{"id":23187,"date":"2021-01-01T12:41:13","date_gmt":"2021-01-01T12:41:13","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=23187"},"modified":"2023-04-12T11:11:49","modified_gmt":"2023-04-12T10:11:49","slug":"dispersion-attraction-effects-on-the-computed-geometry-of-a-leminscular-dodecaporphrin","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23187","title":{"rendered":"Dispersion attraction effects on the computed geometry of a leminscular dodecaporphyrin."},"content":{"rendered":"
\n

In the previous post, I showed the geometries of three large cyclic porphyrins, as part of an article[1]<\/a><\/span> on exploring the aromaticity of large 4n+2 cyclic rings. One of them had been induced into a “figure-eight” or lemniscular conformation, as shown below.<\/p>\n

\"\"

c-P12[b12]_T6f optimised with LC-\u03c9hPBE<\/p><\/div>\n

\"\"

c-P12[b12]_T6f optimised with PM6<\/p><\/div>\n

Any initial inspection of the geometries of these systems suggests they have a high level of symmetry, and the molecule above does have the potential for D2<\/sub> symmetry, typical of such leminscates.[2]<\/a><\/span> The coordinates provided as part of the article however[1]<\/a><\/span> had no symmetry and in the previous post, I asked myself if the coordinates could be symmetrised. That proved possible for the first two molecules shown, and here I ask myself it it can be done for the molecule shown above. My method for symmetrising was to use the PM7 semi-empirical method.[3]<\/a><\/span> For the first time in the PM-series, this latest extension includes a Grimme-style dispersion attraction correction, one that grows in magnitude with the size of the molecule. Since this is a large molecule (720) atoms, dispersion might well have an important role to play. The coordinates provided[1]<\/a><\/span> were obtained using the LC-\u03c9hPBE\/6-31G* method, a functional which in its latest form does not include a built-in dispersion term, although one can be added to the earlier LC-\u03c9PBE version of the functional. We may presume that the calculation used to obtain the coordinates shown above does not include such a dispersion term.<\/p>\n

Here is the PM7 optimised version. Firstly, it has C2<\/sub>-symmetry only and not the higher D2<\/sub>. The reason is that the four porphyrin rings at the point of the ring crossover, which in the original version show no ring-ring stacking, now indeed show stacking of a pair of porphyrin rings when dispersion is included in the calculation.
\n

\"\"

c-P12b12_T6f optimized with PM7<\/p><\/div>
\nWhether such stacking, which does significantly perturb the overall geometry has any impact on the inferred aromaticity, remains to be established. But it reinforces the conclusion that when dealing with large molecules, it is absolutely essential to include a good quality dispersion correction, otherwise the geometries so obtained may differ significantly from reality.<\/p>\n

