Photolabile Dendrimers…

…which are in many ways conceptually similar to Shabat’s self-immmolative dendrimers were published by Kevwitch and McGrath in the recent issue of New J. Chem. (DOI: 10.1039/b617289j). These dendrimers contain o-nitrophenyl linkers in the core, which allow the controlled degradation of the material:

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The photolabile core can be prepared from piperonal in a relatively straightforward way. As was the case for the self-immolative dendrimers, a trigger event – in this case irradiation – leads to the fragmentation of the dendrimer. In this case, the dendrons detach from the core – no complete unraveling of the architecture occurs.

An elegant synthesis…

…of core-shell brush copolymers has just been reported by Wooley et al. (Macromolecules, 40, 2289 (2007)).<img id="image48"

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The exo-norbonene-functionalized raft agent was prepared by esterification of the corresponding alcohol with an acid functionalized raft agent (87 % yield). This was followed by the one pot ROMP and RAFT procedures. The ring-opening metathesis procedure was carried out using a Grubbs catalyst in CH2Cl2 to give a poly(norbonene) derivative with an Mn of 40.6 kDa and a PDI of 1.24.

The RAFT polymerization was then carried out using styrene and maleic acid anhydride as co-monomers and AIBN as the initiator (50 deg C reaction temperature). The comonomer pair was chosen due to their low reactivity ratios, which allows the one-pot preparation of statistical polymers of the type poly(styrene-stat-maleic anhydride)-block-poly(styrene). 1H NMR suggested quantitative conversion of the maleic anhydride after 16 h, but only 8.2 % for styrene. The reaction was allowed to continue for another 16.5 hours and quenched after 12. 8 % styrene conversion to give the desired core-shell brush copolymer (Mn=1200 kDa, PDI = 1.32).

Publishing Volumes

I am currently in the process of preparing a publication on the development of an upper ontology for polymers, that I have been working on for some time. As part of the publication I am arguing that the increasing volume of scientific publication really requires a new information model for chemical and polymer information. To support this with some numbers, I hit SciFinder and did a search on how many journal articles in SciFinder’s database contain either the word “chemistry” or polymers. Here is the graph:

publication-volume.gif

Can you really read from this that the publication volume has doubled over approximately 16 years? In which case….wow….highest highest time we came up with new ways of publishing and mining chemical information.

The Five Minute Polymer Property Videocast: The Crystalline Melting Point – Transcript

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As people seem to like transcripts of the video podcast, here it is. Most of the material in this videocast is taken from van Krevelen’s book.[1]

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Besides the glass transition temperature, the second transition temperature that we need to worry about in connection with polymers is the melting point. Thermodynamically, the melting point is a pure first order transition, at which the energies of the solid and that of the liquid phase are in equilibrium. Or, to put it in an equation: at the melting point, DHm, the enthalpy of fusion is equal to Tm x DSm, DSm being the entropy of fusion. It should be noted, that this first order behaviour is in sharp contrast to the other transition temperature, the glass transition temperature. Thermodynamically, the latter is neither first nor second order as
the amorphous state is thermodynamically never at equilibrium and therefore normal state variables do not apply.

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Besides the molecular structure of the polymer, there are a number of other factors that influence the melting point.

1. Pressure
The melting point of a polymer at a given pressure p can be estimated from its melting point in vacuum, the zero pressure melting point, plus the product of constant sm x the pressure p. For flexible aliphatic polymers, sm has a value of 0.175 K/MPa, whereas for semi rigid and rigid polymers, the value is 0.5 K/MPa.

2. Molecular Mass
Like the glass transition temperature, the melting point, too, is dependent on the molecular weight and increases asymptotically to a high polymer limit. This behaviour is captured in the well-known Flory equation, where Tm is the melting point, Tm(infin) is the melting point at high molecular weight limit, DHm is the heat of fusion per structural unit and Pn is the degree of polymerisation. Intuitively, this behaviour can be understood, as the molecular weight correlates with the length of the crystallizable segments in the polymer. Beyond a certain threshold, the maximum melting point will be reached and any further increases in molecular weight become ineffectual.

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3. Molecular Asymmetry
As a general rule, highly symmetric structural units elevate, asymmetric ones depress the melting point. Again this comprehensible from crystal packing considerations: polymers with symmetric structures will be able to pack more tightly in a crystal than asymmetric ones. The consequence is that more energy will be required to break up the crystal lattice, leading to an increase in melting points.

4. Tacticity
Tacticity is a variation on the same theme and we can derive some empirical rules, which hold for most polymers. Consider the repeat unit fragment on the slide above.If P is a hydrogen atom and Q any other group such as a methyl group, for example, then the rule that the melting points of isotactic polymers is higher than those of syndiotactic polymers generally holds. If, on the other hand P is not a hydrogen atom and has a different structure than Q, the syndiotactic polymer usually has the higher melting point.

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5. The relationship between the glass transition temperature and the crystalline
melting point.

When plotting the experimental glass transition temperatures of polymers contained in the PoLyInfo database against the corresponding crystalline melting point, we can see that there is an approximately linear relationship, albeit with large deviations.

