Archive for the 'nanotech gallery' Category

Finally! A Good Use For The Nano Gallery (Kudos To nanosonic.com)

Wednesday, August 1st, 2012

An unlabeled version of the fused-diamondoid-carbon-nanotube-van-der-waals-crimp-junction found a home in the NanoSonic Nanotechnology Coloring Book, page 8 (I show it below (with mine shown a little more nano-sized)). I think that’s pretty hip.

Kudos to Tom Moore for pointing it out.

Cover Art For The 7 May 2010 Issue Of The Journal Of Organic Chemistry – Notes On Presentation

Tuesday, May 18th, 2010

The cover art for the 7 May 2010 issue of the Journal of Organic Chemistry accompanies the article by (2nd semester organic chemistry professor, co-author, and 2010 American Chemical Society James Flack Norris Award in Physical Organic Chemistry recipient) John E. Baldwin and Alexey P. Kostikov entitled “On the Stereochemical Characteristic of the Thermal Reactions of Vinylcyclobutane.”

This Perspective outlines the stereochemical and mechanistic complexities inherent in the thermal reactions converting vinylcyclobutane to cyclohexene, butadiene, and ethylene. The structural isomerization and the fragmentation processes seem, at first sight, to be obvious and simple. When considered more carefully and investigated with the aid of deuterium-labeled stereochemically well-defined vinylcyclobutane derivatives there emerges a complex kinetic situation traced by 56 structure-to-structure transformations and 12 independent kinetic parameters. Experimental determinations of stereochemical details of stereomutations and [1,3] carbon sigmatropic shifts are now being pursued and will in time contribute to gaining relevant evidence casting light on the reaction dynamics involved as flexible short-lived diradical intermediates trace the paths leading from one d2-labeled vinylcyclobutane starting material to a mixture of 16 structures.

The cover image is meant to convey as much useful information as possible without any verbiage, although this is clearly not a concept meant to be crystal clear to a non-chemist (but kudos if you got the idea without my having to address it).

Included below are the four iterations involved in the cover draft, between which a considerable amount of verbal back-and-forth occurred (that is discussed briefly) to get what was intended to be presented. The iterations are provided both to show how different visions of what might be seen as the most-key of the key points change as content is presented to the client/researcher and, frankly, these all involved quite a bit of busy work and it seems a shame to not have them floating around somewhere accessible.

The original cover idea (above) was quite mundane but provided a bit more information (cryptic as it may appear to the non-mechanistic organic chemist) about what might be occurring in the absence of a brief read of the introduction of the article. This image emphasizes that a constant rearrangement occurs of the vinylcyclobutane (by the many, many arrows and the four different arrangements of deuteriums in the rearrangement) but does not address that the other 12 structures are products of reactions that are generated as the vinylcyclobutane rearranges and undergoes other but simultaneous intramolecular reactions. The absence of the connection between the rearrangement and the formation of products (which include the vinylcyclobutanes) removed this first iteration from the final running.

The second iteration (above) is a significant (well, I think so) improvement in the getting-across of the business end of the research. The vinylcyclobutane rearrangement is still central to the preferred emphasis of the cover (soon to go away) and the connection between the rearrangement and the formation of products is now hinted at directly by the use of the faded arrows. The second-tier information passed along in this image is that the vinylcyclobutane is one of the products, which is not stressed in the image (by the inclusion of four additional arrows from the central graphic (and, with that addition, the inclusion of arrows feeding the vinylcyclobutanes back into the center). If this had been an Angew. Chemie article, the circular design would have been a perfect fit.

It was at this point that a new piece of content was provided in the form of a medium-resolution digital photo of a piece of artwork by Anne Baldwin. The artwork was chosen as much for the colors as for the chaotic quality of the swirls, which was the one aspect of the entire process that the previous two images did not address and which Dr. Baldwin saw as the more significant point to convey. Some Gaussian blurring and a Gaussian basis set later, the new reactant/product combination as scrambled to complement the background and to make clear that one molecule (that at the arrow) lead to everything else in the image, including itself. The slight red halo around the deuterium (dark blue) is a result of an overlay of the blue spheres and red spheres rendered with slightly larger radii.

The arrow color and shading was stolen from Jean-Michel Folon. Example (The Cry) below. If you’ve one of the copies of La morte di un albero (mine is #630), see Comme un aimant (1971).

I admittedly prefer this (that is, the above cover idea) to the final version as the arrow indicates the forward direction of reactions and adds a hint of symmetry to an otherwise jumbled image.

As for the selected cover image (and final iteration, above), the considerable real estate taken up by the vinylcyclobutane in the previous image is recovered, which highlights the starting molecule differently and has the arrow simply angled into a less-busy space.

The final selection may make more sense in light of the image Baldwin chose to use for the graphical abstract.

