{"id":20778,"date":"2019-04-25T19:20:52","date_gmt":"2019-04-25T18:20:52","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=20778"},"modified":"2019-04-25T19:20:52","modified_gmt":"2019-04-25T18:20:52","slug":"imaging-normal-vibrational-modes-of-a-single-molecule-of-cotpp-a-mystery-about-the-nature-of-the-imaged-species","status":"publish","type":"post","link":"https:\/\/www.rzepa.net\/blog\/?p=20778","title":{"rendered":"Imaging normal vibrational modes of a single molecule of CoTPP: a mystery about the nature of the imaged species."},"content":{"rendered":"
\n

Previously<\/a>, I explored (computationally) the normal vibrational modes of Co(II)-tetraphenylporphyrin (CoTPP) as a “flattened” species on copper or gold surfaces for comparison with those recently imaged[1]<\/a><\/span>. The initial intent was to estimate the “flattening” energy. There are six electronic possibilities for this molecule on a metal surface. Respectively positively, or negatively charged and a neutral species, each in either a low or a high-spin electronic state. I reported five of these earlier, finding each had quite high barriers for “flattening” the molecule. For the final 6th possibility, the triplet anion, the SCF (self-consistent-field) had failed to converge, but for which I can now report converged results.\u2020<\/sup><\/p>\n

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

Spin<\/p>\n

Multiplicity<\/p>\n<\/th>\n

\u0394G, Twisted Ph,
\nHartree<\/th>\n		\u0394G, “flattened”,
\nHartree<\/th>\n		\n

\u0394\u0394G,<\/p>\n

kcal\/mol<\/p>\n<\/th>\n<\/tr>\n

-1<\/td>\nTriplet<\/td>\n-3294.68134 (C2<\/sub>)<\/td>\n-3294.64735 (C2v<\/sub>)<\/td>\n21.3<\/strong><\/td>\n<\/tr>\n
-3294.60006 (Cs<\/sub>)<\/td>\n51.0<\/td>\n<\/tr>\n
-3294.37012 (D2h<\/sub>)<\/td>\n195.3<\/td>\n<\/tr>\n
Singlet<\/td>\n-3294.67713 (S4<\/sub>)<\/td>\n-3294.39418 (D4h<\/sub>)<\/td>\n175.6<\/td>\n<\/tr>\n
-3294.39321 (D2h<\/sub>)<\/td>\n178.2<\/td>\n<\/tr>\n
-3294.56652 (D2<\/sub>)<\/span><\/td>\n69.4<\/span><\/td>\n<\/tr>\n
FAIR data at DOI: 10.14469\/hpc\/5486<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

I am exploring the so-called “flattened” mode, induced by the voltage applied at the tip of the STM (scanning-tunnelling microscope) probe and which causes the phenyl rings to rotate as per above. This rotation in turn causes the hydrogen atom-pair encircled above to approach each other very closely.\u2021<\/sup> To avoid these repulsions, the molecule buckles into one of two modes. The first causes the phenyl rings to stack up\/down\/up\/down<\/em>. The second involves an all-up stacking, as shown below. Although these are in fact 4th-order saddle points as isolated molecules, the STM voltage can inject sufficient energy to convert these into apparently stable minima on the metal surface.<\/p>\n

\"\"

All syn mode, Triplet anion<\/p><\/div>\n

The up\/down\/up\/down<\/em> “flattened” form (below) shows a much more modest planarisation energy than all the other charged\/neutral states reported in the previous post<\/a>, whereas the all-up<\/em> isomer (which on the face of it looks a far easier proposition to come into close contact with a metal surface) is far higher in free energy.<\/p>\n

The caption to Figure 3 in the original article[1]<\/a><\/span> does not explicitly mention the nature of the metal surface on which the vibrations were recorded, but we do get “The intensity in the upper right corner of the 320-cm\u22121<\/sup> map is from a neighbouring Cu\u2013CO stretch”<\/em> which suggests it is in fact a copper surface. Coupled with the other observation that in “contrast to gold, the Kondo resonance of cobalt disappears on Cu(100), suggesting that it acquires nearly a full electron from the metal (see Extended Data Fig. 2)<\/em>,” the model below of a triplet-state anion on the Cu surface seems the most appropriate.<\/p>\n

\"\"

