Saturday, February 23, 2013

Short summary of zome-type superbuckyball part II: Superfullerenes

We will move on to our main and original goal of devising this technique: constructing superfullerenes. Readers familiar with zometool would know that C60 can be built with solely blue struts (two fold rotation axes). So here it is.

C60⊗C60 with g=0: C3240

I've borrowed the notation of Kronecker product (⊗) since these two mathematical operations are in some sense similar: each entry (atom) of the matrix (fullerene) before the ⊗ sign is "expanded" into the second matrix times the original entry (the spatial location of that atom). The meaning of g will become clear once you see an example of g=1 as shown below.

C60⊗C60 with g=1: C4680

It is obvious that g indicates the length of the struts (straight CNTs). In the first case the length is essentially zero, so pairs of heptagons "merge" into octagons at the interface. For clarity the rotatable models of four connected superatoms of the above two superbuckyballs are presented below as well. Since all of these superatoms are identical and can be related through mirror symmetries, readers of interest can start with them to build your own models.

For convenience I also show the rotatable models for the superbuckyball proposed and its beaded model constructed by Bih-Yaw in the previous posts.

C60⊗C60 with g=0: C2700

C60⊗C60 with g=1: C4500

Upon close inspection, notice that there is still local threefold symmetry at each of the node in this case. While on the contrary, there are only mirror symmetries in the zome-type superbuckyball. This asymmetry leads to the fact that there is almost no strain when constructing the beaded model of these structures, or even the actual microscopic realization. This is not an issue concerning the 1D structures in the previous post, since they are all simply connected and there is no such thing as commensurability among multiple struts that join at the same node. However, the above two superstructures seem to be pretty stable and beadable, which surprise me a lot in this regard. According to Bih-Yaw, the tension of the five-member rings and the stress in the six-member rings magically balance each other. This is not so for the dodecahedron case, where tension is built everywhere in the model without being compensated by stress.

Having demonstrated the above mentioned, there is nothing so different in constructing other types of superfullerenes. Below I listed a few that I have done coding with.

C20⊗C60 with g=1: C1560

Although I have not tried to build this one with beads yet, I believe that it is quite doable in the sense of stability as mentioned above.

C80⊗C60 with g=1: C6720

C180⊗C60 with g=1: C15480

I'd like to point out in the last two cases you need red struts as well as blue ones. It can be shown that all (n,n) or (n,0) type icosahedral fullerenes are constructable from zometool (with blue and red struts). For now I just manually find out what are the atoms needing to be deleted/connected, well, in an efficient way. I hope one day I can come up with a general automatic routine that does all these for me, which should be taking account of different orbits in a symmetry group. C180 (a (3,0) Ih fullerene) is the largest one I've ever played with.

I plan to talk about other types of regular polyhedra in the next post.

Wednesday, February 20, 2013

Short summary of zome-type superbuckyball part I: 1D Linear and Helical C60 Polymers

Recently I've been playing with all kinds of these superbuckyballs, based on the methodology of replacing balls and struts of zometool by Ih-symmetric fullerenes and straight CNTs. Taking C60 for example, blue struts correspond to removing two atoms next to some particular C2 rotation axes. And the connecting CNTs are of chiral vector (4,0). On the other hand, yellow and red struts correspond to C3 and C5 rotation axes, respectively. In addition, due to the property of the golden field, the algebraic field of zometool, superstructures using yellow or red struts only have the possibility of being polymers of C60. This means that the number of atoms is a multiple of 60, i.e. no atoms needed to be deleted or added when constructing the superbuckyball.

Here I will briefly summarize some of the cases I've done coding with. Hopefully I'd soon come up with a short paper ready to submit to the Bridges 2013 on this topic.

First let us start with the trivial C60 dimers. As mentioned, structures with red or yellow struts cases have the atom-preserving property. The C120 isomers corresponding to joining two C60s along their fivefold and threefold axes are shown below. I should mention that they were also discussed in Diudea and Nagy's book . In particular for the C3-joined case there are two possibilities of local atomic connectivity.