References<\/h2>\n
  1. M. Rickhaus, M. Jirasek, L. Tejerina, H. Gotfredsen, M.D. Peeks, R. Haver, H. Jiang, T.D.W. Claridge, and H.L. Anderson, \"Global aromaticity at the nanoscale\", Nature Chemistry<\/i>, vol. 12, pp. 236-241, 2020. https:\/\/doi.org\/10.1038\/s41557-019-0398-3<\/a>\n\n<\/li>\n
  2. H.S. Rzepa, \"A Double-Twist M\u00f6bius-Aromatic Conformation of [14]Annulene\", Organic Letters<\/i>, vol. 7, pp. 4637-4639, 2005. https:\/\/doi.org\/10.1021\/ol0518333<\/a>\n\n<\/li>\n
  3. J.J.P. Stewart, \"Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters\", Journal of Molecular Modeling<\/i>, vol. 19, pp. 1-32, 2012. https:\/\/doi.org\/10.1007\/s00894-012-1667-x<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    In the previous post, I showed the geometries of three large cyclic porphyrins, as part of an article on exploring the aromaticity of large 4n+2 cyclic rings. One of them had been induced into a “figure-eight” or lemniscular conformation, as shown below. Any initial inspection of the geometries of these systems suggests they have a […]<\/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":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_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":[4],"tags":[],"ppma_author":[2661],"class_list":["post-23187","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry"],"yoast_head":"\nDispersion attraction effects on the computed geometry of a leminscular dodecaporphyrin. - 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=23187\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Dispersion attraction effects on the computed geometry of a leminscular dodecaporphyrin. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In the previous post, I showed the geometries of three large cyclic porphyrins, as part of an article on exploring the aromaticity of large 4n+2 cyclic rings. One of them had been induced into a “figure-eight” or lemniscular conformation, as shown below. Any initial inspection of the geometries of these systems suggests they have a […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23187\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2021-01-01T12:41:13+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-04-12T10:11:49+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/12\/c-P12b12_T6f.jpg\" \/>\n<meta name=\"author\" content=\"Henry Rzepa\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Henry Rzepa\" \/>\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Dispersion attraction effects on the computed geometry of a leminscular dodecaporphyrin. - Henry Rzepa's Blog","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23187","og_locale":"en_GB","og_type":"article","og_title":"Dispersion attraction effects on the computed geometry of a leminscular dodecaporphyrin. - Henry Rzepa's Blog","og_description":"In the previous post, I showed the geometries of three large cyclic porphyrins, as part of an article on exploring the aromaticity of large 4n+2 cyclic rings. 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As I noted, these have an associated\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\/2022\/12\/cavitand.png?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":10870,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10870","url_meta":{"origin":23187,"position":1},"title":"The butterfly effect in chemistry: aromaticity on the edge of chaos.","author":"Henry Rzepa","date":"July 11, 2013","format":false,"excerpt":"The butterfly effect\u00a0summarises how a small change to a system may result in very large and often unpredictable (chaotic) consequences. If the system is merely on the edge of chaos, the consequences are predictable, but nevertheless finely poised between e.g. two possible outcomes. Here I ask how a molecule might\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":"","width":0,"height":0},"classes":[]},{"id":23134,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23134","url_meta":{"origin":23187,"position":2},"title":"Global aromaticity at the nanoscale.","author":"Henry Rzepa","date":"December 31, 2020","format":false,"excerpt":"Here is another of the \"large\" molecules in the c&e news shortlist for molecule-of-the-year, 2020. This one is testing the H\u00fcckel 4n+2 rule out to a value never before seen (n = 40, or 162 \u03c0-electrons). The take-home message is that this rule seems to behave well in predicting global\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.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/12\/c-P6e6_neutral.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":25043,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25043","url_meta":{"origin":23187,"position":3},"title":"Geometries of proton transfers: modelled using total energy or free energy?","author":"Henry Rzepa","date":"April 18, 2022","format":false,"excerpt":"Proton transfers are amongst the most common of all chemical reactions. They are often thought of as \"trivial\" and even may not feature in many mechanistic schemes, other than perhaps the notation \"PT\".\u00a0The types with the lowest energy barriers for transfer often involve heteroatoms such as N and O, and\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\/2022\/04\/plot-1024x734.png?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":29711,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29711","url_meta":{"origin":23187,"position":4},"title":"Mechanism of reaction between titanocene pentasulfide and sulfenyl chloride: The effect of continuum solvation on the energy surface.","author":"Henry Rzepa","date":"December 16, 2025","format":false,"excerpt":"An investigation of the kinetics of the reaction between titanocene pentasulfide and sulfenyl chloride leading to the formation of the S7 allotrope of sulfur was accompanied by supporting DFT calculations which led to the conclusion\u00a0that of five possible\u00a0mechanisms for the reaction, the most probable corresponded to a variant of 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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2025\/11\/BL12-17.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2025\/11\/BL12-17.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2025\/11\/BL12-17.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2025\/11\/BL12-17.jpg?resize=700%2C400&ssl=1 2x"},"classes":[]},{"id":27476,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=27476","url_meta":{"origin":23187,"position":5},"title":"Mechanism of the Masamune-Bergman reaction. Part 2: a possible 3D Model for Calicheamicin revealing the non-covalent-interactions (NCI) present.","author":"Henry Rzepa","date":"August 26, 2024","format":false,"excerpt":"Calicheamicin is a natural product with antitumour properties discovered in the 1980s, with the structure shown below. As noted elsewhere, this structure has many weird properties, including amongst other features an unusual \"enedidyne\" motif and the presence of an iodo group on an aromatic ring. Its\u00a0isolated 3D structure is quite\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":"","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","author_category":"1","first_name":"Henry","last_name":"Rzepa","user_url":"https:\/\/orcid.org\/0000-0002-8635-8390","job_title":"","description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London."}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/23187","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=23187"}],"version-history":[{"count":14,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/23187\/revisions"}],"predecessor-version":[{"id":26002,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/23187\/revisions\/26002"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=23187"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=23187"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=23187"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=23187"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}