{"id":811,"date":"2009-09-23T10:21:54","date_gmt":"2009-09-23T09:21:54","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=811"},"modified":"2011-04-03T06:18:06","modified_gmt":"2011-04-03T06:18:06","slug":"capturing-penta-coordinate-carbon-part-2","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=811","title":{"rendered":"Capturing penta-coordinate carbon! (Part 2)."},"content":{"rendered":"
\n

In this follow-up to the previous post, I will try to address the question what is the nature of the bonds in penta-coordinate carbon<\/strong>?<\/p>\n

This is a difficult question to answer with any precision, largely because our concept of a bond derives from trying to define what the properties of the electrons located in the region between any two specified atoms are. Such a local<\/strong> picture is somewhat at variance with the idea of electrons being delocalized across the entire molecule. Two procedures for analyzing the local electronic behaviour which we have been using recently are AIM (Atoms-in-Molecules) and ELF (the topology of the Electron localization function). There are many useful published articles which elaborate these concepts; if you want to read some of them, start at DOI 10.1021\/ct8001915<\/a> and follow the cited articles.<\/p>\n

Firstly, the AIM analysis of the system below, where X=cyclopentadienyl anion and Y=CN.<\/p>\n

\"The

The Sn2 transition state<\/p><\/div>\n

This is shown below. If you click on the image, you will see a rotatable version of this diagram. The coloured (red, yellow and green) dots represent so-called critical points in the curvature of the electron density function \u03c1(r). The red dots are known as bond critical points, or BCPs. These (almost) always are found along the line connecting two atoms which we tend to refer to as a bond. You will see two that have been circled in the diagram below, and these appear to show a bond connecting the central 5-coordinate carbon atom and a carbon of each of the cyclopentadienyl rings (which themselves are revealed as rings by the presence of a yellow dot). Indeed, that central carbon atom does seem to have five red dots radiating out along lines connecting it to five carbon atoms.<\/p>\n

\"AIM

AIM analysis (red = bond critical points, yellow = ring, green = cage)<\/p><\/div>So is the case proven for pentavalent carbon? Well, no. Firstly, one has to inspect the value of \u03c1(r) at the circled red dot. This has a (calculated) value of 0.022 au and a calculated bond length of ~2.7\u00c5.\u00a0We need to calibrate this against a real system as reported in DOI: 10.1021\/ja710423d<\/a> (below):<\/p>\n

\"Hexa-coordinate

Hexa-coordinate carbon. Click for 3D model<\/p><\/div>Here, the electron density \u03c1(r) was actually measured using X-ray diffraction, and found to be ~0.017 for bond critical points found connecting the central carbon and each of the four oxygen atoms. The length of these “bonds” was measured as \u00a0~2.7\u00c5. The agreement with our frozen transition state is quite striking.<\/p>\n

One can go a little further and inspect the (2nd) derivative of the electron density at the bond critical point, termed the Laplacian, or \u22072<\/sup>\u03c1, which tells what kind of “bond” one might have. The measured value of \u22072<\/sup>\u03c1 for the system above was ~0.06 au, and the calculated value for our pentacoordinate system is 0.04 au, which again suggests we are dealing with a very similar interaction in both systems (one hypothetical and calculated, the other real and measured). The use of the term \u00a0interaction<\/strong> was deliberate. \u00a0It is less loaded than the term \u00a0bond<\/strong>. Thus the value of \u03c1(r) for an undisputed C-C single bond is around 0.28 au, around ten times higher than our putative bonds. Since we do not really wish to grace a \u03c1(r) value of 0.022 with the term decibond <\/em>(or any other fraction of a single bond) <\/em>perhaps it is best to call it just an interaction, and leave open the question of how strong that interaction is! So, despite the \u00a0AIM analysis \u00a0finding a\u00a0bond critical point<\/em>, we shall settle for interpreting that merely as an interaction, and not a bond! \u00a0Well, is an interaction (or come to that, a decibond) worthy of counting towards a coordination? \u00a0Perhaps!<\/p>\n

So AIM can provide information about the curvature and density of the electrons in the region of a bond\/interaction. But it does not provide any information about another simple question which the term bond implies. How many electrons might be involved? Ever since \u00a0G. N. Lewis coined the term two-electron bond in 1916, \u00a0we have become used to interpreting bonds in terms of simple (often integer) numbers of electrons. \u00a0A carbon-carbon single bond shares two electrons; a double bond four electrons, and so on. We use this concept all the time in the technique known \u00a0as arrow-pushing, which helps us delineate mechanisms of reactions. Might it be possible to \u00a0identify how\u00a0many<\/strong> electrons are involved in bonds\/interactions of the captured \u00a0SN<\/sub>2\u00a0species above? Enter the ELF technique.\u00a0It would not be appropriate to delve into the theory of this method here; suffice to say that \u00a0(approximately), the \u00a0bond-critical-point of the \u00a0AIM analysis in this case would map to a disynaptic basin for ELF.\u00a0Thus a two-electron single bond will reveal a disynaptic basin (the centroid of which approximately matches the position of the \u00a0AIM BCP), which can be integrated to approximately two electrons. Shown below are the centroids of the disynaptic basins calculated for our SN<\/sub>2 species:<\/p>\n

