{"id":17702,"date":"2017-03-16T13:53:00","date_gmt":"2017-03-16T13:53:00","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=17702"},"modified":"2017-03-17T07:24:35","modified_gmt":"2017-03-17T07:24:35","slug":"how-does-methane-invert-its-configuration","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17702","title":{"rendered":"How does methane invert (its configuration)?"},"content":{"rendered":"
\n

This is a spin-off from the table I constructed here<\/a> for further chemical examples of the classical\/non-classical norbornyl cation conundrum. One possible entry would include the transition state for inversion of methane via<\/em> a square planar geometry as compared with e.g.<\/em> NiH4<\/sub> for which the square planar motif is its minimum. So is square planar methane a true transition state for inversion (of configuration) of carbon?<\/p>\n

The history of this topic is nicely told as far back as 1993[1]<\/a><\/span>, when square planar methane was shown to be a\u00a04th-order saddle point (i.e.<\/em> four negative force constants) and not the first order one required of a transition state. A true transition state was located,\u2021<\/sup> and here I show it as part of an animated IRC (intrinsic reaction coordinate). Go to DOI:\u00a010.14469\/hpc\/2288<\/a>\u00a0for the calculation outputs.<\/p>\n

\"\"<\/p>\n

To convince yourself that the configuration really does invert, focus on the CIP rule. With atom 1 pointing behind, atoms 2 \u2192 3\u00a0 \u2192 4 rotate in a clockwise direction. Now focus on the final point at the end of the IRC, when\u00a02 \u2192 3\u00a0 \u2192 4 rotate anti-clockwise. The configuration has inverted! The barrier as can be seen below is ~118 kcal\/mol. At this value the half-life\u00a0for the process would be far longer than the age of the universe.<\/p>\n

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

The process can be described as an interesting variation on\u00a0pseudorotation, for which the classic example is of course PF5<\/sub>.\u2020<\/sup> Alternatively it can be thought of as the partial extrusion of H2<\/sub> to give carbene, followed by re-addition of the H2<\/sub> to reform methane. Partial because the extrusion is never fully achieved.<\/p>\n

I have to say I did not expect anything quite so interesting to be associated with methane; \u00a0one can learn from the simplest of molecules!<\/p>\n

\n

\u2021<\/sup> It was not entirely trivial to recover appropriate coordinates for recomputing this TS from the article. But it is in fact an easy one to find from scratch. Hopefully with the files at 10.14469\/hpc\/2288<\/a> to help, this will not be an issue here.<\/p>\n

\u2020<\/sup>There are many kinds of pseudo-rotations. For others see here.[2]<\/a><\/span> and [3]<\/a><\/span><\/p>\n

