{"id":21579,"date":"2019-12-07T09:40:14","date_gmt":"2019-12-07T09:40:14","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21579"},"modified":"2019-12-21T07:33:04","modified_gmt":"2019-12-21T07:33:04","slug":"what-effect-do-explicit-solvent-molecules-have-on-calculated-optical-rotation-d-glyceraldehyde","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21579","title":{"rendered":"What effect do explicit solvent molecules have on calculated optical rotation: D-(“+”)-Glyceraldehyde."},"content":{"rendered":"
\n

In this series of posts<\/a> on optical rotations,\u00a0I firstly noted Kirkwood’s 1937 attempt to correlate the optical rotation of butan-2-ol with its absolute configuration. He had identified as essential knowing the relative orientation (the term conformation was not yet in common use) of the two methyl groups (the modern terms are gauche<\/em> vs anti<\/em>) and also that of the hydroxyl group, noting that anisotropy from this group could influence his result (he had assumed it was linear, or axially symmetric). I then looked at D-(+)-glyceraldehyde, noting that this species itself has a strongly negative rotation and that it is the hydrated diol that results in a positive rotation and hence the (+) designation. Here I take another look at this latter system to see what effect adding explicit water molecules to the unhydrated form of glyceraldehyde might have on its computed rotation, on the premise that strong hydrogen bonds can also contribute anisotropy to the system.<\/p>\n

Firstly, here again are the computed results for glyceraldehyde on its own, albeit encased in a continuum solvent field for water (SCRF=water). At 303K and 589nm, the computed rotation is -193\u00b0 compared to -147\u00b0 inferred from the population of the aldehyde.[1]<\/a><\/span><\/p>\n

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

Here are the new values (FAIR data DOI: 10.14469\/hpc\/6445<\/a>)\u00a0obtained by adding an explicit water molecule to the original conformations. This also introduces extra conformations, some of which are included below. This reduces the calculated value by ~25\u00b0 to improve the agreement with measurement (-147\u00b0). The value at 436nm is -411 (calc), -380 (obs).<\/p>\n

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

So a 25\u00b0 correction is not entirely insignificant, but does not change the overall conclusion that the optical rotation of D-(+) glyceraldehyde is (-). How might the model be improved further?<\/p>\n

    \n
  1. Adding more water molecules, in theory until a limit is reached where further anisotropy is not added to the model. But the major disadvantage is that each extra water molecule increases the conformational space to be explored. With say seven added water molecules, there are probably 100s of conformations that would have to be searched, now a major undertaking.<\/li>\n
  2. Another interesting avenue to explore is the temperature dependence of the optical rotation. The experimental values are shown below. This is due to the change in Boltzmann populations as a function of temperature.\"\"<\/a>\n

    At 343K, the original calculations without inclusion of a water molecule reduce the calculated rotation changes from -193 to -182.5, or about 10\u00b0. The observed value is a change of 39\u00b0. However, with the model including an extra water molecule, the value changes from -168.5 to -171\u00b0. So it might well be that reproduction of the temperature effects will require more water molecules added to the model.<\/p>\n<\/li>\n<\/ol>\n

