{"id":16758,"date":"2016-09-11T08:55:52","date_gmt":"2016-09-11T07:55:52","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16758"},"modified":"2016-09-17T13:34:48","modified_gmt":"2016-09-17T12:34:48","slug":"whats-in-a-name-carbenes-a-reality-check","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16758","title":{"rendered":"What’s in a name? Carbenes: a reality check."},"content":{"rendered":"
\n

To quote<\/a> from Wikipedia: in chemistry, a carbene is a molecule containing a neutral carbon atom with a valence of two and two unshared valence electrons<\/em>. The most ubiquitous type of carbene of recent times is the one shown below as 1<\/strong>, often referred to as a resonance stabilised or persistent carbene<\/a><\/em>. This type is of interest because of its\u00a0ability to act as a ligand to an astonishingly wide variety of metals, with many of the resulting complexes being\u00a0important catalysts. The Wiki page on persistent carbenes shows them throughout in form 1<\/strong> below, thus reinforcing the belief that they have a valence of two and by implication six (2×2 shared + 2 unshared) electrons in the valence shell of carbon. Here I consider whether this name is really appropriate.<\/p>\n

\"carbenes\"<\/a><\/p>\n

Let us start by counting the\u00a0electrons in the 2p atomic orbitals on the ring atoms of 1<\/strong>, forming what we call a \u03c0-system. There are six; two from the carbons shown connected by a double bond, C=C and a further four from the two nitrogen lone pairs. Now in benzene, we also have six\u00a0\u03c0-electrons in a ring and this molecule is of course famously aromatic due to the diatropic ring current created by the circulation of these six electrons. Moreover, all the C-C bonds are equal in length, ~1.4\u00c5 long (although the reasons for this equality<\/a> are subtle).<\/p>\n

So does\u00a01<\/strong> behave similarly? A \u03c9B97XD\/Def2-TZVPP calculation[1]<\/a><\/span> shows the following calculated structure, in which all the bonds are clearly intermediate between single and double. The N-C(“carbene”) length of 1.357\u00c5 in particular is much shorter than a C-N\u00a0single bond (~1.44A\u00c5), which tends to suggest that the resonance form 2<\/strong> is a better representation than 1<\/strong>. This form is also pretty similar to pyrrole, itself a well-known hetero-aromatic species.\"nhc1\"<\/p>\n

An alternative reality check is crystal structures. There are 42 examples (no errors, no disorder, R < 0.05) in the Cambridge structure database (CSD) and the distribution of C-N bond lengths\u00a0below is indeed quite similar to the calculation shown above for the unsubstituted parent, with the lhs “hot-spot” almost exactly coincident. The C-C length similarly corresponds.<\/p>\n

\"nhc2\"<\/p>\n

\"nhc3\"<\/p>\n

Let us try a\u00a0technique for explicitly counting electrons, the ELF (electron localisation method), which works directly on a function of the electron density to identify the centroids of\u00a0localized “basins” containing the integrated density. The three surrounding the “carbene” atom sum to 7.54e (with small\u00a0seepage also into the carbon 1s core; 2.08e). A “normal” carbon on the C=C bond is 7.65e. The localization below\u00a0turns out to\u00a0closely resemble resonance structure 2<\/strong> above.<\/p>\n

\"nhc4\"<\/p>\n

Further in-silico<\/em> experiments can be carried out with species 3<\/strong> and 4<\/strong>, in which a carbon atom replaces each of the nitrogens. This reduces the total electron count by two and now this poor molecule has a difficult choice to make. Should it be the\u00a0\u03c0-system that sacrifices these two electrons, or could it be the \u03c3-lone-pair found on the two-coordinate carbon? We will let the quantum mechanical solution decide[2]<\/a><\/span> (with a constraint that the molecule be planar). The electrons arrange themselves to resemble the resonance form 4, <\/strong>choosing to retain the six\u00a0\u03c0-electrons and sacrifice the carbene “unshared pair”. The 2-coordinate carbon as a vinyl cation now does have ~6 valence electrons (ELF indicates 5.23e).\u00a0\"nhc5\"<\/p>\n

