{"id":17771,"date":"2017-03-20T16:57:32","date_gmt":"2017-03-20T16:57:32","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=17771"},"modified":"2017-03-20T17:05:11","modified_gmt":"2017-03-20T17:05:11","slug":"reaction-coordinates-vs-dynamic-trajectories-as-illustrated-by-an-example-reaction-mechanism","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17771","title":{"rendered":"Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"17771\">\n<p>The example <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=17702\">a few posts back<\/a> of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic <strong>reaction coordinate<\/strong>\u00a0(IRC). Here I explore an alternative method based instead on computing a molecular dynamics trajectory (MD).<\/p>\n<p>I have used ethane instead of methane, since it is now possible to envisage two outcomes:<\/p>\n<p><a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/md-page001.svg\"><img decoding=\"async\" class=\"aligncenter size-large wp-image-17786\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/md-page001.svg\" alt=\"\" width=\"350\" \/><\/a><\/p>\n<p>An animation of the IRC starting from the located transition state is shown below (DOI: <a href=\"https:\/\/doi.org\/10.14469\/hpc\/2331\">10.14469\/hpc\/2331<\/a>).\u00a0This is based purely on the computed potential energy surface of the molecule. The IRC is computed from the forces experienced on the atoms as they are displaced from an initial set of coordinates corresponding to the located transition state and then following the direction indicated by the eigenvectors of the negative force constant required of a transition state. Importantly, there is no time component; the path is based entirely on energies and forces.<\/p>\n<p><!-- img class=\"aligncenter size-full wp-image-17781\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/ethane-irc.gif\" alt=\"\" width=\"450\" \/--><\/p>\n<p><video class=\"aligncenter\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/ethane-irc.m4v\" poster=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/161.jpg\" preload=\"none\" autoplay=\"autoplay\" loop=\"loop\" controls=\"controls\" width=\"450\" height=\"252\"><\/video><\/p>\n<p>Next, a molecular dynamics simulation (\u03c9B97XD\/6-31G(d,p), DOI: <a href=\"https:\/\/doi.org\/10.14469\/hpc\/2330\">10.14469\/hpc\/2330<\/a>).\u00a0 This uses the <a href=\"http:\/\/gaussian.com\/admp\/\">ADMP method<\/a>, which requests a classical\u00a0trajectory calculation\u00a0using the &#8220;atom-centered density matrix propagation molecular dynamics model&#8221;. This integrates kinetic energy contributions from the molecular vibrations and so explicitly now includes a time component. In this example the evolution of the system from the transition state is charted over a period of 100 femtoseconds (1000 integrated steps). As it happens this is a relatively short period of evolution; sometimes periods of picoseconds may be required to get a realistic model, especially if one is also dealing with explicit solvent molecules (of which perhaps\u00a0500 might be required).<\/p>\n<p><video class=\"aligncenter\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/ethane-md.m4v\" poster=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/160.jpg\" preload=\"none\" autoplay=\"autoplay\" loop=\"loop\" controls=\"controls\" width=\"450\" height=\"253\"> <\/video><\/p>\n<p>Such explicit inclusion of the kinetic energy from molecular vibrations in effect allows the molecule to &#8220;jump&#8221; over shallow barriers. In this case, the barrier for a [1,2] hydrogen shift from the methyl group to the adjacent carbene (watch atom 8). Simultaneously, the path taken by two hydrogens no longer corresponds to their transposition but to their elimination as a hydrogen molecule. So this quite different outcome from the IRC is very probably also a much more realistic one.<\/p>\n<p>If the MD method is so much more realistic than the IRC, then why is it not always used? The simple answer is computational time! For this very small molecule and using quite a modest basis set (6-31G(d,p)), the relatively short 1000 time steps took about three times as long to compute as the IRC. The factor gets worse as the size of the molecule increases and the number of time steps for a realistic result increases. Perhaps, as technology gets better and new computer architectures emerge, MD simulations of ever increasingly complex reactions will become far more common. In ten years time, I expect most of the examples on this blog will use this method!<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 17771 -->","protected":false},"excerpt":{"rendered":"<p>The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate\u00a0(IRC). Here I explore an alternative method based instead on computing a molecular dynamics trajectory (MD). I have [&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":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":[1086],"tags":[152,984,1395,34,2071,24,2069,1960,2072,2073,2063,859,1837,1512,2070,721,1631],"ppma_author":[2661],"class_list":["post-17771","post","type-post","status-publish","format-standard","hentry","category-reaction-mechanism-2","tag-animation","tag-chemical-reaction","tag-chemistry","tag-computational-chemistry","tag-computed-potential-energy-surface","tag-energy","tag-gaseous-signaling-molecules","tag-hydrogen","tag-kinetic-energy","tag-kinetic-energy-contributions","tag-methane","tag-molecular-dynamics","tag-physical-chemistry","tag-quantum-chemistry","tag-reaction-coordinate","tag-simulation","tag-theoretical-chemistry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism. - 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=17771\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate\u00a0(IRC). Here I explore an alternative method based instead on computing a molecular dynamics trajectory (MD). I have [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17771\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2017-03-20T16:57:32+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2017-03-20T17:05:11+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/md-page001.svg\" \/>\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":"Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism. - Henry Rzepa&#039;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=17771","og_locale":"en_GB","og_type":"article","og_title":"Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism. - Henry Rzepa&#039;s Blog","og_description":"The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate\u00a0(IRC). 