{"id":3621,"date":"2011-03-05T09:02:36","date_gmt":"2011-03-05T09:02:36","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=3621"},"modified":"2011-06-30T14:23:59","modified_gmt":"2011-06-30T14:23:59","slug":"the-thermodynamic-energies-of-left-and-right-handed-dna","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3621","title":{"rendered":"The thermodynamic energies of left and right handed DNA."},"content":{"rendered":"
\n

In this earlier post<\/a>, I noted some aspects of the calculated structures of both Z- and B-DNA duplexes. These calculations involved optimising the positions of around 250-254 atoms, for d(CGCG)2<\/sub> and d(ATAT)2, <\/sub>an undertaking which has taken about two months of computer time! The geometries are finally optimised to the point where 2nd derivatives can be calculated, and which reveal up to 756 all-positive force constants and 6 translations and rotations which are close to zero! This now lets one compute the thermodynamic relative energies using \u03c9B97XD\/6-31G(d) (for 2nd derivatives) and 6-31G(d,p) (for dispersion terms). All geometries are optimized using a continuum solvent field (water), and are calculated, without a counterion, as hexa-anions.<\/p>\n\n\n\n\n\n\n\n\n\n
Relative thermodynamic energies (kcal mol-1<\/sup>) of DNA duplexes.<\/span><\/span><\/th>\n<\/tr>\n<\/thead>\n
system<\/th>\nTotal energy (duplex)<\/th>\nDispersion term<\/th>\n\u0394\u0394H298<\/sub><\/th>\n\u0394(-T.\u0394S298<\/sub>)<\/th>\n\u0394\u0394G298<\/sub> duplex<\/th>\n\u0394G298<\/sub> single chain<\/th>\n\u0394\u0394G298<\/sub> (Duplex)<\/th>\n<\/tr>\n
Z-CGCG<\/td>\n0.0 <\/td>\n0.0<\/td>\n0.0<\/td>\n0.0<\/td>\n0.0<\/td>\n0.0<\/td>\n-60.3<\/td>\n<\/tr>\n
B-CGCG<\/td>\n6.2 <\/td>\n-4.2<\/td>\n8.0<\/td>\n3.9<\/td>\n11.9<\/td>\n+3.1<\/td>\n-54.7<\/td>\n<\/tr>\n
Z-ATAT<\/td>\n0.0<\/td>\n0.0<\/td>\n0.0<\/td>\n0.<\/td>\n0.0<\/td>\n0.0<\/td>\n-44.9<\/td>\n<\/tr>\n
B-ATAT<\/td>\n-7.6<\/td>\n-12.8<\/td>\n-7.0<\/td>\n2.7<\/td>\n-4.3<\/td>\n-1.8<\/td>\n-45.7<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Note how the CGCG duplex is more stable as a Z-helix, whilst the ATAT duplex prefers the B-helix. I will discuss the precise reasons for this elsewhere.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

In this earlier post, I noted some aspects of the calculated structures of both Z- and B-DNA duplexes. These calculations involved optimising the positions of around 250-254 atoms, for d(CGCG)2 and d(ATAT)2, an undertaking which has taken about two months of computer time! The geometries are finally optimised to the point where 2nd derivatives can […]<\/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":[472,494,390,493,258,24,470,373,572,471,378],"ppma_author":[2661],"class_list":["post-3621","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-6-31gd","tag-atat-duplex","tag-b-dna","tag-cgcg-duplex","tag-dispersion-energy-corrections","tag-energy","tag-thermodynamic-stability","tag-tutorial-material","tag-watoc11","tag-wb97xd","tag-z-dna"],"yoast_head":"\nThe thermodynamic energies of left and right handed DNA. - 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=3621\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The thermodynamic energies of left and right handed DNA. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In this earlier post, I noted some aspects of the calculated structures of both Z- and B-DNA duplexes. These calculations involved optimising the positions of around 250-254 atoms, for d(CGCG)2 and d(ATAT)2, an undertaking which has taken about two months of computer time! 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They chose a right-handed turn, on the grounds that their attempts at left-handed models all \"violated permissible van der Waals contacts\". No details of\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\/2011\/01\/CGCG.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":3235,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3235","url_meta":{"origin":3621,"position":1},"title":"The handedness of DNA: an unheralded connection.","author":"Henry Rzepa","date":"December 29, 2010","format":false,"excerpt":"Science is about making connections. Plenty are on show in Watson and Crick's famous 1953 article on the structure of DNA but often with the tersest of explanations. Take for example their statement \"Both chains follow right-handed helices\". Where did that come from? This post will explore the subtle implications\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\/2010\/12\/tartrate.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":23187,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23187","url_meta":{"origin":3621,"position":2},"title":"Dispersion attraction effects on the computed geometry of a leminscular dodecaporphyrin.","author":"Henry Rzepa","date":"January 1, 2021","format":false,"excerpt":"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\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-P12b12_T6f.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":3746,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3746","url_meta":{"origin":3621,"position":3},"title":"The Cyclol Hypothesis for protein structure: castles in the air.","author":"Henry Rzepa","date":"April 4, 2011","format":false,"excerpt":"Most scientific theories emerge slowly, over decades, but others emerge fully formed virtually overnight as it were (think Einstein in 1905). A third category is the supernova type, burning brightly for a short while, but then vanishing (almost) without trace shortly thereafter. The structure of DNA (of which I have\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.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/04\/cyclol.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":4089,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4089","url_meta":{"origin":3621,"position":4},"title":"The inner secrets of the DNA structure.","author":"Henry Rzepa","date":"May 18, 2011","format":false,"excerpt":"In earlier posts, I alluded to what might make DNA wind into a left or a right-handed helix. Here I switch the magnification of our structural microscope up a notch to take a look at some more inner secrets. The 3D coordinates of this fragment were obtained by taking a\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/CGCG.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":21128,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21128","url_meta":{"origin":3621,"position":5},"title":"A Non-nitrogen Containing Morpholine Isostere; an application of FAIR data principles.","author":"Henry Rzepa","date":"August 4, 2019","format":false,"excerpt":"In the pipeline reports on an intriguing new ring system acting as an isostere for morpholine. I was interested in how the conformation of this ring system might be rationalised electronically and so I delved into the article. Here I recount what I found. The basis for the isosteric claim\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/08\/jm-2019-00348p_0004-2.gif?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","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\/3621","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=3621"}],"version-history":[{"count":1,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/3621\/revisions"}],"predecessor-version":[{"id":16625,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/3621\/revisions\/16625"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=3621"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=3621"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=3621"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=3621"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}