54 nets and nothing fishy

Prof Batten tells a tale of why it’s always healthy to be skeptical!

What is it?

One of the most important qualities of a scientist is scepticism. The predisposition to doubt conclusions without solid supporting evidence is vital. Nowhere does this apply more than to your own work.

So when one of my colleagues requested my help with a structure that they thought contained 54 interpenetrating three-dimensional networks my initial reaction was that, in polite terms, they’d made a mistake somewhere and I’d need to find it. Yes, interpenetration of networks is quite common in framework structures – see, for example, the two interpenetrating diamond nets in the structures of zinc cyanide and cadmium cyanide, discussed previously on this blog. But the previous ‘record’ was only 18 nets, an exceptional number in itself. This was three times that – there was no way that so many independent 3D networks could pass through each other without bumping into themselves, nevermind the incredible self-assembly process that must happen for such a structure to form. It simply defied belief.

I was wrong.

The structure did, of course, contain 54 interpenetrating, independent networks. Each network was composed of silver atoms bridged by tri(4-imidazolylphenyl)amine ligands. The ligands bridged in two different ways – one was bound to three metals, while the other coordinated to only two. Furthermore, all the silver atoms connected to only two ligands, meaning that the branching points of the networks, the centres of the 3-connecting ligands, were interconnected by parts of two 3-connecting ligands, pairs of silver atoms, and a 2-connecting ligand. As the ligands themselves were quite large, the nodes were therefore an enormous 36.85 Å apart. This very large distance between the nodes meant that an individual net was extremely spacious, and gave the necessary room for 53 other networks to form and entangle with the first. So a few hours and one headache later I found myself confirming that yes, the structure did indeed have that many unconnected networks all tangled up together.

Another interesting feature of this structure was that the networks formed had the “(10,3)-a” topology. This network is of particular interest because it is chiral – i.e. there are two different versions of the net that are mirror images of each other (in the same way that your left and right hands are mirror images and different). Remarkably, nets of both “handedness” were present in this structure – 27 of each – to give an arrangement that was overall nonchiral (or racemic – see the tartaric acid blog post for an explanation of this applied to discrete molecules rather than infinite networks).

What does it look like?

54_nets

Two of the 54 interpenetrating networks are shown schematically in the figure. Although distorted from the most symmetrical version of the (10,3)-a topology, the chirality of the nets can be seen in the rectangular spirals. Those of the blue net spiral into the page in an anti-clockwise fashion, while those of the red net spiral into the page in a clockwise fashion. The real structure, of course, squeezes another 52 nets into the space you see here.

Where did the structure come from?

“An Exceptional 54-Fold Interpenetrated Coordination Polymer with 103-srs Network Topology”, H. Wu, J. Yang, Z.-M. Su, S.R. Batten and J.-F. Ma, J. Am. Chem. Soc., 2011, 133, 11406-11409. DOI: dx.doi.org/10.1021/ja202303b

CCDC Refcode: OYEYOH

 

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Pasteurized Crystals – Tartaric acid.

What is it?

December 27 marks the 192nd birthday of Louis Pasteur, which means that (a) he’d be really old if he hadn’t died in 1895, and (b) today is the perfect day to talk about tartaric acid.

Tartaric acid occurs naturally in many plants, particularly grapes. You’ve already read about ‘wine diamonds’ (potassium bitartrate), but you may not be aware of the contribution tartaric acid has made to scientific language.

Naturally occurring tartaric acid, first isolated in 1769, was found to rotate plane polarized light to the right. When it was prepared synthetically, tartaric acid had identical properties, except that it didn’t rotate plane polarized light. The synthetic material was thought to be a different compound, and was named racemic acid (from racemus, Latin for ‘a bunch of grapes’). It was subsequently determined that tartaric acid can exist in two different forms; and that naturally occurring tartaric acid was L-tartaric acid, while ‘racemic acid’ was actually an equal mixture of D and L-tartaric acid, mirror image isomers (enantiomers). These enantiomers were optically active in opposing directions, appearing optically inactive; this explained the otherwise identical properties of tartaric acid and racemic acid.

