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	<title>Comments on: The conformation of cyclohexane</title>
	<atom:link href="http://www.ch.imperial.ac.uk/rzepa/blog/?feed=rss2&#038;p=1587" rel="self" type="application/rss+xml" />
	<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587</link>
	<description>Chemistry with a twist</description>
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		<title>By: Ring-flipping in cyclohexane in a different light &#171; Henry Rzepa</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-11556</link>
		<dc:creator>Ring-flipping in cyclohexane in a different light &#171; Henry Rzepa</dc:creator>
		<pubDate>Fri, 12 Oct 2012 13:42:35 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-11556</guid>
		<description><![CDATA[[...] conformational analysis of cyclohexane is a mainstay of organic chemistry. Is there anything new that can be said about it? Let us start [...]]]></description>
		<content:encoded><![CDATA[<p>[...] conformational analysis of cyclohexane is a mainstay of organic chemistry. Is there anything new that can be said about it? Let us start [...]</p>
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	<item>
		<title>By: The Cyclol Hypothesis for protein structure: castles in the air. &#171; Henry Rzepa</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-6697</link>
		<dc:creator>The Cyclol Hypothesis for protein structure: castles in the air. &#171; Henry Rzepa</dc:creator>
		<pubDate>Mon, 04 Apr 2011 12:54:10 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-6697</guid>
		<description><![CDATA[[...] to this mathematician (the interesting symmetrical and conformational properties of the central cyclohexane-like ring were still to be fully recognised by [...]]]></description>
		<content:encoded><![CDATA[<p>[...] to this mathematician (the interesting symmetrical and conformational properties of the central cyclohexane-like ring were still to be fully recognised by [...]</p>
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	<item>
		<title>By: danial</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-6491</link>
		<dc:creator>danial</dc:creator>
		<pubDate>Tue, 01 Mar 2011 17:42:17 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-6491</guid>
		<description><![CDATA[Working on the give topic is really a difficult task but your this tutorial made it easy for me to handle it without any problem. If anyone seeking information then this blog is the best place for him as it has quality content for your required information. Thanks for sharing. 
&lt;a href=&quot;http://bestbabyswingreviews.com/&quot; rel=&quot;nofollow&quot;&gt;best baby swing&lt;/a&gt;]]></description>
		<content:encoded><![CDATA[<p>Working on the give topic is really a difficult task but your this tutorial made it easy for me to handle it without any problem. If anyone seeking information then this blog is the best place for him as it has quality content for your required information. Thanks for sharing.<br />
<a href="http://bestbabyswingreviews.com/" rel="nofollow">best baby swing</a><img src="http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/plugins/zlinks/imgs/mini_rdf.gif" border="0" style="cursor: pointer; padding:0px 0px 0px 1px; margin:0px;" onmouseover="assignPopup(this, 'http://bestbabyswingreviews.com/', 'http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/plugins/zlinks/');" alt="" /></p>
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	<item>
		<title>By: What is OCD</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-6335</link>
		<dc:creator>What is OCD</dc:creator>
		<pubDate>Sun, 23 Jan 2011 18:21:39 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-6335</guid>
		<description><![CDATA[I really enjoyed reading this write-up and have recently been checking out your web site for some months now. I manage a website devoted to the fight against OCD (obsessive compulsive disorder) and would like to include your webblog within my information section for the advantage of my readers. There is certainly a great deal of falsehoods these days on the internet and anytime I happen across a very good high quality web-site similar to this I like to distribute these onto my readership -- I am hoping this is alright with you, I&#039;ve inserted your hyperlink within my highly valued resources section (on this page; http://www.whatisocd.org/resources/). Thank you - be sure to keep up the quality work it is very much valued.]]></description>