What about the other choice? By promoting two electrons from HOMO to LUMO one can also calculate 3<\/strong>\u00a0(again constrained to planarity)[3]<\/a><\/span> which finally does correspond to the classical description of a carbene.<\/p>\n

\"nhc6\"<\/p>\n

The arrow connecting 3<\/strong> and 4<\/strong>\u00a0in the scheme at the top is NOT<\/strong> in this case an electronic resonance, but a a real equilibrium between two different species separated by an energy barrier. With only four\u00a0\u03c0-electrons in a cycle it is also antiaromatic<\/em>, and so the two localised alkene bonds avoid any conjugation with each other.\u00a0This form has a\u00a0free energy some 5.7 kcal\/ml higher than the aromatic form. In fact, the molecule is very keen to avoid all antiaromaticity<\/a> and hence if the planar constraint is lifted, it will distort with no activation to a non-planar diene (just as cyclo-octatetraene does to a non-planar tetra-ene). And to complete the tale, even though 4<\/strong> is aromatic, it too distorts without activation to an odd-looking non-planar form with no symmetry[4]<\/a><\/span>,[5]<\/a><\/span>,[6]<\/a><\/span> (but that is another story).<\/p>\n

The final word should be that the naming of these types of persistent carbene does need a reality check; they should not be called this at all! They are really dipolar species or carbon-ylides as shown in 2<\/strong>. As it happens, a very closely related species in which one sulfur replaces one nitrogen is a very familiar compound, vitamin B1 or thiamine<\/a>. The only example of a\u00a0stable deprotonated thiamine derivative\u00a0is referred to as a carbene[7]<\/a><\/span>, perhaps because with an acid catalyst it can dimerise in the manner expected of a real carbene. Significantly however, without acid catalyst this does not happen; a true carbene would not require such a catalyst.<\/p>\n