Syn\/anti mode, Triplet anion with C2v symmetry<\/p><\/div>\n

There is one final remark made in the article worth repeating here: “This suggests that the vibronic functions are complex-valued in this state, as expected for Jahn\u2013Teller active degenerate orbitals of the planar porphyrin.26<\/sup><\/em>” Orbital degeneracy can only occur if the molecule has e.g.<\/i> D4h<\/sub> point group symmetry, whereas the triplet anion stationary-point shown in the figure above has only C2v<\/sub> symmetry for which no orbital degeneracies (E) are expected. Enforcing D4h<\/sub> symmetry on Co(II) tetraphenylporphyrin results in eight pairs of H…H contacts of 1.34\u00c5,\u2021<\/sup> which is an impossibly short distance (the shortest known is ~1.5\u00c5). Moreover this geometry has an equally impossible free energy 176 kcal\/mol above the relaxed free molecule. Visually from Figure 3, the H…H contact distance looks even shorter (below, circled in red)! A D2h<\/sub> form (with no E-type orbitals) can also be located.<\/p>\n\n\n\n\n
\n
\"\"

Singlet, Calculated with D4h<\/sub> symmetry. Click for vibrations.<\/strong><\/p><\/div>\n<\/td>\n

\n
\"\"

Singlet, Calculated with D2h<\/sub> symmetry. Click for vibrations.<\/strong><\/p><\/div>\n<\/td>\n<\/tr>\n

\n
\"\"

Taken from Figure 3 (Ref 1).<\/strong><\/p><\/div>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

These totally flat species are calculated to be at 13 or 12th-order saddle points, with the eight most negative force constants having vectors which correspond to up\/down avoidance motions of the proximate hydrogen pairs encircled above and the remaining being buckling modes of the entire ring.<\/p>\n

So to the mystery, being the nature of the “flattened” CoTPP on the copper metal surface, as represented in Figure 3 of the article.[1]<\/a><\/span> Is it truly flat, as implied by the article? If so, the energy of such a species would be beyond the limits of what is normally considered feasible. Moreover, it would represent a species with truly mind-blowing short H…H contacts. Or could it be a saddle-shaped geometry, where the phenyl rings are not lying flat in contact with the metal but interacting via<\/em> the phenyl para-hydrogens? That geometry has not only a much more reasonable energy above the unflattened free molecule, but also acceptable H…H contacts (~2.0.Å) However, would such a shape correspond to the visualised vibrational modes also shown in Figure 3? I have a feeling that there must be more to this story.<\/p>\n

\n

\u2020<\/sup>These convergence problems were solved by improving the basis set via<\/em> adding “diffuse” functions, as in (u)\u03c9B97XD\/6-311+G(d,p). \u2021<\/sup>If the crystal structure for these species is flattened without geometry optimisation, the H-H distance is around 0.8\u00c5<\/p>\n

References<\/h2>\n
  1. J. Lee, K.T. Crampton, N. Tallarida, and V.A. Apkarian, \"Visualizing vibrational normal modes of a single molecule with atomically confined light\", Nature<\/i>, vol. 568, pp. 78-82, 2019. https:\/\/doi.org\/10.1038\/s41586-019-1059-9<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    Previously, I explored (computationally) the normal vibrational modes of Co(II)-tetraphenylporphyrin (CoTPP) as a “flattened” species on copper or gold surfaces for comparison with those recently imaged. The initial intent was to estimate the “flattening” energy. There are six electronic possibilities for this molecule on a metal surface. Respectively positively, or negatively charged and a neutral […]<\/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,"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":[6],"tags":[2514,1999,2531,2542,510,2544,1416,1422,1423,2551,2552,2554,2560,147,164,185,2578,1463,1467,2582,2587,246,2589,2591,1987,2595,2603,2604,2605,2615,1604,2626,2635,2637,2638],"class_list":["post-20778","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-019-1059-9","tag-10-1038","tag-biomolecules","tag-chelating-agents","tag-chemical-bonding","tag-chemical-compounds","tag-chemistry","tag-coordination-chemistry","tag-coordination-complex","tag-copper","tag-copper-metal-surface","tag-cu-co","tag-e-type","tag-energy","tag-free-energy","tag-higher-energy","tag-impossible-free-energy","tag-inorganic-chemistry","tag-jahn-teller-effect","tag-lowest-energy-electronic-state","tag-metabolism","tag-metal","tag-metal-surface","tag-modest-planarisation-energy","tag-molecule","tag-natural-sciences","tag-physical-sciences","tag-planarisation","tag-porphyrin","tag-reasonable-energy","tag-resonance","tag-solid-state-chemistry","tag-sufficient-energy","tag-teller","tag-tetraphenylporphyrin"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p1gPyz-5p8","jetpack_likes_enabled":true,"_links":{"self":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/20778","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=20778"}],"version-history":[{"count":0,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/20778\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=20778"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=20778"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=20778"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}