		<content:encoded><![CDATA[<p>I really enjoyed reading this write-up and have recently been checking out your web site for some months now. I manage a website devoted to the fight against OCD (obsessive compulsive disorder) and would like to include your webblog within my information section for the advantage of my readers. There is certainly a great deal of falsehoods these days on the internet and anytime I happen across a very good high quality web-site similar to this I like to distribute these onto my readership &#8212; I am hoping this is alright with you, I&#8217;ve inserted your hyperlink within my highly valued resources section (on this page; <a href="http://www.whatisocd.org/resources/" rel="nofollow">http://www.whatisocd.org/resources/</a><img src="http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/plugins/zlinks/imgs/mini_rdf.gif" border="0" style="cursor: pointer; padding:0px 0px 0px 1px; margin:0px;" onmouseover="assignPopup(this, 'http://www.whatisocd.org/resources/', 'http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/plugins/zlinks/');" alt="" />). Thank you &#8211; be sure to keep up the quality work it is very much valued.</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Conformational analysis of biphenyls: an upside-down view &#171; Henry Rzepa</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-3404</link>
		<dc:creator>Conformational analysis of biphenyls: an upside-down view &#171; Henry Rzepa</dc:creator>
		<pubDate>Fri, 02 Apr 2010 16:08:06 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-3404</guid>
		<description><![CDATA[[...] any distance less than ~2.1Å now represents a genuine repulsion between the hydrogens (see also this post). This represents a somewhat more quantitative judgement on what used to be called steric [...]]]></description>
		<content:encoded><![CDATA[<p>[...] any distance less than ~2.1Å now represents a genuine repulsion between the hydrogens (see also this post). This represents a somewhat more quantitative judgement on what used to be called steric [...]</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Conformational analysis of cyclotriborazane &#171; Henry Rzepa</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-2536</link>
		<dc:creator>Conformational analysis of cyclotriborazane &#171; Henry Rzepa</dc:creator>
		<pubDate>Sun, 14 Feb 2010 18:41:55 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-2536</guid>
		<description><![CDATA[[...] an earlier post, I re-visited the conformational analysis of cyclohexane by looking at the vibrations of the [...]]]></description>
		<content:encoded><![CDATA[<p>[...] an earlier post, I re-visited the conformational analysis of cyclohexane by looking at the vibrations of the [...]</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Henry Rzepa</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-2453</link>
		<dc:creator>Henry Rzepa</dc:creator>
		<pubDate>Wed, 10 Feb 2010 16:14:53 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-2453</guid>
		<description><![CDATA[In answer to the previous post, if you resolve the  DOI for the calculation, it will take you to a repository where you can check any details of the calculation. In this case, it was done at the  DFT level, B3LYP/6-31G(d).  Of course, this was not  intended to provide energies at the  state-of-the-art level.]]></description>
		<content:encoded><![CDATA[<p>In answer to the previous post, if you resolve the  DOI for the calculation, it will take you to a repository where you can check any details of the calculation. In this case, it was done at the  DFT level, B3LYP/6-31G(d).  Of course, this was not  intended to provide energies at the  state-of-the-art level.</p>
]]></content:encoded>
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	<item>
		<title>By: Abraha</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-2452</link>
		<dc:creator>Abraha</dc:creator>
		<pubDate>Wed, 10 Feb 2010 14:51:07 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-2452</guid>
		<description><![CDATA[what are the different methods used to measure the energy difference of substituted cyclohexanes?]]></description>
		<content:encoded><![CDATA[<p>what are the different methods used to measure the energy difference of substituted cyclohexanes?</p>
]]></content:encoded>
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	<item>
		<title>By: sjb</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-2338</link>
		<dc:creator>sjb</dc:creator>
		<pubDate>Wed, 03 Feb 2010 13:05:13 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-2338</guid>
		<description><![CDATA[Is there a missing 1 in the DOI link to the Cp dimerisation?]]></description>
		<content:encoded><![CDATA[<p>Is there a missing 1 in the DOI link to the Cp dimerisation?</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Henry Rzepa</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-2256</link>
		<dc:creator>Henry Rzepa</dc:creator>
		<pubDate>Fri, 29 Jan 2010 15:10:16 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-2256</guid>
		<description><![CDATA[re: repository. Thanks for noticing.  We are the only group  in computational chemistry who does this to my knowledge  (although  I did hear that the comp chem group at  Erlangen has an archive of perhaps  300,000 calculations. Sadly however, its private).  So it is nice to hear that you found it useful! That was indeed the intention.

