Most Complex Nanoparticle Crystal Ever Made

By Benedette Cuffari, M.Sc.Mar 7 2017

                                                                                                                          NTA88/Shutterstock

Clathrates are complex structures consisting of polyhedral cages with large pores, where the guest molecules are housed^1,5. These clathrates with complex structures are known to be formed naturally, and synthesizing such structures in laboratories has been challenging. Recently, researchers at Northwestern University’s Department of Chemistry have developed the most complex clathrate crystal built from nanoparticles. Chad A. Mirkin and his team showed that these complex structures can be intentionally created by controlling the shape of the particles and the way these particles connect².

Compounds that form clathrates naturally associate with each other by forming hydrogen bonds to form the complex structure. For example, in methane clathrates or clathrate hydrates (CH), the water molecules forms a lattice to house the methane molecules. Although these clathrates appear like ice, they form cages to trap individual methane molecules³. These CHs prefer to house carbon dioxide (CO₂) over methane, therefore, potentially serving as a bridging fuel capable of capturing CO₂ while releasing methane, which could be used as an energy source³. Similarly, urea molecules could be linked with each other by hydrogen bonds to form clathrates with hexagonal channels that can host 1, 6 dichloro hexane⁴.

Mirkin’s lab pioneered the art of forming colloidal crystals using nucleic acids combined with isostructural nanoparticles as the template to form a masterpiece of such deliberate clathrates². Due to the incredibly small size of the NPs, which measure less than 100 nm each, they are capable of exhibiting physicochemical properties which differ greatly from their bulk counterparts. Such custom-built crystals made from nanoparticles can have many special properties which are difficult to obtain from the naturally-occurring clathrates. These clathrate colloidal crystals have the ability to absorb, transmit and amplify a selective range of light wavelengths, while blocking the others, changing colors and patterns, capturing pollutants and thus, can be used in optical, storing, delivering and sensing materials for environmental, diagnostic and therapeutic application².

Due to the magnificent crystal symmetry and lattice parameters achievable with DNA Programmable Assembly (DPA), more than 500 different colloidal crystal structures with 36 different symmetries were developed using this method⁵. However, most of these structures were made up of spherical-shaped nanoparticle building blocks called Programmable Atom Equivalents (PAEs). Such spherical PAEs may not be suitable for making symmetrical and complex structures, such as clathrates, however, anisotropic PAEs can make this possible. The cages of the clathrates are formed by the atomic or molecular nodes with bond angles between 100° - 125° ⁵. By employing the DPA method, Mirkin’s lab used trigonal bipyramid structured gold nanoparticles (TBPs) capable of forming a bond angle of 110° to develop a complex colloidal clathrate⁶.

After synthesis and purification, the TBPs were functionalized with 28 base hexylthiol-modified DNA, which recognizes the linker DNA. The linker DNAs are comprised of varying lengths ranging from 23-228 bases, however, all strands end with same self-complimentary GCGC sticky ends. The complimentary duplexer strand is then allowed to bind with the long-linker DNA⁵. Due to the inability of the complimentary DNA to bind to the specific single base sites, otherwise known as flexors, on the linker DNA, the assembly is flexible⁵. This flexibility of the sufficiently long DNA helps in reducing the strain imposed during the assembly of the clathrate.

At high temperatures, these PAEs formed a disordered state, and when the temperature is slowly reduced, the PAEs aggregate due to DNA hybridization⁵. The DNA length was fine-tuned by varying the length of the number of duplexed block segments. Scanning electron microscopy (SEM) images of the assembly quality of the PAEs with varying block lengths of 1 – 5 revealed that the assembly quality improved with the increase in the number of block segments⁵. The cavities in the clathrate were observed using transmission electron microscopy (TEM). Molecular simulations and geometric analysis were also used to identify ordered assemblies in the clathrates formed.

Mirkin’s group of researchers believe that the clathrates formed by using the anisotropic gold TBPs are of the most complex nanoparticle crystal structures ever made. They are hopeful that this research will allow for the development of other complex crystal structures in the future.

References:

1. "Clathrates." IUPAC Gold Book. Web. http://goldbook.iupac.org/C01097.html.
2. "Most Complex Nanoparticle Crystal Ever Made by Design." Phys.org. Web. https://phys.org/news/2017-03-complex-nanoparticle-crystal.html.
3. Marshall, Michael. "Ice That Burns Could Be a Green Fossil Fuel." New Scientist. 26 Mar. 2009. Web. https://www.newscientist.com/article/dn16848-ice-that-burns-could-be-a-green-fossil-fuel/.
4. Hollingsworth, U.Werner-Zwanziger; Brown, J.D.Chaney; Huffman, K.D.M.Harris (1999). "Spring-Loading at the Molecular Level:  Relaxation of Guest-Induced Strain in Channel Inclusion Compounds". J. Am. Chem. Soc. 121: 9732.
5. Lin, Haixin, Sangmin Lee, Lin Sun, Matthew Spellings, Michael Engel, Sharon C. Glotzer, and Chad A. Mirkin. "Chemists Create Colloidal Clathrate Crystals." C&EN Global Enterprise 95.10 (2017): 10-11. Web.
6. Samanta, Dipak, and Rafal Klajn. "Clathrates Grow up." Science 355.6328 (2017): 912. Web.

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