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	<title>Esemplastic thermoplastic &#187; chemistry</title>
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	<link>http://drzubkov.com</link>
	<description>chemists are reactive scientists</description>
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		<title>Things I won&#8217;t work with, either</title>
		<link>http://drzubkov.com/2010/03/things-i-wont-work-with-either/</link>
		<comments>http://drzubkov.com/2010/03/things-i-wont-work-with-either/#comments</comments>
		<pubDate>Fri, 05 Mar 2010 23:01:19 +0000</pubDate>
		<dc:creator>cubbi</dc:creator>
				<category><![CDATA[chemistry]]></category>

		<guid isPermaLink="false">http://drzubkov.com/?p=997</guid>
		<description><![CDATA[I was randomly linked to an awesome blog of an organic chemist who wrote, among other things, several posts titled &#8220;Things I won&#8217;t work with&#8221;. Here: http://pipeline.corante.com/archives/things_i_wont_work_with/ Even if you&#8217;re a non-chemist, you will appreciate the compounds that can force evacuation of a village when their scent wafts over from an open flask in a [...]]]></description>
			<content:encoded><![CDATA[<p>I was randomly linked to an awesome blog of an organic chemist who wrote, among other things, several posts titled &#8220;Things I won&#8217;t work with&#8221;. Here: http://pipeline.corante.com/archives/things_i_wont_work_with/</p>
<p>Even if you&#8217;re a non-chemist, you will appreciate the compounds that can force evacuation of a village when their scent wafts over from an open flask in a nearby college, compounds that set concrete, sand, bricks, water, and people on fire as they happily burn through them, or compounds that just blow up while standing undisturbed in the dark at cryogenic temperatures.</p>
<p>Fun stuff.. And no, I didn&#8217;t work with any of the title compounds either <img src='http://drzubkov.com/wp-includes/images/smilies/icon_smile.gif' alt=':)' class='wp-smiley' /> </p>
<p><small>Crossposted from <a href="http://cubbi.livejournal.com/74167.html">Livejournal</a></small></p>
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		<title>Microscopes show C-H bonds now O.o</title>
		<link>http://drzubkov.com/2009/08/pentacene/</link>
		<comments>http://drzubkov.com/2009/08/pentacene/#comments</comments>
		<pubDate>Mon, 31 Aug 2009 21:25:37 +0000</pubDate>
		<dc:creator>cubbi</dc:creator>
				<category><![CDATA[chemistry]]></category>

		<guid isPermaLink="false">http://drzubkov.com/?p=962</guid>
		<description><![CDATA[As BBC reports on this article in Science published by a bunch of crazy IBM researchers from Zurich, atomic force microscopes can be tuned so insanely well now that even C-H bonds become (kinda) visible! (the molecule on the picture is pentacene) Crossposted from LiveJournal]]></description>
			<content:encoded><![CDATA[<p><img src="http://cubbi.org/tmp/lj/pentacene_anatomy.jpg" alt="Pentacene image from IBM press release" /><br />
<img src="http://cubbi.com/pentacene2.jpg" alt="Pentacene image from Science 325, 1110 (2009)><br />
<br clear=all><br />
As <a href="http://news.bbc.co.uk/2/hi/science/nature/8225491.stm">BBC</a> reports on <a href="http://www.sciencemag.org/cgi/content/abstract/325/5944/1110">this article</a> in Science published by a bunch of crazy IBM researchers from Zurich, atomic force microscopes can be tuned so insanely well now that even C-H bonds become (kinda) visible! (the molecule on the picture is <a href="http://en.wikipedia.org/wiki/Pentacene">pentacene</a>)<br />
<small>Crossposted from <a href="http://cubbi.livejournal.com/69189.html">LiveJournal</a></small></p>
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		<title>Evolution of the scientific language</title>
		<link>http://drzubkov.com/2008/09/evolution-of-the-scientific-language/</link>
		<comments>http://drzubkov.com/2008/09/evolution-of-the-scientific-language/#comments</comments>
		<pubDate>Fri, 12 Sep 2008 02:15:40 +0000</pubDate>
		<dc:creator>cubbi</dc:creator>
				<category><![CDATA[chemistry]]></category>

		<guid isPermaLink="false">http://drzubkov.com/?p=929</guid>
		<description><![CDATA[Someone asked on IRC if aniline is planar and I wasn&#8217;t sure, so I looked it up and found it amusing to see the changes in the language of the abstracts from 1966, 1985, 1993, and 2007: 1966: &#8220;Aniline-planar or nonplanar?&#8221; J Mol Spectrosc, 20(2):193-195 The question whether the NH2 group of aniline is coplanar [...]]]></description>
			<content:encoded><![CDATA[<p>Someone asked on IRC if aniline is planar and I wasn&#8217;t sure, so I looked it up and found it amusing to see the changes in the language of the abstracts from 1966, 1985, 1993, and 2007:</p>
<p>1966: &#8220;Aniline-planar or nonplanar?&#8221; <i>J Mol Spectrosc</i>, <b>20</b>(2):193-195<br />
The question whether the NH2 group of aniline is coplanar with the aromatic ring has been raised many times (1) but the configuration has not yet been established beyond doubt. Evidence from the electronic band system near 2940 Å appears to settle this point, not only for the ground state of aniline but for its first electronically-excited state (1B2) also.</p>
<p>1985: &#8220;A molecular orbital study of nitrogen inversion in aniline with extensive geometry optimization&#8221; <i>Theor Chim Acta</i> <b>69</b>(3):235-245<br />
The geometry and energy of aniline have been calculated using the 6-31G and 6-31G*(5D) basis sets for the planar structure and various pyramidal structures, assuming that the ring and the N-atom bonded to it lie in the same plane, but otherwise with full geometry optimization. With the 6-31G basis set the planar structure is predicated to be the most stable, whereas the inclusion of polarization functions in the 6-31G*(5D) basis set finds a pyramidal structure with the out-of-plane angle phgr=42.3° to be most stable</p>
<p>1993: &#8220;The structure of aniline by ab initio studies&#8221; <i>J Mol Struct</i> <b>281</b>:91-98<br />
The structure of aniline has been studied by ab initio calculations. Complete geometry optimization of (1) the energy minimum structure and the transition states for (2) internal rotation and (3) inversion of the amino group were carried out at the SCF level using several different basis sets. For these three stationary geometries vibrational frequencies were calculated at the SCF/6-31G** level. The effect of electron correlation was estimated by single point MP4(SDQ) calculations using the 6-311G** basis set. To satisfactorily describe the conformation and orientation of the amino group a fully polarized (6-31G**) basis set is required</p>
<p>2007: &#8220;Simulation of inversion motion and N-H stretching overtone spectra of aniline.&#8221; <i>J Chem Phys</i> <b>126</b>(6):064309<br />
A curvilinear internal coordinate Hamiltonian is used to simulate the N-H stretching overtone spectra and the associated inversion splittings in aniline. A simple local mode type model is applied to the N-H stretching and H-N-H bending modes. Geometric algebra is employed to derive the kinetic energy operator for the large amplitude inversion motion. Electronic structure calculations at the Moller-Plesset second order perturbation theory and correlation consistent aug-cc-pVTZ basis set level are used to obtain model parameters, some of which have been optimized with the least-squares method using experimental vibrational term values as data. The observed N-H stretching overtone vibrational levels and the inversional tunneling splittings are well reproduced with our approach.</p>
<p>Isn&#8217;t it awesome?</p>
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