.4, following the stages described in Section 1. The volume of the simulation box is kept constant. The cluster is automatically centered in the simulation box. Four snapshots of the movie are shown in Fig. S6.
    Movie S2
    A system of 2274 PAEs with n = 5 DNA shell (68.7 nm length) self-assemble over 21 million time steps. Visualized using (left) DNA-tethered nanoparticles, (middle) TBP cores, and (right) the clathrate network. Temperature is varied from T* = 2.8 to T* = 2.5, following the stages described in Section 1. The volume of the simulation box is kept constant. The cluster is automatically centered in the simulation box.

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