re: Magnitude. Its really related to the hyperpolarisability rather than havng a stereogenic centre. Thus  the  &quot;lemniscular&quot; form of  [14] annulene, that also  has no stereogenic centre, has a rotation of around  3500 degrees. I have seen systems with no stereogenic centres with rotations &gt; 100,000 degrees (sic). 

Its the hyperpolarizability that does it, and  &#960;-electrons are particularly polarizable. Thus any system with (di)symmetric  &#960; electrons is going to have large rotations. It is also fair to say that such systems also have enormously variable optical dispersivity, ie frequency dependence. Thus some systems with rotations &gt; 20,000 can go from  -20,000, thru zero,  to  + 20,000 over  400 nm or so.]]></description>
		<content:encoded><![CDATA[<p>re: repository. Thanks for noticing.  We are the only group  in computational chemistry who does this to my knowledge  (although  I did hear that the comp chem group at  Erlangen has an archive of perhaps  300,000 calculations. Sadly however, its private).  So it is nice to hear that you found it useful! That was indeed the intention.</p>
<p>re: Magnitude. Its really related to the hyperpolarisability rather than havng a stereogenic centre. Thus  the  &#8220;lemniscular&#8221; form of  [14] annulene, that also  has no stereogenic centre, has a rotation of around  3500 degrees. I have seen systems with no stereogenic centres with rotations > 100,000 degrees (sic). </p>
<p>Its the hyperpolarizability that does it, and  &pi;-electrons are particularly polarizable. Thus any system with (di)symmetric  &pi; electrons is going to have large rotations. It is also fair to say that such systems also have enormously variable optical dispersivity, ie frequency dependence. Thus some systems with rotations > 20,000 can go from  -20,000, thru zero,  to  + 20,000 over  400 nm or so.</p>
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	<item>
		<title>By: Eutactic</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-2255</link>
		<dc:creator>Eutactic</dc:creator>
		<pubDate>Fri, 29 Jan 2010 14:18:26 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-2255</guid>
		<description><![CDATA[That repository software is very cool and thanks for making the logfiles available - being able to open the structure in Avogadro really helps with visualising the species&#039; helicity.

Not being very familiar with the theory that gives rise to the magnitude of optical rotation, I take it that you would have expected a smaller rotation for a species lacking a stereogenic center and not being *massively* distorted from the C2h point group?

I know a spectroscopist who does a bit of CD (well, protein MCD) who I imagine may find this quite interesting.]]></description>
		<content:encoded><![CDATA[<p>That repository software is very cool and thanks for making the logfiles available &#8211; being able to open the structure in Avogadro really helps with visualising the species&#8217; helicity.</p>
<p>Not being very familiar with the theory that gives rise to the magnitude of optical rotation, I take it that you would have expected a smaller rotation for a species lacking a stereogenic center and not being *massively* distorted from the C2h point group?</p>
<p>I know a spectroscopist who does a bit of CD (well, protein MCD) who I imagine may find this quite interesting.</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Henry Rzepa</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-2252</link>
		<dc:creator>Henry Rzepa</dc:creator>
		<pubDate>Fri, 29 Jan 2010 08:38:09 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-2252</guid>
		<description><![CDATA[As promised, here are the calculated chiro-optical properties of  D&lt;sub&gt;2&lt;/sub&gt;-symmetric cyclohexane. 

The [&#945;]&lt;sub&gt;D&lt;/sub&gt; is  +38&#176; (for the absolute configuration corresponding to this rotation, see  DOI: &lt;a href=&quot;http://hdl.handle.net/10042/to-3719&quot; target=&quot;new&quot; rel=&quot;nofollow&quot;&gt;10042/to-3719&lt;/a&gt;), calculated for a chloroform solution at the frequency dependent value of  589nm (B3LYP/6-311G(d,p)  level using Gaussian 09).

The circular dichroism (for the same absolute configuration)  using time-dependent DFT  is archived at &lt;a href=&quot;http://hdl.handle.net/10042/to-3720&quot; target=&quot;new&quot; rel=&quot;nofollow&quot;&gt;10042/to-3720&lt;/a&gt;  and is feature-full (I cannot post a graphic  here in the comments),  with positive phased peaks at 152, 142 and 133nm,  and a negative phase peak at 128nm. The Cotton effect is also large (&#916;&#949; ~200).  (I rather doubt that commercial  CD spectrometers can go so far into the  UV however). 

Whilst it is very unlikely that either value could be verified experimentally, it is  interesting that the optical rotation is as high as it is!]]></description>
		<content:encoded><![CDATA[<p>As promised, here are the calculated chiro-optical properties of  D<sub>2</sub>-symmetric cyclohexane. </p>
<p>The [&alpha;]<sub>D</sub> is  +38&deg; (for the absolute configuration corresponding to this rotation, see  DOI: <a href="http://hdl.handle.net/10042/to-3719" target="new" rel="nofollow">10042/to-3719</a><img src="http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/plugins/zlinks/imgs/mini_rdf.gif" border="0" style="cursor: pointer; padding:0px 0px 0px 1px; margin:0px;" onmouseover="assignPopup(this, 'http://hdl.handle.net/10042/to-3719', 'http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/plugins/zlinks/');" alt="" />), calculated for a chloroform solution at the frequency dependent value of  589nm (B3LYP/6-311G(d,p)  level using Gaussian 09).</p>
<p>The circular dichroism (for the same absolute configuration)  using time-dependent DFT  is archived at <a href="http://hdl.handle.net/10042/to-3720" target="new" rel="nofollow">10042/to-3720</a><img src="http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/plugins/zlinks/imgs/mini_rdf.gif" border="0" style="cursor: pointer; padding:0px 0px 0px 1px; margin:0px;" onmouseover="assignPopup(this, 'http://hdl.handle.net/10042/to-3720', 'http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/plugins/zlinks/');" alt="" />  and is feature-full (I cannot post a graphic  here in the comments),  with positive phased peaks at 152, 142 and 133nm,  and a negative phase peak at 128nm. The Cotton effect is also large (&Delta;&epsilon; ~200).  (I rather doubt that commercial  CD spectrometers can go so far into the  UV however). </p>
<p>Whilst it is very unlikely that either value could be verified experimentally, it is  interesting that the optical rotation is as high as it is!</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Eutactic</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-2225</link>
		<dc:creator>Eutactic</dc:creator>
		<pubDate>Thu, 28 Jan 2010 14:06:58 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-2225</guid>
		<description><![CDATA[Whoops, that should be the cp radical C5H5.

