Zhang, Chen, Yuan, Ji, Cheng, and Qui

Mine is not a science blog and it is not my intent that it should become one, but I could not help but follow up on a post I made a bit ago the focus of which was the Anthropic Principle and which relied heavily on discussion of the significance of the hydrogen bond to life on Earth. In that post I described hydrogen bonds as weak interactions which occur between a hydrogen atom attached to an electronegative atom, such as oxygen, and an electronegative atom of another molecule. Imagine my surprise when I received an email from a colleague the other day which included a link to an article entitled Real-Space Identification of Intermolecular Bonding with Atomic Force Microscopy. The piece described a technique which allows for the visualization of hydrogen bonds forming between molecules of 8-hydroxyquinoline. How, you may well ask, were these folks able to visualize an electrical interaction? The authors, whose names comprise the title of this post, had tweaked their microscope and their computers in such a way that they were able to measure and to then visualize the electron densities about interacting atoms. The image below shows a molecule of 8-hydroxyquinoline: white balls are hydrogen atoms, black ones are carbon, red are oxygen, and blue is nitrogen.


The image below, left, is a micrograph of hydrogen bonds. The figure on the right shows the hydrogen bonds (dotted lines) which form between four adjacent  molecules of 8-hydroxyquinoline. Do you see how bonds form between hydrogen and oxygen (four instances) and between hydrogen and nitrogen (three instances)? Now look to the left at the micrograph and at these same interactions. Look more closely and you will see the same seven hydrogen bonds we just enumerated! Fascinating, truly, and really, really impressive. For reference, the frame size of each of the images below is approximately 2 nanometers, or 20 ångströms; a nanometer is one billionth of a meter while an ångström is one ten-billionth of a meter. Totally crazy … but I do love this stuff.


4 thoughts on “Zhang, Chen, Yuan, Ji, Cheng, and Qui

  1. Very interesting to last week’s follow-up! Elke raises an interesting point so maybe I should chime in with my pet peeve. Math on the web. I can’t believe that the web and browsers have come so far and we still do not have a nice, simple, standard way of marking up math. When this first became an issue for me around 15 years ago (after I got sick of using gif images) I learned of MathML. I also learned of how it would not work directly in a browser – you either had to write an XML page and be browser-specific or resort to plug-ins. Here we still are – same thing. Very frustrating! Yes, there are various ways of putting math online but no simple standard browser-neutral way. I can’t believe it!

    • I don’t know enough about mark-ups to offer an opinion. Is this not simply a matter of the market? Perhaps if there hasn’t been some critical mass of need expressed no one has bothered to develop the browser-neutral piece of software? Hey … there’s something you can do in your retirement? Generate an open-source, browser-neutral piece of math mark-up software! You’ll be famous … and rich even! D

  2. This is very impressive – it seems AFM has been improved a lot since I was involved with it about 20 years ago (I did not do microscopy myself but did fabricate thin films which were analyzed by our partners in their lab). Since the original article is behind a paywall I have a question – probably to be answered in a new post (?). What is your opinion – as a professor and as a science enthusiast – about open access? Supporters say that most research is governmentally funded and should be available to tay payers at no cost; objectors say that the distribution of scientific knowledge is a task that must not be underestimated. I think it is a hard question. I tend to argue in favor of the objectors; I have worked as a distributor as in a sense, too (as a consultant you are – consolidating existing knowledge into something easier to digest or applicable to a problem). On the other hand I could name lots of governmentally funded initiatives (in renewable energy in particular) that I consider unnecessary, unjust, and simply funding self-perpetuating pseudo-businesses which only live off funding only. As a science enthusiast I would like to see that money go into open access. I don’t understand why Austria’s official patents’ database cannot be accessed openly. Sorry, this was a random diatribe 🙂 But – as in previous science post – you have pushed a button!

    • Very interesting question. I’m sure others have discussed it at length. But Yes … part of the scientific method dictates that we disseminate our findings … for the ‘greater good.’ Having to pay for the findings seems not to be in the best interest of dissemination. I think that there are market forces lurking in the shadows here Elke. The publishers of the journals in which these results are being published need to make a dollar too! No? Science is an expensive undertaking and it seems that it isn’t the funding agencies however that are looking to make a buck … but, rather the publishers of the information themselves? I’m not well enough versed in the topic to offer a learned opinion! I remember a line from the Ruby radio broadcast series in which Nikola Tesla himself is quoted as saying, “Free electricity for ALL!.” So, the same could be said here, “Free access to scientific knowledge for ALL.” D

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