{"id":17279,"date":"2016-12-24T08:19:43","date_gmt":"2016-12-24T08:19:43","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=17279"},"modified":"2017-01-07T09:37:20","modified_gmt":"2017-01-07T09:37:20","slug":"the-dipole-moments-of-highly-polar-molecules-glycine-zwitterion","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17279","title":{"rendered":"The dipole moments of highly polar molecules: glycine zwitterion."},"content":{"rendered":"
\n

The previous posts produced discussion<\/a> about the dipole moments of highly polar molecules<\/a>. Here to produce some reference points for further discussion I look at the dipole moment of glycine, the classic\u00a0zwitterion (an internal ion-pair).<\/p>\n

Dielectric<\/span> relaxation<\/span> studies of glycine<\/span>–water<\/span> mixtures yield values that range from\u00a015.7D<\/span><\/strong>[1]<\/a><\/span> to 11.9D<\/span><\/strong>[2]<\/a><\/span> although these have to be derived using various approximations and assumptions for up to\u00a04 independent Debye<\/span> processes.\u00a0Before proceeding to calculations, I looked at the properties of ionized\u00a0amino acids\u00a0in the solid state, using the following search query for the Cambridge structure database (CSD).\u00a0<\/p>\n

\"\"<\/p>\n

The distance measures hydrogen bonds to the carboxylate oxygens and the torsion their orientation. The O…H hydrogen bond distances vary between 1.7-1.85\u00c5, which are short. The orientation of the hydrogen bond can be to the in-plane oxygen “\u03c3-lone pair” (torsion 0 or 180\u00b0) and also an out-of-plane ~\u03c0 form (torsion ~60-90\u00b0).<\/p>\n

\"\"<\/p>\n

In aqueous solution, it is normally assumed that glycine sustains five such strong H-bonds (three to the H3<\/sub>N+<\/sup> group and two[3]<\/a><\/span> to the carboxylate anion), forming a polarised “salt bridge” across the ion-pair. Two model types were subjected to calculation using \u03c9B97XD\/Def2-TZVPP\/SCRF=water. Aqueous glycine without any added explicit water molecules yields a dipole moment of 12.9D<\/span><\/strong> (DOI:\u00a010.14469\/hpc\/2000<\/a>), which is\u00a0within the range noted above.\u2021<\/sup><\/p>\n

<\/p>\n

The solvated form is shown below, in one specific conformation of the three studied (\u03c9B97XD\/Def2-TZVPP\/SCRF=water). The calculated O…H hydrogen bond lengths fall into the range revealed from crystal structures. The calculated dipole moments range from 12.6<\/span><\/strong>\u00a0(DOI:\u00a010.14469\/hpc\/2007<\/a>), 15.3<\/span><\/strong> (DOI:\u00a010.14469\/hpc\/2006<\/a>) and 14.9<\/span><\/strong>D (DOI:\u00a010.14469\/hpc\/2005<\/a>), which is a modest increase over the model with no explicit water molecules. The actual dipole is of course a Boltzmann average over these and other as yet unexplored conformations, as well as other values for the number of water molecules.<\/p>\n

\"\"<\/p>\n

Given the difficulties in interpreting the\u00a0dipole moment of a complex Debye system such as hydrated glycine,\u00a0the agreement between the limited range of\u00a0solvated models and the measured values seems reasonable, and provides at least some measure of “calibration” for the polar molecules commented on previously.<\/p>\n

\n

\u2021<\/sup>Optimized with the solvent field on. If a vacuum model is used, the proton transfers from the N to the O.<\/p>\n