A word to the perspective cover artist – This is a point that should be obvious but is often not until it is made obvious by an editor when it is much too late. Your images should be as LARGE as possible. Each of the images above is a 200 MB Photoshop file that would print without pixilation or granularity at 600 dpi on a 24” x 36” poster.

POV-Ray The Error Number Is -199 Potential Remedy For OSX

Wednesday, November 21st, 2007

This post provides a possible fix for an OSX POV-Ray error with precious little information available about it anywhere online. The error,

The Error number is -199. (For internal reference only!)

appears upon startup and exits from the program proper, such that POV-Ray becomes useless (not pleasant when you need that last minute image 30 seconds before lecturing).


The only mention online (if you search by the message text) can be found at


The error itself is not diagnosed, only noting that a corrupted file is not being accessed upon startup and that running a Disk Utility verification/fixing and reinstalling POV-Ray solves the problem. If this has happened to you, you may have noted that verification/fixing and re-installation does not do the trick.

The origin of the problem on my machine could be traced to a crashed POV-Ray rendering run of a number of images and the retention of the file POV-Ray Mac 3.6.plist in my /[USER]/Library/Preferences/ directory, which typically only contains the file POV-Ray Preferences 3.5 (why an installation of POV-Ray 3.6 would still leave a 3.5 Preference file is beyond the scope of this post).

Deleting the POV-Ray Mac 3.6.plist file fixes the problem.


Recent Appearances, Hessen-Nanotech and Institute of Physics

Friday, July 20th, 2007

Not since Arthur Eddington‘s confirmation (from luck, skill, expectation, selective bias, or other) of space curvature by the Sun as predicted by Einstein‘s General Relativity have English and German scientists agreed so closely on a matter of scientific importance. Yes, the NanoEngineer-1 energy-minimized, POVRay-rendered fused diamondoid carbon nanotube van dew Waals crimp junction wins the eye candy prize yet again out of all the molecular mechanics-based structures in the gallery. Now that I’m trying more with Qutemol, we’ll see how subsequent selections go. Links and pdfs are provided below for bookkeeping purposes, as they’re already google-able.


NE-1 and POVray
NE-1 and Qutemol

As standard procedure, I’m happy to provide free, hi-res graphics to interested parties of anything already in the gallery and have no problem with their general use provided that I know where they are showing up if they’re going to be put into paper-print.

The junction is floating on the back page (note the ruler to the left!) of the latest Science In Focus magazine issue on “The Future for Nanoscience and Nanotechnology” at the kind request of Nina Hall, who I knew previously as the editor of the book “The New Chemistry.”

http://www.iop.org/activity/policy/Publications/file_22332.pdf (local copy)

The German site, hessen-nanotech.de, recently used the image as part of a publication on “Nanotechnologien für die optische Industrie,” “Nanotechnology for the Optics Industry,” which is about as far as my conversational German will get me at this point. In French, that would have been “Industrie optische,” which is about as far as my conversation French grammar gets me at this point. C’est dommage.

From the website:

Grundlagen für zukünftige Innovationen in Hessen\r\n\r\nDie Nanotechnologie und die Optik gelten als entscheidende Zukunftsfelder für die deutsche Industrie und als wichtige Jobmotoren. In Zukunft wird die NanoOptik nach Expertenmeinung unser Leben ähnlich grundlegend verändern wie das Auto oder die Computertechnologie. Fensterscheiben, die sich bei Sonnenlicht automatisch im gewünschten Farbton verdunkeln, sich selbst reinigen, Sonnenenergie effektiv in Strom umwandeln oder sich bei Bedarf in Bildschirme oder Beleuchtungselemente verwandeln. Das ist keine Science Fiction, sondern NanoOptik von morgen. Die vom Kompetenznetz für Optische Technologien in Hessen/Rheinland-Pfalz Optence e.V. erstellte Broschüre “Nanotechnologien für die optische Industrie – Grundlagen für zukünftige Innovationen in Hessen” der Aktionslinie Hessen-Nanotech des Hessischen Wirtschaftsministeriums erläutert bestehende Anwendungen der Nanotechnologien in der Optik und zeigt zukünftige Anwendungspotenziale für Unternehmen auf.

http://www.hessen-nanotech.de/mm/NanoOptik_final_Internet.pdf (local copy)

The Brazilians, however, seem to prefer their nanotube-free Drexlerian nanotech (local copy).



NanoEngineer-1 + QuteMol Local Gallery Addition

Tuesday, June 5th, 2007

Simply posting the addition of new gallery contents rendered with QuteMol. A number of these are included in the Nanorex Carbon Nanotube and Molecular Manufacturing Galleries, now provided here in significantly larger versions for your viewing pleasure. The carbon nanotube gallery contents have also been featured at Tom Moore‘s machine-phase.blogspot.com site and the previously posted A Low-Friction Molecular Bearing Assembly Tutorial, v1.

qutemol gallery



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