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I have [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17771","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2017-03-20T16:57:32+00:00","article_modified_time":"2017-03-20T17:05:11+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/md-page001.svg","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=17771#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17771"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism.","datePublished":"2017-03-20T16:57:32+00:00","dateModified":"2017-03-20T17:05:11+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17771"},"wordCount":477,"commentCount":2,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17771#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/md-page001.svg","keywords":["animation","chemical reaction","Chemistry","computational chemistry","computed potential energy surface","energy","Gaseous signaling molecules","Hydrogen","kinetic energy","kinetic energy contributions","Methane","Molecular dynamics","Physical chemistry","Quantum chemistry","Reaction coordinate","simulation","Theoretical chemistry"],"articleSection":["reaction mechanism"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17771#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17771","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17771","name":"Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism. - 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The mechanism involves an initial equilibrium between React and Int1, followed by capture of the hydrogen by Int1 to form a 5-coordinate borane intermediate (Int2 below, as\u2026","rel":"","context":"In &quot;reaction mechanism&quot;","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":5114,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5114","url_meta":{"origin":17771,"position":1},"title":"Mechanism of the reduction of a carboxylic acid by borane: revisited and revised.","author":"Henry Rzepa","date":"October 16, 2011","format":false,"excerpt":"I asked a while back\u00a0whether blogs could be considered a serious form of scholarly scientific communication (and so has Peter Murray-Rust more recently). A case for doing so might be my post of about a year ago, addressing why borane reduces a carboxylic acid, but not its ester, where I\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":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/acyloxy1-page001.svg","width":350,"height":200},"classes":[]},{"id":17710,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17710","url_meta":{"origin":17771,"position":2},"title":"How does silane invert (its configuration)?","author":"Henry Rzepa","date":"March 16, 2017","format":false,"excerpt":"In the previous post, I found intriguing the mechanism by which methane (CH4) inverts by transposing two of its hydrogens. Here I take a look at silane, SiH4. It appears it is a three-stage process! Firstly, silane eliminates molecular hydrogen to form a molecular complex between H2\u00a0and SiH2 (DOI:\u00a010.14469\/hpc\/2290). The\u2026","rel":"","context":"In &quot;reaction mechanism&quot;","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/gaussian-78_tot_ener.svg","width":350,"height":200},"classes":[]},{"id":20354,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20354","url_meta":{"origin":17771,"position":3},"title":"Epoxidation of ethene: a new substituent twist.","author":"Henry Rzepa","date":"December 21, 2018","format":false,"excerpt":"Five years back,\u00a0I speculated about the mechanism of the epoxidation of ethene by a peracid, concluding that kinetic isotope effects provided interesting evidence that this mechanism is highly asynchronous and involves a so-called \"hidden intermediate\". Here I revisit this reaction in which a small change is applied to the atoms\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\/2018\/12\/imine2.gif?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":4837,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4837","url_meta":{"origin":17771,"position":4},"title":"Anatomy of a simple reaction: the hydration of an alkene.","author":"Henry Rzepa","date":"September 4, 2011","format":false,"excerpt":"The hydration of an alkene by an acid is one of those fundamental reactions, taught early on in most chemistry courses. What can quantum mechanics teach us about the mechanism of the reaction? The diagram below shows us the IRC, or intrinsic reaction coordinate for the process (for definitions, see\u2026","rel":"","context":"In \"alkene\"","block_context":{"text":"alkene","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=alkene"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/09\/hydration.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17702,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17702","url_meta":{"origin":17771,"position":5},"title":"How does methane invert (its configuration)?","author":"Henry Rzepa","date":"March 16, 2017","format":false,"excerpt":"This is a spin-off from the table I constructed here for further chemical examples of the classical\/non-classical norbornyl cation conundrum. One possible entry would include the transition state for inversion of methane via a square planar geometry as compared with e.g. NiH4 for which the square planar motif is its\u2026","rel":"","context":"In &quot;reaction mechanism&quot;","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"","width":0,"height":0},"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\/17771","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=17771"}],"version-history":[{"count":16,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17771\/revisions"}],"predecessor-version":[{"id":17798,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17771\/revisions\/17798"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=17771"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=17771"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=17771"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=17771"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}