{"id":276,"date":"2020-12-25T17:19:54","date_gmt":"2020-12-25T17:19:54","guid":{"rendered":"https:\/\/sciting.eu\/sciting\/?page_id=276"},"modified":"2020-12-27T07:59:46","modified_gmt":"2020-12-27T07:59:46","slug":"organic-chemistry-iii","status":"publish","type":"page","link":"https:\/\/sciting.eu\/sciting\/samples\/pedagogical-resources\/organic-chemistry-iii\/","title":{"rendered":"Organic chemistry (III)"},"content":{"rendered":"\n<p>The mechanism of the <strong>H<sup>5<\/sup>C<sup>5x<\/sup> <\/strong>(free radical intramolecular hydrogen abstraction followed by intramolecular addition to an alkene) reaction represented as an animation of the energy profile as well as the SOMO (singly occupied molecular orbital) wave functions.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large is-style-default\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"768\" src=\"https:\/\/sciting.eu\/sciting\/wp-content\/uploads\/2020\/12\/cube.066.SOMOE_-1024x768.png\" alt=\"\" class=\"wp-image-277\" srcset=\"https:\/\/sciting.eu\/sciting\/wp-content\/uploads\/2020\/12\/cube.066.SOMOE_-1024x768.png 1024w, https:\/\/sciting.eu\/sciting\/wp-content\/uploads\/2020\/12\/cube.066.SOMOE_-300x225.png 300w, https:\/\/sciting.eu\/sciting\/wp-content\/uploads\/2020\/12\/cube.066.SOMOE_-768x576.png 768w, https:\/\/sciting.eu\/sciting\/wp-content\/uploads\/2020\/12\/cube.066.SOMOE_-1536x1152.png 1536w, https:\/\/sciting.eu\/sciting\/wp-content\/uploads\/2020\/12\/cube.066.SOMOE_.png 1920w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>We provide the animation in three formats in case that the two first are not compatible with all browsers. If any given image is not animated, please, move down to the next format (they should work in recent versions of Firefox and Chrome). The animated images are too heavy to be embedded here, they can be downloaded from the following links:<\/p>\n\n\n\n<p><a href=\"https:\/\/sciting.eu\/sciting\/wp-content\/uploads\/pics\/H5C5x_energy_SOMO.png\" target=\"_blank\" rel=\"noreferrer noopener\">APNG<\/a> version.<\/p>\n\n\n\n<p><a href=\"https:\/\/sciting.eu\/sciting\/wp-content\/uploads\/pics\/H5C5x_energy_SOMO.webp\" target=\"_blank\" rel=\"noreferrer noopener\">WEBP<\/a> version.<\/p>\n\n\n\n<p>Video: <\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-4-3 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"Mechanism of an intramolecular free radical chain reaction\" width=\"500\" height=\"375\" src=\"https:\/\/www.youtube.com\/embed\/z-LZZ5v9p7w?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<p>CREDITS<\/p>\n\n\n\n<p>The QM calculations were carried out with <a href=\"https:\/\/orcaforum.kofo.mpg.de\/app.php\/portal\">ORCA<\/a> at the UHF\/RI-MP2\/ma-def2-TZVP level of theory, whereas the <a href=\"https:\/\/sites.google.com\/site\/orcainputlibrary\/printing-and-visualization\">orca_plot<\/a> program was used to generate the Cube files that were subsequently rendered with <a href=\"https:\/\/www.ks.uiuc.edu\/Research\/vmd\/\">VMD<\/a> with the help of a customised <a href=\"https:\/\/github.com\/psi4\/psi4\/blob\/master\/psi4\/share\/psi4\/scripts\/vmd_cube.py\">vmd_cube<\/a> script (Python 2).<\/p>\n\n\n\n<p>Other tools employed include <a href=\"http:\/\/gabedit.sourceforge.net\/\">Gabedit<\/a>, ImageMagick, Inkscape, img2webp, ffmpeg and Matplotlib, powered by Manjaro Linux.<\/p>\n\n\n\n<p>This work is inspired by the second part of my <a href=\"https:\/\/doi.org\/10.1021\/ol060231w\" target=\"_blank\" rel=\"noreferrer noopener\">PhD thesis<\/a>.<\/p>\n\n\n\n<p>Even though they are not intended for distribution, I can make available the Python 3 and Bash scripts I wrote in order to automatise the tasks.<\/p>\n\n\n\n<p><\/p>\n\n\n\n<div class=\"wp-block-image is-style-default\"><figure class=\"aligncenter size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"286\" height=\"361\" src=\"https:\/\/sciting.eu\/sciting\/wp-content\/uploads\/2020\/12\/sciting_logo_medium.png\" alt=\"\" class=\"wp-image-280\" srcset=\"https:\/\/sciting.eu\/sciting\/wp-content\/uploads\/2020\/12\/sciting_logo_medium.png 286w, https:\/\/sciting.eu\/sciting\/wp-content\/uploads\/2020\/12\/sciting_logo_medium-238x300.png 238w\" sizes=\"auto, (max-width: 286px) 100vw, 286px\" \/><\/figure><\/div>\n","protected":false},"excerpt":{"rendered":"<p>The mechanism of the H5C5x (free radical intramolecular hydrogen abstraction followed by intramolecular addition to an alkene) reaction represented as an animation of the energy profile as well as the SOMO (singly occupied molecular orbital) wave functions. We provide the animation in three formats in case that the two first are not compatible with all [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":246,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-276","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/pages\/276","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/comments?post=276"}],"version-history":[{"count":8,"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/pages\/276\/revisions"}],"predecessor-version":[{"id":293,"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/pages\/276\/revisions\/293"}],"up":[{"embeddable":true,"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/pages\/246"}],"wp:attachment":[{"href":"https:\/\/sciting.eu\/sciting\/wp-json\/wp\/v2\/media?parent=276"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}