For this reason, ‘racemic’ came to mean ‘an equal mixture of enantiomers’, and this term continues to be ubiquitous in organic chemistry today.

So where does Pasteur fit into this story? Early in his career, before he discovered vaccination, microbial fermentation and invented the process which still bears his name (pasteurization), Pasteur studied crystals of tartaric acid and ‘paratartaric acid’ obtained from wine sediments. In particular, he wondered why (as described above) tartaric acid rotated light, while paratartaric acid did not, even though the chemistry and elemental composition of the two were identical. In one of the most beautiful and famous experiments in the history of science, Pasteur noticed, while squinting down a microscope, that there were two subtlety different types of crystals in the samples of paratartaric acid, each the mirror image of the other (see diagram below). He very carefully (and tediously) separated the two types of crystals into separate piles, redissolved each pile, and found that each did indeed rotate light, but in opposite directions. He had, in effect, separated the two enantiomers from the paratartaric acid (a.k.a. racemic acid) and discovered molecular chirality.

The two types of crystals found in paratartaric acid, which are mirror images of each other.

The two types of crystals found in paratartaric acid, which are mirror images of each other.

What does it look like?

The structure of D-tartaric acid (left) and its mirror image, L-tartaric acid (right).

The structure of D-tartaric acid (left) and its mirror image, L-tartaric acid (right).

 

Where did the structure come from?

D-tartaric acid can be found under CCDC refcode TARTAC, while L-tartaric acid is at CCDC refcode TARTAL.

Pinene – It’s beginning to smell a lot like Christmas!

What does it look like?

Pinene crystallises in an Orthorhombic P212121 space group. Graphics created using CrystalExplorer

Pinene crystallises in an Orthorhombic P212121 space group. Graphics created using CrystalExplorer

What is it?

pinnie_2As I write this post, sitting in a very wintery northern hemisphere, the nights are drawing in and the temperature is dropping to the low single figures (being the UK, it is also raining, but we’ll try to forget that bit). However, being a native to these shores, there’s nothing quite like it to make you feel like Christmas is getting close.

A decorated Christmas tree, with its twinkling lights and colourful decorations, is probably one of the most iconic Christmas images. Although it may be unwise to start a debate about the merits of natural vs. artificial, it is hard to deny that a fresh tree definitely wins in the scent department.

That smell comes from Pinene. Pinene is a naturally occurring hydrocarbon, part of the terpene family, and is most commonly found in tree resin – the thick, sticky liquid secreted by conifers when they’ve been cut or wounded. Pinene is predominantly used by these trees to seal and protect wounds, and to act as a repellent to harmful insects. Pinene is also found in many essential oils (such as ironwort or sage), used as flavour additives in food, perfumery and in medicines and alternative medicines. It is also the main component of turpentine paint thinner, and can be used as a feedstock for jet fuel!

Where did it come from?

This structure was determined and published by Andrew Bond and John Davies of the University of Cambridge in 2001 (A. D. Bond, J. E. Davies, Acta Crys., 2001, E57, o1039). Graphics were produced using CrystalExplorer. Further facts were also found on http://www.explorecuriocity.org.

Cellulose – the inner strength of plants

What is it?

CelluloseCellulose is the most abundant natural polymer on Earth comprised of glucose molecules joined together into long chains. It is a key component of plant materials for example comprising 40-50% of wood. Naturally, cellulose is known to form into two crystal structures and it is the 1β form which is primarily found in plants. It is the cellulose that makes wood the strong building material that it is. The long chains of cellulose are bundled together into microfibrils and the way in which this happens can be related to the stage of growth that the plant is in (saplings have to be flexible to withstand wind but older plants tend to have stiffer stems) and also to the species of plant and the relative strengths. By studying the cellulose structure, we can understand how it provides strength and stiffness and use this to help us design better building materials; composite materials using fused synthetic and cellulose polymer chains are already being investigated. In strong wood like sitka spruce (also known as aircraft spruce) the cellulose chains are very well aligned with the direction of the trunk.