References<\/h2>\n
  1. M.W. Aaron, and E.H. Grant, \"Dielectric relaxation of glycine in water\", Transactions of the Faraday Society<\/i>, vol. 59, pp. 85, 1963. https:\/\/doi.org\/10.1039\/tf9635900085<\/a>\n\n<\/li>\n
  2. T. Sato, R. Buchner, ?. Fernandez, A. Chiba, and W. Kunz, \"Dielectric relaxation spectroscopy of aqueous amino acid solutions: dynamics and interactions in aqueous glycine\", Journal of Molecular Liquids<\/i>, vol. 117, pp. 93-98, 2005. https:\/\/doi.org\/10.1016\/j.molliq.2004.08.001<\/a>\n\n<\/li>\n
  3. T. Shikata, \"Dielectric Relaxation Behavior of Glycine Betaine in Aqueous Solution\", The Journal of Physical Chemistry A<\/i>, vol. 106, pp. 7664-7670, 2002. https:\/\/doi.org\/10.1021\/jp020957j<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    The previous posts produced discussion about the dipole moments of highly polar molecules. Here to produce some reference points for further discussion I look at the dipole moment of glycine, the classic\u00a0zwitterion (an internal ion-pair). Dielectric relaxation studies of glycine–water mixtures yield values that range from\u00a015.7D to 11.9D although these have to be derived using […]<\/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":[1745,4],"tags":[1362,1957,1395,431,1463,1965,1669,1963,1964,1871,1962,1872,1670,667],"ppma_author":[2661],"class_list":["post-17279","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","category-interesting-chemistry","tag-aqueous-solution","tag-chemical-polarity","tag-chemistry","tag-dielectric","tag-dipole","tag-electric-dipole-moment","tag-electromagnetism","tag-magnetism","tag-moment","tag-nature","tag-physical-quantities","tag-physics","tag-potential-theory","tag-zwitterion"],"yoast_head":"\nThe dipole moments of highly polar molecules: glycine zwitterion. - 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=17279\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The dipole moments of highly polar molecules: glycine zwitterion. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The previous posts produced discussion about the dipole moments of highly polar molecules. Here to produce some reference points for further discussion I look at the dipole moment of glycine, the classic\u00a0zwitterion (an internal ion-pair). Dielectric relaxation studies of glycine–water mixtures yield values that range from\u00a015.7D to 11.9D although these have to be derived using […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17279\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-12-24T08:19:43+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2017-01-07T09:37:20+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/12\/053.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":"The dipole moments of highly polar molecules: glycine zwitterion. - 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=17279","og_locale":"en_GB","og_type":"article","og_title":"The dipole moments of highly polar molecules: glycine zwitterion. - Henry Rzepa's Blog","og_description":"The previous posts produced discussion about the dipole moments of highly polar molecules. Here to produce some reference points for further discussion I look at the dipole moment of glycine, the classic\u00a0zwitterion (an internal ion-pair). Dielectric relaxation studies of glycine–water mixtures yield values that range from\u00a015.7D to 11.9D although these have to be derived using […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17279","og_site_name":"Henry Rzepa's Blog","article_published_time":"2016-12-24T08:19:43+00:00","article_modified_time":"2017-01-07T09:37:20+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/12\/053.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17279#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17279"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"The dipole moments of highly polar molecules: glycine zwitterion.","datePublished":"2016-12-24T08:19:43+00:00","dateModified":"2017-01-07T09:37:20+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17279"},"wordCount":393,"commentCount":1,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17279#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/12\/053.jpg","keywords":["aqueous solution","Chemical polarity","Chemistry","dielectric","Dipole","Electric dipole moment","Electromagnetism","Magnetism","Moment","Nature","Physical quantities","Physics","Potential theory","zwitterion"],"articleSection":["crystal_structure_mining","Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17279#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17279","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17279","name":"The dipole moments of highly polar molecules: glycine zwitterion. - 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Such was the case here, when a question about the dipole moment of cyclopropenylidene arose. It turned out to be 3.5D, but this question sparked a thought about the related molecule below. Of the two resonance forms show above,\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\/2021\/07\/C5H5-esp-1024x690.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":21436,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21436","url_meta":{"origin":17279,"position":1},"title":"The Structure of Tetrodotoxin as a free base.","author":"Henry Rzepa","date":"November 9, 2019","format":false,"excerpt":"The notorious neurotoxin Tetrodotoxin is often chemically represented as a zwitterion, shown below as 1. This idea seems to originate from a famous article written in 1964 by the legendary organic chemist, Robert Burns Woodward. This structure has propagated on to Wikipedia and is found in many other sources. With\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\/2019\/11\/MEP-1024x749.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":13394,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13394","url_meta":{"origin":17279,"position":2},"title":"How many water molecules does it take to ionise HCl?","author":"Henry Rzepa","date":"February 14, 2015","format":false,"excerpt":"According to Guggemos, Slavicek and Kresin, about 5-6!. This is one of those simple ideas, which is probably quite tough to do experimentally. It involved blasting water vapour through a pinhole, adding HCl and\u00a0measuring the dipole-moment induced deflection by an electric field. They\u00a0found\u00a0\"evidence for a noticeable rise in the dipole\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":17205,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17205","url_meta":{"origin":17279,"position":3},"title":"Molecules of the year? The most polar neutral compound synthesized…","author":"Henry Rzepa","date":"December 18, 2016","format":false,"excerpt":"This, the fourth candidate provided by C&EN for a vote for the molecule of the year\u00a0as discussed here,\u00a0lays claim to the World's most polar neutral molecule (system 1 shown below). Here I explore\u00a0a strategy for extending that record. The claim for 1 (3 in\u00a0) is on the basis of its\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":19550,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19550","url_meta":{"origin":17279,"position":4},"title":"A record polarity for a neutral compound?","author":"Henry Rzepa","date":"April 13, 2018","format":false,"excerpt":"In several posts a year or so ago I considered various suggestions for the most polar neutral molecules, as measured by the dipole moment. A record had been claimed for a synthesized molecule of ~14.1\u00b10.7D. I pushed this to a calculated 21.7D for an admittedly hypothetical and unsynthesized molecule. Here\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":14944,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14944","url_meta":{"origin":17279,"position":5},"title":"A tutorial problem in stereoelectronic control. A Grob alternative to the Tiffeneau-Demjanov rearrangement?","author":"Henry Rzepa","date":"November 28, 2015","format":false,"excerpt":"In answering tutorial problems, students often need skills in deciding how much time to spend on explaining what does not happen, as well as what does. Here I explore alternatives to the mechanism outlined in the previous post to see what computation\u00a0has to say about what does (or might) not\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":"Alt1","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/11\/Alt1.gif?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\/17279","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=17279"}],"version-history":[{"count":20,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17279\/revisions"}],"predecessor-version":[{"id":17304,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17279\/revisions\/17304"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=17279"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=17279"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=17279"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=17279"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}