I look forward to the rotation and dichroism results.]]></description>
		<content:encoded><![CDATA[<p>Whoops, that should be the cp radical C5H5.</p>
<p>I look forward to the rotation and dichroism results.</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Henry Rzepa</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-2223</link>
		<dc:creator>Henry Rzepa</dc:creator>
		<pubDate>Thu, 28 Jan 2010 12:56:03 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-2223</guid>
		<description><![CDATA[re the question about how to prepare enantiomers of twis-boat cyclohexane,  I think magic is probably the best bet.  But  the twist-boat is normally prepared by rapid quench of   high temperature cyclohexane on a super-cold surface. If that surface was itself chiral, one might at least be able to detect spectroscopically two  distinct  twist-boat sets of signals.

I will in fact calculate both  [&#945;]D  and the  OCD spectrum of the twist boat, to see exactly how large the optical properties are.]]></description>
		<content:encoded><![CDATA[<p>re the question about how to prepare enantiomers of twis-boat cyclohexane,  I think magic is probably the best bet.  But  the twist-boat is normally prepared by rapid quench of   high temperature cyclohexane on a super-cold surface. If that surface was itself chiral, one might at least be able to detect spectroscopically two  distinct  twist-boat sets of signals.</p>
<p>I will in fact calculate both  [&alpha;]D  and the  OCD spectrum of the twist boat, to see exactly how large the optical properties are.</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Eutactic</title>
		<link>http://www.ch.imperial.ac.uk/rzepa/blog/?p=1587&#038;cpage=1#comment-2221</link>
		<dc:creator>Eutactic</dc:creator>
		<pubDate>Thu, 28 Jan 2010 11:36:40 +0000</pubDate>
		<guid isPermaLink="false">http://www.ch.ic.ac.uk/rzepa/blog/?p=1587#comment-2221</guid>
		<description><![CDATA[A thought-provoking post. I&#039;m trying to get my head around how one might prepare the enantiomers of the twist-boat conformer mentioned. Heteroepitaxy on a chiral substrate? Magic?

There seems to be a dearth of discussion of symmetry breaking within the context of chemical structure. An interesting paper by Applegate, Barckholtz and Miller (DOI: &lt;a href=&quot;http://dx.doi.org/10.1039/a910269h&quot; target=&quot;new&quot; rel=&quot;nofollow&quot;&gt;10.1039/a910269h&lt;/a&gt;) on Jahn-Teller distortions of cyclopenadienyl radical depicts a PES gratifyingly akin to the &#039;Mexican Hat Function&#039; and how it gives rise to fluxional &#039;pseudo-rotary&#039; sequences of equienergetic allylic and dienic structures. This post reminded me of that.]]></description>
		<content:encoded><![CDATA[<p>A thought-provoking post. I&#8217;m trying to get my head around how one might prepare the enantiomers of the twist-boat conformer mentioned. Heteroepitaxy on a chiral substrate? Magic?</p>
<p>There seems to be a dearth of discussion of symmetry breaking within the context of chemical structure. An interesting paper by Applegate, Barckholtz and Miller (DOI: <a href="http://dx.doi.org/10.1039/a910269h" target="new" rel="nofollow">10.1039/a910269h</a><img src="http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/plugins/zlinks/imgs/mini_rdf.gif" border="0" style="cursor: pointer; padding:0px 0px 0px 1px; margin:0px;" onmouseover="assignPopup(this, 'http://dx.doi.org/10.1039/a910269h', 'http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/plugins/zlinks/');" alt="" />) on Jahn-Teller distortions of cyclopenadienyl radical depicts a PES gratifyingly akin to the &#8216;Mexican Hat Function&#8217; and how it gives rise to fluxional &#8216;pseudo-rotary&#8217; sequences of equienergetic allylic and dienic structures. This post reminded me of that.</p>
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