{"id":2230,"date":"2010-07-15T08:50:36","date_gmt":"2010-07-15T07:50:36","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2230"},"modified":"2011-06-30T14:27:56","modified_gmt":"2011-06-30T14:27:56","slug":"non-covalent-interactions-nci-revisiting-pirkle","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2230","title":{"rendered":"Non-covalent interactions (NCI): revisiting  Pirkle"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"2230\">\n<p>NCI (non-covalent interactions) is the name of a fascinating new technique for identifying exactly these. Published <a href=\"http:\/\/dx.doi.org\/10.1021\/ja100936w\" target=\"_blank\">recently<\/a> by  Johnson, Keinan,  Mori-Snchez, Contreras-Garca, Cohen and Yang, it came to my attention at a conference to celebrate the 20th birthday of ELF when <a href=\"http:\/\/wiki.lct.jussieu.fr\/workshop\/index.php\/ELF_abstracts_page#J._Contreras-Garc.C3.ADa\" target=\"_blank\">Julia Contreras-Garcia<\/a> talked about the procedure. It is one of those methods which may seem as if it merely teases out the obvious about a molecule, but it is surprising how difficult seeing the obvious can be sometimes. I have blogged about this <a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=221\" target=\"_blank\">previously<\/a>, in discussing the so-called Pirkle reagent. On that occasion, I used the QTAIM technique to identify so-called critical points in the electron density. NCI goes one stage further in identifying surfaces of interaction rather than just single points, the idea being that this focuses attention on regions in molecules which are primarily responsible for binding, stereoselection and other aspects of molecular selectivity.<\/p>\n<div id=\"attachment_222\" style=\"width: 160px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-222\" class=\"size-full wp-image-222\" title=\"pirkle\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/pirkle.jpg\" alt=\"The Pirkle reagent\" width=\"150\" height=\"119\" \/><p id=\"caption-attachment-222\" class=\"wp-caption-text\">The Pirkle reagent<\/p><\/div>\n<p>So I was intrigued as to whether the  NCI method might find something that my analysis using the QTAIM procedure might have missed. The required program  is available for <a href=\"http:\/\/www.chem.duke.edu\/~yang\/Software\/softwareNCI.html\" target=\"_blank\">download<\/a>. I will not go into the theory behind the program, but like AIM, it uses the properties of the electron density via a combination of the first and second derivatives to concentrate on the non-bonded or weakly interacting regions of a molecule.<\/p>\n<div id=\"attachment_2234\" style=\"width: 426px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/pirkle2.jpg\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2234\" class=\"size-full wp-image-2234\" title=\"pirkle2\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/pirkle2.jpg\" alt=\"\" width=\"416\" height=\"399\" \/><\/a><p id=\"caption-attachment-2234\" class=\"wp-caption-text\">NCI interactions in the  Pirkle reagent<\/p><\/div>\n<p>The results of the analysis (using the SCF option in the program, and a  B3LYP\/6-31G calculation) are displayed using <a href=\"http:\/\/www.ks.uiuc.edu\/Research\/vmd\/\" target=\"_blank\">VMD<\/a>, and I cannot pull my usual trick of displaying the surface within the page of a blog via Jmol (although it seems Jmol with some effort could probably be persuaded to also render the information). So the above cannot be rotated. I have therefore circled one (there are others) interesting region in red. This encloses two surfaces. I should explain the colour coding adopted by the program. Red would be a repulsive interaction, and blue attractive. Weak interactions are shown in green. In the diagram above, these include the \u03c0-\u03c0 stacking  and various hydrogen bonds. But concentrating on the two surfaces inside the red circle, one occurs between the two hydrogens shown below. It catches the eye because there is a blue-tinge to the colour coding! This might mean it is a bit stronger than just &#8220;weak&#8221;.<\/p>\n<div id=\"attachment_2236\" style=\"width: 225px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/pirkle.jpg\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2236\" class=\"size-full wp-image-2236\" title=\"pirkle\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/pirkle.jpg\" alt=\"\" width=\"215\" height=\"173\" \/><\/a><p id=\"caption-attachment-2236\" class=\"wp-caption-text\">A Weak interaction in the  Pirkle reagent<\/p><\/div>\n<p>The NCI method I do not think is meant to provide a definitive answer to the question;  is that interaction real\/strong? It serves, as  I noted earlier, to  spike interest. Here, it does that, since this particular interaction had indeed never previously been identified for attention (the obvious had been missed!). Highlighting such potential regions of a molecule and perhaps then helping in the design of experiments to test if the interactions are real is what the NCI program is meant to do (IMHO)!