     <\/p>\n

    References<\/h2>\n
    1. M. Fedoro\u0148ko, \"Optical activity of D-glyceraldehyde in aqueous solutions\", Collection of Czechoslovak Chemical Communications<\/i>, vol. 49, pp. 1167-1172, 1984. https:\/\/doi.org\/10.1135\/cccc19841167<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      In this series of posts on optical rotations,\u00a0I firstly noted Kirkwood’s 1937 attempt to correlate the optical rotation of butan-2-ol with its absolute configuration. He had identified as essential knowing the relative orientation (the term conformation was not yet in common use) of the two methyl groups (the modern terms are gauche vs anti) and […]<\/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_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":[2644,4],"tags":[],"ppma_author":[2661],"class_list":["post-21579","post","type-post","status-publish","format-standard","hentry","category-chiroptics","category-interesting-chemistry"],"yoast_head":"\nWhat effect do explicit solvent molecules have on calculated optical rotation: D-("+")-Glyceraldehyde. - 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.imperial.ac.uk\/rzepa\/blog\/?p=21579\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"What effect do explicit solvent molecules have on calculated optical rotation: D-("+")-Glyceraldehyde. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In this series of posts on optical rotations,\u00a0I firstly noted Kirkwood’s 1937 attempt to correlate the optical rotation of butan-2-ol with its absolute configuration. He had identified as essential knowing the relative orientation (the term conformation was not yet in common use) of the two methyl groups (the modern terms are gauche vs anti) and […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21579\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2019-12-07T09:40:14+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2019-12-21T07:33:04+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/12\/glyceraldehyde-rotations-1-1024x310.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":"What effect do explicit solvent molecules have on calculated optical rotation: D-(\"+\")-Glyceraldehyde. - 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.imperial.ac.uk\/rzepa\/blog\/?p=21579","og_locale":"en_GB","og_type":"article","og_title":"What effect do explicit solvent molecules have on calculated optical rotation: D-(\"+\")-Glyceraldehyde. - Henry Rzepa's Blog","og_description":"In this series of posts on optical rotations,\u00a0I firstly noted Kirkwood’s 1937 attempt to correlate the optical rotation of butan-2-ol with its absolute configuration. He had identified as essential knowing the relative orientation (the term conformation was not yet in common use) of the two methyl groups (the modern terms are gauche vs anti) and […]","og_url":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21579","og_site_name":"Henry Rzepa's Blog","article_published_time":"2019-12-07T09:40:14+00:00","article_modified_time":"2019-12-21T07:33:04+00:00","og_image":[{"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/12\/glyceraldehyde-rotations-1-1024x310.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.imperial.ac.uk\/rzepa\/blog\/?p=21579#article","isPartOf":{"@id":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21579"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"What effect do explicit solvent molecules have on calculated optical rotation: D-(“+”)-Glyceraldehyde.","datePublished":"2019-12-07T09:40:14+00:00","dateModified":"2019-12-21T07:33:04+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21579"},"wordCount":457,"commentCount":0,"image":{"@id":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21579#primaryimage"},"thumbnailUrl":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/12\/glyceraldehyde-rotations-1-1024x310.jpg","articleSection":["Chiroptics","Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21579#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21579","url":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21579","name":"What effect do explicit solvent molecules have on calculated optical rotation: D-(\"+\")-Glyceraldehyde. - 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The measured optical rotatory dispersion curve at low wavelengths is shown below\u2026","rel":"","context":"In "Chiroptics"","block_context":{"text":"Chiroptics","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2644"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":21592,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21592","url_meta":{"origin":21579,"position":2},"title":"Sign inversions in optical rotation as a function of wavelength (ORD spectra)","author":"Henry Rzepa","date":"December 9, 2019","format":false,"excerpt":"I have been discussing some historical aspects of the absolute configuration of molecules and how it was connected to their optical rotations. The nomenclature for certain types of molecules such as sugars and less commonly amino acids includes the notation (+) to indicate that the specific optical rotation of the\u2026","rel":"","context":"In "Chiroptics"","block_context":{"text":"Chiroptics","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2644"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":25869,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25869","url_meta":{"origin":21579,"position":3},"title":"Determining absolute configuration: Cylindricine.","author":"Henry Rzepa","date":"February 1, 2023","format":false,"excerpt":"Nature has produced most natural molecules as chiral objects, which means the molecule can come in two enantiomeric forms, each being the mirror image of the other. 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Here theory\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":"A 34-Octaphyrin. Click to see molecule","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/qarfar.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":21499,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21499","url_meta":{"origin":21579,"position":5},"title":"Prediction preceding experiment in chemistry – how unlucky was John Kirkwood?","author":"Henry Rzepa","date":"November 30, 2019","format":false,"excerpt":"Some areas of science progressed via very famous predictions that were subsequently verified by experiments. Think of Einstein and gravitational waves or of Dirac and the positron. There are fewer well-known examples in chemistry; perhaps Watson and Crick's prediction of the structure of DNA, albeit based on the interpretation of\u2026","rel":"","context":"In "Chiroptics"","block_context":{"text":"Chiroptics","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2644"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/12\/butan-2-ol-ORP-1024x312.jpg?resize=350%2C200&ssl=1","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","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\/21579","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=21579"}],"version-history":[{"count":10,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21579\/revisions"}],"predecessor-version":[{"id":21591,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21579\/revisions\/21591"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=21579"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=21579"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=21579"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=21579"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}