References<\/h2>\n
  1. M.S. Gordon, and M.W. Schmidt, \"Does methane invert through square planar?\", Journal of the American Chemical Society<\/i>, vol. 115, pp. 7486-7492, 1993. https:\/\/doi.org\/10.1021\/ja00069a056<\/a>\n\n<\/li>\n
  2. H.S. Rzepa, and M.E. Cass, \"A Computational Study of the Nondissociative Mechanisms that Interchange Apical and Equatorial Atoms in Square Pyramidal Molecules\", Inorganic Chemistry<\/i>, vol. 45, pp. 3958-3963, 2006. https:\/\/doi.org\/10.1021\/ic0519988<\/a>\n\n<\/li>\n
  3. H.S. Rzepa, and M.E. Cass, \"In Search of the Bailar and R\u00e2y\u2212Dutt Twist Mechanisms That Racemize Chiral Trischelates:\u2009 A Computational Study of Sc<sup>III<\/sup>, Ti<sup>IV<\/sup>, Co<sup>III<\/sup>, Zn<sup>II<\/sup>, Ga<sup>III<\/sup>, and Ge<sup>IV<\/sup> Complexes of a Ligand Analogue of Acetylacetonate\", Inorganic Chemistry<\/i>, vol. 46, pp. 8024-8031, 2007. https:\/\/doi.org\/10.1021\/ic062473y<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    This is a spin-off from the table I constructed here for further chemical examples of the classical\/non-classical norbornyl cation conundrum. One possible entry would include the transition state for inversion of methane via a square planar geometry as compared with e.g. NiH4 for which the square planar motif is its minimum. So is square planar […]<\/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":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}},"categories":[1086],"tags":[1395,2063,1630,2065,2064,2062,1560],"ppma_author":[2661],"class_list":["post-17702","post","type-post","status-publish","format-standard","hentry","category-reaction-mechanism-2","tag-chemistry","tag-methane","tag-molecular-geometry","tag-orbital-hybridisation","tag-planar","tag-square-planar-molecular-geometry","tag-stereochemistry"],"yoast_head":"\nHow does methane invert (its configuration)? - 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=17702\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"How does methane invert (its configuration)? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"This is a spin-off from the table I constructed here for further chemical examples of the classical\/non-classical norbornyl cation conundrum. 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One possible entry would include the transition state for inversion of methane via a square planar geometry as compared with e.g. NiH4 for which the square planar motif is its minimum. 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A ten minute exploration.","author":"Henry Rzepa","date":"April 30, 2014","format":false,"excerpt":"I love experiments where the insight-to-time-taken ratio is high. This one pertains to exploring the coordination chemistry of the transition metal region of the periodic table; specifically the tetra-coordination of the series headed by\u00a0Mn-Ni. Is the geometry tetrahedral, square planar, or other? One can get a statistical answer in about\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":"Tet-SP.jpg","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/04\/Tet-SP.jpg.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":21883,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21883","url_meta":{"origin":17702,"position":1},"title":"Molecules of the year 2019: Hexagonal planar crystal structures.","author":"Henry Rzepa","date":"January 23, 2020","format":false,"excerpt":"Here is another selection from the Molecules-of-the-Year shortlist published by C&E News, in which hexagonal planar transition metal coordination is identified. This was a mode of metal coordination first mooted more than 100 years ago, but with the first examples only being discovered recently.\u00a0The C&E News example comprises a central\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":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/01\/norloy-300x263.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":4952,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4952","url_meta":{"origin":17702,"position":2},"title":"The importance of being complete.","author":"Henry Rzepa","date":"September 26, 2011","format":false,"excerpt":"To (mis)quote Oscar Wilde again, \"\u201cTo lose one methyl group may be regarded as a misfortune; to lose both looks like carelessness.\u201d Here, I refer to the (past) tendency of molecular modellers to simplify molecular structures. Thus in 1977, quantum molecular modelling, even at the semi-empirical level, was beset by\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":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/09\/cbdzw1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":16619,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16619","url_meta":{"origin":17702,"position":3},"title":"Pyrophoric metals + the mechanism of thermal decomposition of magnesium oxalate.","author":"Henry Rzepa","date":"March 19, 2017","format":false,"excerpt":"A pyrophoric metal is one that burns spontaneously in oxygen; I came across this phenomenon as a teenager doing experiments at home. Pyrophoric iron for example is prepared by heating anhydrous iron (II) oxalate in a sealed test tube (i.e. to 600\u00b0 or higher). When the tube is broken open\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":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/155-1024x363.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17710,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17710","url_meta":{"origin":17702,"position":4},"title":"How does silane invert (its configuration)?","author":"Henry Rzepa","date":"March 16, 2017","format":false,"excerpt":"In the previous post, I found intriguing the mechanism by which methane (CH4) inverts by transposing two of its hydrogens. Here I take a look at silane, SiH4. It appears it is a three-stage process! Firstly, silane eliminates molecular hydrogen to form a molecular complex between H2\u00a0and SiH2 (DOI:\u00a010.14469\/hpc\/2290). The\u2026","rel":"","context":"In "reaction mechanism"","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/gaussian-78_tot_ener.svg","width":350,"height":200},"classes":[]},{"id":17771,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17771","url_meta":{"origin":17702,"position":5},"title":"Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism.","author":"Henry Rzepa","date":"March 20, 2017","format":false,"excerpt":"The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate\u00a0(IRC). Here I explore an alternative method based instead on computing a molecular\u2026","rel":"","context":"In "reaction mechanism"","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"","width":0,"height":0},"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\/17702","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=17702"}],"version-history":[{"count":3,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17702\/revisions"}],"predecessor-version":[{"id":17708,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17702\/revisions\/17708"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=17702"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=17702"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=17702"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=17702"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}