\"ELF

ELF basins (purple dots) for the SN2 system. Click for 3D model<\/p><\/div>The most striking difference with the AIM analysis is that that the central carbon is surrounded only by three<\/strong>, not five<\/strong> disynaptic basins. The BCPs found for the two di-axial interactions have no counterpart in synaptic basins. Of course, that does not mean that there are no electrons that can be integrated in that region, just that the curvature of the density in that region is not sufficiently well defined to define a bounded volume of space which can be clearly integrated. Perhaps that condition is what we might mean by a bond!<\/p>\n

The three disynaptic basins that do surround the central carbon integrate to a total of 7.85 electrons, which is close enough to 8 for us to say that this carbon is NOT<\/strong> hypervalent!<\/p>\n

So what is our final conclusion? The frozen SN<\/sub>2 species is not<\/strong> hypervalent.\u00a0It could reasonably be said to be coordinated by three bonds, and two diaxial substituents that interact with the central carbon weakly.\u00a0Perhaps rather than penta-coordinate, the central carbon could be described as pentacoordinaloid<\/strong>!<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

In this follow-up to the previous post, I will try to address the question what is the nature of the bonds in penta-coordinate carbon? This is a difficult question to answer with any precision, largely because our concept of a bond derives from trying to define what the properties of the electrons located in the […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":5,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[7,4],"tags":[138,2649,2648,42],"ppma_author":[2661],"class_list":["post-811","post","type-post","status-publish","format-standard","hentry","category-hypervalency","category-interesting-chemistry","tag-aim-bcp","tag-hypervalency","tag-interesting-chemistry","tag-x-ray"],"yoast_head":"\nCapturing penta-coordinate carbon! (Part 2). - Henry Rzepa's Blog<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=811\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Capturing penta-coordinate carbon! (Part 2). - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In this follow-up to the previous post, I will try to address the question what is the nature of the bonds in penta-coordinate carbon? 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This is characterised by a central carbon with five coordinated ligands. The original suggestion included two astatine atoms as ligands (X=At), but in my post I suggested an alternative\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"The Sn2 transition state","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/sn2.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":10801,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10801","url_meta":{"origin":811,"position":1},"title":"Is CLi6 hypervalent?","author":"Henry Rzepa","date":"July 5, 2013","format":false,"excerpt":"A comment made on the previous post on the topic of hexa-coordinate carbon cited an article entitled \"Observation of hypervalent CLi6\u00a0by Knudsen-effusion mass spectrometry\" by Kudo as a amongst the earliest of evidence that such species can exist (in the gas phase). It was a spectacular vindication of the earlier\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/CLi6-Lp.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":878,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=878","url_meta":{"origin":811,"position":2},"title":"It’s Hexa-coordinate carbon Spock – but not as we know it!","author":"Henry Rzepa","date":"October 2, 2009","format":false,"excerpt":"Science is about making connections. And these can often be made between the most unlikely concepts. Thus in the posts I have made about pentavalent carbon, one can identify a series of conceptual connections. The\u00a0first, by Matthias\u00a0Bickelhaupt and co, resulted in the suggestion of a possible frozen\u00a0SN2 transition state. They\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"The HOMO orbital","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/C5-homo1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":783,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=783","url_meta":{"origin":811,"position":3},"title":"Capturing penta-coordinate carbon! (Part 1).","author":"Henry Rzepa","date":"September 22, 2009","format":false,"excerpt":"The bimolecular nucleophilic substitution reaction at saturated carbon is an icon of organic chemistry, and is better known by its mechanistic label, SN2. It is normally a slow reaction, with half lives often measured in hours. This implies a significant barrier to reaction (~15-20 kcal\/mol) for the transition state, shown\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"The Sn2 transition state","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/sn2.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17829,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17829","url_meta":{"origin":811,"position":4},"title":"First, hexacoordinate carbon – now pentacoordinate nitrogen?","author":"Henry Rzepa","date":"March 25, 2017","format":false,"excerpt":"A few years back I followed a train of thought here which ended with hexacoordinate carbon, then a hypothesis rather than a demonstrated reality. That reality was recently confirmed via a crystal structure,\u00a0DOI:10.5517\/CCDC.CSD.CC1M71QM. Here is a\u00a0similar proposal for\u00a0penta-coordinate nitrogen. First, a search of the CSD (Cambridge structure database) for such\u00a0nitrogen.\u2026","rel":"","context":"In "Bond slam"","block_context":{"text":"Bond slam","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2237"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":936,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=936","url_meta":{"origin":811,"position":5},"title":"Full circle with carbon hypervalencies","author":"Henry Rzepa","date":"October 2, 2009","format":false,"excerpt":"The previous post talked about making links or connections. And part of the purpose for presenting this chemistry as a blog is to expose how these connections are made, or or less as it happens in real time (and\u00a0not the chronologically sanitized version of discovery that most research papers are).\u00a0So\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"C4-symmetric pentavalent carbon","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/10\/c4.jpg?resize=350%2C200","width":350,"height":200},"classes":[]}],"jetpack_likes_enabled":false,"authors":[{"term_id":2661,"user_id":1,"is_guest":0,"slug":"admin","display_name":"Henry Rzepa","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/811","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=811"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/811\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=811"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=811"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=811"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=811"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}