Cellulose is a polymer made up of glucose units joined together into a long chain.  In strong plants such as trees, the cellulose chains all lie along the direction of growth in the crystal

Cellulose is a polymer made up of glucose units joined together into a long chain. In strong plants such as trees, the cellulose chains all lie along the direction of growth in the crystal

That isn’t the end of the importance of cellulose though. It is also being used as a source of biofuel! Cellulose grown in plants can be broken down into cellulosic ethanols by enzymes and these can be used as biofuels. Understanding how the cellulose forms into a solid is important to understand which plants will be best to use and also to help us understand how the break-down process works.

Where did the structure come from?

Fibre diffraction patterns of cellulose from tunicate (left) from which the crystal structure of cellulose 1β was determined, sitka spruce (middle) and the fibre diffraction pattern of DNA (right).

Fibre diffraction patterns of cellulose from tunicate (left) from which the crystal structure of cellulose 1β was determined, sitka spruce (middle) and the fibre diffraction pattern of DNA (right).

Naturally occurring cellulose doesn’t form terribly good crystals so it took a long time before the crystal structure could be determined. Yoshiharu Nishiyama, Paul Langan and Henri Chanzy used a technique called fibre diffraction to determine the structure of very crystalline cellulose from tunicates and they had to use a combination of X-rays and neutrons to get to a solution [1]. This is similar to the way in which the structure of DNA was determined. Using this result, it has been possible for many groups to study the structure of cellulose in different plant materials and make some significant break-throughs in our understanding of the function of cellulose in plants [2,3] with future implications in biofuels.

1. Y. Nishiyama, P. Langan, and H. Chanzy. Crystal Structure and Hydrogen-Bonding System in Cellulose Iβ from Synchrotron X-ray and Neutron Fiber Diffraction. J. Am. Chem. Soc. 2002, 124, 9074-9082. http://dx.doi.org/ 10.1021/ja0257319

2. A. Fernandes , L.H. Thomas, C.M. Altaner, P. Callow, V.T. Forsyth, D.C. Apperley, C.J. Kennedy and M.C. Jarvis. Nanostructure of cellulose microfibrils in spruce wood. PNAS 2011, 108, E1195-E1203. http://dx.doi.org/10.1073/pnas.1108942108

3. M. J. Jarvis. Cellulose Biosynthesis: Counting the Chains. Plant Physiology 2013, 163, 1485-1486. http://dx.doi.org/10.1104/pp.113.231092

A big water cage, sH clathrate hydrate.

What does it look like?

The three host water cages found in sH clathrate hydrates.  Image from Loveday and Nelmes 2008 http://pubs.rsc.org/en/content/articlelanding/2008/cp/b704740a#!divAbstract

The three host water cages found in sH clathrate hydrates and how they fit together. Image from Loveday and Nelmes 2008 http://pubs.rsc.org/en/content/articlelanding/2008/cp/b704740a#!divAbstract

What is it?

Water is an incredible material for lots of reasons, but a further one is the shear number of materials it will form new compounds with. Known as hydrates, we’ve featured quite a lot of them on the blog so far. Most of the time the water molecules are able to bond with the materials it’s forming with, for instance in copper sulfate hydrate. But sometimes water forms a solid with a material it can’t bond to, often very small organic molecules like methane and propane, so what do those structures look like?

We’ve met these before, a class of materials called clathrate hydrates. These are three dimensional host guest materials where the water molecules form into a giant host cage that trap the small molecular guests. The structure we met before was one of the two cubic (i.e. very symmetrical) clathrates that form when you freeze methane and water. This one is a bit different. It’s named sH clathrate, where the H indicates that it has hexagonal symmetry, and is special because it forms a very big cage able to fit some pretty large molecules in.

It was thought for many years that this material was only synthetic; it was discovered in the laboratory. This structure has been of interest to a range of scientists, especially as it could also be used to stored CO2. But a few years ago researchers pluming the margins of the Gulf of Mexico discovered that the hexagonal big cage form of clathrate could form in nature too.

Where did the structure come from?

sH clathrate hydrates were first discovered by Ripmeester et al., and were reported in Nature in 1987.