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Early on it was observed by a number of scientists that for most polymers, the ratio of
the glass transition temperature and the crystalline melting point is approximately 2/3,
i.e. approximately 0.67. Boyer later refined this somewhat and claimed that the ratio for most symmetrical polymers is 1/2 and 2/3 for unsymmetrical ones. Unsymmetrical polymers in this context are polymers, having two non-identical main chain substituents. However, even with this refinement, there are still significant deviations from this rule. Further refinement yielded the following rules:

The majority of both symmetrical and unsymmetrical polymers have Tg/Tm ratios between 0.56 and 0.76, with a maximum number of values centered around 2/3.

Polymers with ratios below 0.5 are usually highly symmetrical, with short repeating units. These usually only consist of one or two main chain atoms, carrying substituents of only a single atom. They are usually very crystalline.

Polymers with ratios above 0.76 are unsymmetrical and all have relatively complex structures. They can be highly crystalline.

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6. Copolymers
A discussion of the factors determining the melting points and Tg/Tm ratio would merit a separate presentation and anybody interested in delving deeper into the subject should refer to van Krevelen and other textbooks. At this point suffice it to say, that for random copolymers the melting point is usually depressed w.r.t. to the
corresponding homopolymers and intermediate between them. Tg/Tm ratios are
usually high.
Block copolymers can have high melting points, particularly if one of the blocks is crystallizable and of sufficient length. Tg/Tm ratios are usually low.

References
[1] van Krevelen, D. W.; Properties of Polymers: Their Correlation with Chemical Structure; Elsevier 1990 (3rd Edition)

The Five Minute Polymer Property Videocast: The Crystalline Melting Point

Now (almost) by definition, one has an awful lot of people knowing an awful lot about computers in a polymer informatics group, but rather less about polymers. One of the “educational” things that we therefore started here was the “polymer property of the week.” At each meeting of the polymer group, someone prepares a five minute talk about a particular polymer property that they happen to find sexy on that day and presents it to the rest of the group.

I think some of this material is interesting and useful to the polymer community at large and hence I have experimented with getting it into a videocast format, which you can either watch on your computer or download from Google Video directly onto your iPod without any fuss (hence I didn’t upload to YouTube). So please go ahead and watch it and tell me what you think….at this stage things are very experimental and I would be grateful for constructive feedback.

Polymer Informatics and The Semantic Web – The Solution, Part 1: Adding Structure: Chemical Markup Language

In my last post concerning our work on polumer informatics, I started to discuss how one can add structure to documents in the form of metadata, in order to help correct information retrieval. In particular, I introduced the notion of markup languages to structure information and used an example of a bread recipe, to discuss some general features of XML. So having been through all of that, how can we hold chemical information in a marked-up way.

Being chemists, one of the assumptions that is fundamentally engrained into all of our thinking, is that the structure of a molecule is related to the physical properties of that molecule. Therefore, the most important information a chemist might wish to hold in a marked-up way is probably structural information about a molecule. Well, fortunately, over the past decade or so, Peter Murray-Rust, Henry Rzepa and others have worked on an XML dialect called CML – Chemical Markup Language. Let’s have a look at a small molecule, styrene in our case, and see what some basic CML looks like.

Here’s a representation of styrene (InChI=1/C8H8/c1/h2-7H,1H2) that every chemist will be familiar with:

Styrene

and here’s how the same molecule would be represented in CML:

StyreneInCML

As was the case for our bread recipe, you can see that we have three containers here, namely “atomArray” and “bondArray” enclosed by the container “molecule”. Both arrays are essentially lists of atoms (with attributes specifying which element we are talking about, what id that particular atom has and what it’s 2D coordinates are) and bonds (with attributes telling us between which atom IDs the bond was formed, what the ID of the bond is and also what the bond order is). All of this taken together is what computational chemists call a “connection table”.

Neither hard, nor scary, is it? And the simplest way of holding chemical information in a semantically rich format. In future posts I will delve somewhat deeper into the bowels of CML and show you what else it is capable of.

Polymer Snakes…

…is what I came across during tonight’s post-midnightly journey through the wild wild web. When searching for the keyword polymer in YouTube, I found a short animation about polymer reptation. I had to chuckle, because I had seen this movie before when someone taught me about the reptation model in a very elegant and wonderfully entertaining way.

The reptation model was developed by de Gennes and explains some of the behaviour of high molecular weight polymers in the melt. Consider a polymer chain, surrounded by other chains. Now the movements of such a polymer chain are constrained by the presence of other chains surrounding it and therefore the chain is only free to move within what is essentially a topological tube. Within that tube, it can carry out snake like motions (hence reptation) and only advance by diffusing it’s stored lengths.

de Gennes, by the way, is a polymath. A physicist by training, he made substantive contributions to such diverse areas as magnetism, liquid crystals, superconductivity and polymer physics. Though he formally retired in 2002, at the moment he is working on the comprehension of living systems and cellular mechanisms. Go and look him up, he is a fascinating character.