C3-fused C120, case 1 (with octagons and pentagons at the interface)

C3-fused C120, case 2 (with heptagons at the interface)

C5-fused C120

For the case of blue struts (twofold rotation axes)

C2-fused C116

C2-fused C132

Some of them were already made previously by us, see here for example. But we did not realize back then this particular connection with zometool. To my knowledge, there has not been any experimental characterization of such dimers. Synthetic chemists do make C60 dimers but those are of partial sp3 characteristics, i.e. some interfacial atoms have four neighbors instead of three. Please refer to Diudea and Nagy's book for further details if you are interested.

One can come up with the one dimensional C60 chains without too much effort by enforcing periodic boundary condition. So the structure repeats itself indefinitely along the direction of polymerization. See for example below.

Also, it is one step away from constructing the 2D analog of this kind of structure.

A little bit more sophisticated extension of the above scheme is to consider helical screw symmetry. A (discrete) helical curve is defined by the angle between adjacent unit cells and the dihedral angle between next-nearest neighbors. I recommend readers of interest to play with the awesome virtual zome program vZome developed by Scott Vorthmann. You have to write Scott an email for the license of the full version of vZome. Anyway, here are some examples of helical C60 polymers.

C3-fused fourfold C60 helix

C5-fused fivefold C60 helix

Notice that if you are looking along the axes of the helices, the C60s that are four/five unit cells away lie exactly on top of each other. Curiously, this result is actually symmetry-determined, since I've tested with the relaxation scheme that does not require such symmetry. In other words, even if I optimize the geometries with full degrees of freedom of a general helix, the screw angles will still be 2*pi/4 or 2*pi/5 in the above cases.

Monday, February 4, 2013

Carbon star and other clover-shaped carbon nanotori

I recently saw a post on the clover-shaped carbon tori by my facebook friend, Tetsuaki Hirata, who is an artist from Himi, Japan and seems to be a frequent visitor of this blog. After I showed Chern about his works, Chern told me he has thought about this kind of clover-shaped carbon nanotori quite some times ago. Indeed, Chern has published a number of papers on the tubular graphitic structures. He is probably one of few people who know a lot about this kind of graphitic structures, especially on how the nonhexagons could influence the structures of a carbon nanotube. I am not surprised that he thought about this kind of structures.

1. Chuang, C.; Fan, Y.-C.; Jin, B.-Y.* Generalized Classification of Toroidal and Helical Carbon Nanotubes J. Chem. Info. Model. 2009, 49, 361-368.
2. Chuang, C; Fan, Y.-C.; Jin, B.-Y.* Dual Space Approach to the Classification of Toroidal Carbon Nanotubes J. Chem. Info. Model. 2009, 49, 1679-1686.
3. Chuang, C; Jin, B.-Y.* Hypothetical toroidal, cylindrical, helical analogs of C60 J. Mol. Graph. Model. 2009, 28, 220-225.
4. Chuang, C.; Fan, Y.-C.; Jin, B.-Y.* On the structural rules of helically coiled carbon nanotubes, J. Mol. Struct. 2012 1008, 1-7.
5. Chuang, C.; Fan, Y.-J.; Jin, B.-Y. Comments on structural types of toroidal carbon nanotubes, arXiv:1212.4567, 2013 submitted to J. Chin. Chem. Soc.

In the first two and the 5th papers, we talked about general structural rules of carbon nanotori and only touched helices briefly. In the next two papers, we discussed very generally how the horizontal and vertical shifts (HS and VS) can be exploited to change the direction of a straight carbon nanotube in order to obtain an arbitrary helically coiled carbon nanotubes. In Chern's Ms thesis, he also showed how to take advantage of HS and VS to create trefoil knots or torus knots in general, which was later summarized in a brief review we wrote, "Systematics of Toroidal, Helically-Coiled Carbon Nanotubes, High-Genus Fullerenes, and Other Exotic Graphitic Materials."  (Procedia Engineering, 2011, 14,  2373-2385).

Clover-shaped TCNTs are just a special class of more general curved carbon nanotubes we considered. A simple strategy is to introduce 180 twists along the tube direction (i.e. 180 degree VS) at suitable positions. I got a few nice figures of clover-shaped TCNTs from Chern the other days.
Among all these clover-shaped tori, I particularly like the five-fold carbon star.