<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 2230 -->","protected":false},"excerpt":{"rendered":"<p>NCI (non-covalent interactions) is the name of a fascinating new technique for identifying exactly these. Published recently by Johnson, Keinan, Mori-Snchez, Contreras-Garca, Cohen and Yang, it came to my attention at a conference to celebrate the 20th birthday of ELF when Julia Contreras-Garcia talked about the procedure. It is one of those methods which may [&hellip;]<\/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,"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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[4],"tags":[2648,249,572],"ppma_author":[2661],"class_list":["post-2230","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-interesting-chemistry","tag-julia-contreras-garcia","tag-watoc11"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Non-covalent interactions (NCI): revisiting Pirkle - Henry Rzepa&#039;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=2230\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Non-covalent interactions (NCI): revisiting Pirkle - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"NCI (non-covalent interactions) is the name of a fascinating new technique for identifying exactly these. Published recently by Johnson, Keinan, Mori-Snchez, Contreras-Garca, Cohen and Yang, it came to my attention at a conference to celebrate the 20th birthday of ELF when Julia Contreras-Garcia talked about the procedure. 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Each achieves its chiral magic by control of the geometry at the transition state for\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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":4254,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4254","url_meta":{"origin":2230,"position":1},"title":"Conformational restriction involving formyl CH&#8230;F hydrogen bonds.","author":"Henry Rzepa","date":"May 31, 2011","format":false,"excerpt":"The title of this post paraphrases E. J. Corey's article in 1997 (DOI:\u00a010.1016\/S0040-4039(96)02248-4) which probed the origins of conformation restriction in aldehydes. The proposal was of (then) unusual hydrogen bonding between the O=C-H...F-B groups. Here I explore whether the NCI (non-covalent-interaction) method can be used to cast light on this\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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\/05\/RUGYEX-x.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":4196,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4196","url_meta":{"origin":2230,"position":2},"title":"The inner secrets of an ion-pair: Isobornyl chloride rearrangements.","author":"Henry Rzepa","date":"May 29, 2011","format":false,"excerpt":"Observation of the slow racemization of isobornyl chloride in a polar solvent in 1923-24 by Meerwein led\u00a0to the recognition that mechanistic interpretation is the key to understanding chemical reactivity. The hypothesis of ion pairs in which a chloride anion is partnered by a carbocation long ago entered the standard textbooks\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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\/05\/isobornyl.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":4153,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4153","url_meta":{"origin":2230,"position":3},"title":"D\u00e9j\u00e0 vu: Pirkle for a third time!","author":"Henry Rzepa","date":"May 25, 2011","format":false,"excerpt":"This molecule is not leaving me in peace. It and I first met in 1990 (DO:\u00a010.1039\/C39910000765), when we spotted the two unusual \u03c0-facial bonds formed when it forms a loose dimer. The next step was to use QTAIM to formalise this interaction, and this led to spotting a second one\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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\/2010\/07\/pirkle.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":4038,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4038","url_meta":{"origin":2230,"position":4},"title":"Updating a worked problem in conformational analysis. Part 2: an answer.","author":"Henry Rzepa","date":"May 17, 2011","format":false,"excerpt":"The previous post set out a problem in conformational analysis. Here is my take, which includes an NCI (non-covalent interaction) display as discussed in another post. The lowest energies of the four diastereomers A-D, each in two conformations (1\/2) were calculated at the \u03c9B97D\/6-311G(d,p)\/SCRF=ethanol level, and are shown here relative\u2026","rel":"","context":"In \"conformational analysis\"","block_context":{"text":"conformational analysis","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=conformational-analysis"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/problem_sheet_answer42.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":4224,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4224","url_meta":{"origin":2230,"position":5},"title":"D\u00e9j\u00e0 vu all over again. Are H&#8230;H interactions attractive or repulsive?","author":"Henry Rzepa","date":"May 31, 2011","format":false,"excerpt":"The Pirkle reagent is a 9-anthranyl derivative (X=OH, Y=CF3). The previous post on the topic had highlighted DIST1, the separation of the two hydrogen atoms shown below. The next question to ask is how general this feature is. Here we take a look at the distribution of lengths found in\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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\/05\/9-anthranyl1.jpg?resize=350%2C200","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\/2230","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=2230"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/2230\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2230"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2230"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2230"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=2230"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}