References<\/h2>\n
  1. H. Rzepa, \"NHC wfn\", 2016. https:\/\/doi.org\/10.14469\/hpc\/1473<\/a>\n\n<\/li>\n
  2. H. Rzepa, \"butadiene carbene aromatic -192.700746\", 2016. https:\/\/doi.org\/10.14469\/hpc\/1581<\/a>\n\n<\/li>\n
  3. H. Rzepa, \"butadiene carbene antiaromatic guess=alter -192.691607\", 2016. https:\/\/doi.org\/10.14469\/hpc\/1582<\/a>\n\n<\/li>\n
  4. H. Rzepa, \"C5H4 non-planar, Cs symmetry\", 2016. https:\/\/doi.org\/10.14469\/hpc\/1583<\/a>\n\n<\/li>\n
  5. H. Rzepa, \"C5H4 non-planar, C2 symmetry\", 2016. https:\/\/doi.org\/10.14469\/hpc\/1584<\/a>\n\n<\/li>\n
  6. H. Rzepa, \"C5H4 non-planar, no symmetry\", 2016. https:\/\/doi.org\/10.14469\/hpc\/1585<\/a>\n\n<\/li>\n
  7. A.J. Arduengo, J.R. Goerlich, and W.J. Marshall, \"A Stable Thiazol\u20102\u2010ylidene and Its Dimer\", Liebigs Annalen<\/i>, vol. 1997, pp. 365-374, 1997. https:\/\/doi.org\/10.1002\/jlac.199719970213<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    To quote from Wikipedia: in chemistry, a carbene is a molecule containing a neutral carbon atom with a valence of two and two unshared valence electrons. The most ubiquitous type of carbene of recent times is the one shown below as 1, often referred to as a resonance stabilised or persistent carbene. This type is […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":true,"_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":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[1745,1],"tags":[1411,557,939,40,1412,1552,1853,1848,1850,1854,1849,1852,1634,1851],"ppma_author":[2661],"class_list":["post-16758","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","category-general","tag-carbenes","tag-chemical-bonding","tag-energy-barrier","tag-free-energy","tag-functional-groups","tag-ligand","tag-mesoionic-carbene","tag-organometallic-chemistry","tag-persistent-carbene","tag-quantum-mechanical-solution","tag-reactive-intermediates","tag-transition-metal-carbene-complex","tag-valence","tag-valence-electron"],"yoast_head":"\nWhat's in a name? 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Stabilised “nitrenes”.","author":"Henry Rzepa","date":"September 19, 2016","format":false,"excerpt":"I previously explored stabilized \"carbenes\" with the formal structures (R2N)2C:, concluding that perhaps the alternative ionic representation R2N+=C-NR2\u00a0might reflect their structures better. Here I take a broader look at the \"carbene\" landscape before asking the question \"what about nitrenes?\" The top row shows the compounds for which no crystal structure\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"nitrene1","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/nitrene1-1024x655.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":19307,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19307","url_meta":{"origin":16758,"position":1},"title":"Are diazomethanes hypervalent molecules? An attempt into more insight by more “tuning” with substituents.","author":"Henry Rzepa","date":"December 26, 2017","format":false,"excerpt":"Recollect the suggestion\u00a0that diazomethane has hypervalent character. When I looked into this, I came to the conclusion that it probably was mildly hypervalent, but on carbon and not nitrogen. Here I try some variations with substituents to see what light if any this casts. I have expanded the resonance forms\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/12\/H2CNCCN_ELF-1024x258.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":14037,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14037","url_meta":{"origin":16758,"position":2},"title":"R-X\u2261X-R: G. N. Lewis’ 100 year old idea.","author":"Henry Rzepa","date":"May 22, 2015","format":false,"excerpt":"As I have noted elsewhere, Gilbert N. Lewis wrote a famous paper entitled \"the atom and the molecule\", the centenary of which is coming up. In a short and rarely commented\u00a0upon remark, he speculates about the shared electron pair structure of acetylene,\u00a0\u00a0R-X\u2261X-R (R=H, X=C). It could, he suggests, take up\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1423,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1423","url_meta":{"origin":16758,"position":3},"title":"Contriving aromaticity from S\u2261C Triple bonds","author":"Henry Rzepa","date":"January 1, 2010","format":false,"excerpt":"In the previous post, the molecule F3S-C\u2261SF3 was found to exhibit a valence bond isomerism, one of the S-C bonds being single, the other triple, and with a large barrier (~31 kcal\/mol, \u03bd 284i cm-1) to interconversion of the two valence-bond forms. So an interesting extension of this phenomenon is\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/01\/S3C3F6.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":11421,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11421","url_meta":{"origin":16758,"position":4},"title":"Six vs ten aromatic electrons?","author":"Henry Rzepa","date":"October 20, 2013","format":false,"excerpt":"Homoaromaticity is a special case of\u00a0aromaticity\u00a0in which\u00a0\u03c0-conjugation\u00a0is interrupted by a single sp3\u00a0hybridized\u00a0carbon atom (it is sometimes referred to as a suspended \u03c0-bond with no underlying \u03c3-foundation).\u00a0But consider the carbene shown below. This example comes from a recently published article which was highlighted on Steve Bachrach's blog. Here aromaticity has resulted\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/10\/B10-sigma.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":26601,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26601","url_meta":{"origin":16758,"position":5},"title":"Molecules of the year: 2023","author":"Henry Rzepa","date":"December 28, 2023","format":false,"excerpt":"The Science education unit at the ACS publication C&EN publishes its list of molecules of the year (as selected by the editors and voted upon by the readers) in December. Here are some observations about three of this year's batch. Diberyllocene with its unusual Be-Be bond has already beeen covered\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2023\/12\/CF.gif?resize=350%2C200&ssl=1","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\/16758","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=16758"}],"version-history":[{"count":38,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16758\/revisions"}],"predecessor-version":[{"id":16818,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16758\/revisions\/16818"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16758"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16758"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16758"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16758"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}