{"id":1174,"date":"2009-11-29T10:20:17","date_gmt":"2009-11-29T09:20:17","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1174"},"modified":"2011-04-05T10:13:54","modified_gmt":"2011-04-05T10:13:54","slug":"the-fine-tuned-principle-in-chemistry","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1174","title":{"rendered":"The Fine-tuned principle in chemistry"},"content":{"rendered":"
\n

The \u00a0so-called \u00a0Fine tuned<\/a> model of the universe asserts that any small change in several of the\u00a0dimensionless fundamental physical constants would make the universe radically different (and hence one in which life as we know it could not exist). I suggest here that there may be molecules which epitomize the same principle in chemistry. Consider for example dimethyl formamide<\/a>. The NMR spectra of this molecule reveal that at room temperature, the two methyl groups are inequivalent, indicating that the rate constant for rotation about the C-N bond has a very particular range of values at the temperatures at which most living organisms exist on our planet.<\/p>\n

\"Dimethyl

Dimethyl formamide<\/p><\/div>\n

The half-restricted room-temperature rotation about the C-N bond arises from exactly the right amount of resonance contribution from the ionic form shown on the right, and this in turn depends on the relative energies of the nitrogen pair and the \u03c0 system of the carbonyl group having the correct relationship. It is probably also true that the environment that this grouping finds itself in will alter the contribution (i.e. stabilize the ionic form over the neutral one). \u00a0 A little less contribution and the C-N bond would rotate much more easily, a little more and it would be much more rigid. Since this peptide bond is an essential and repeated feature of the structure of most biological proteins and enzymes, one might speculate that if that bond could rotate more easily, most enzymes would be much floppier than they are, and may not be easily induced to fold in a repeatable manner into the conformations that enable all the metabolic processes and make them the efficient catalysts they are. If the bond rotated less easily, it might be that the same enzymes would end up being too rigid, and this may prevent them from flexing sufficiently to allow key metabolites to enter or leave the active site.<\/p>\n

Nowadays, the flexing of proteins is commonly studied using techniques of molecular dynamics, \u00a0the driving forces for which are specified using molecule mechanics force fields. Here, the rotation about the C-N bond is defined by simple mechanical force constants or torsional barriers. I ask here how sensitive the dynamics of protein folding and catalysis are to the C-N rotational barrier? Is this truly a fine-tuned molecule, or might it be that the existence of life as we know it has a wide tolerance to the strength of the C-N bond?<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

The \u00a0so-called \u00a0Fine tuned model of the universe asserts that any small change in several of the\u00a0dimensionless fundamental physical constants would make the universe radically different (and hence one in which life as we know it could not exist). I suggest here that there may be molecules which epitomize the same principle in chemistry. Consider […]<\/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":[156,2648],"ppma_author":[2661],"class_list":["post-1174","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-active-site","tag-interesting-chemistry"],"yoast_head":"\nThe Fine-tuned principle in chemistry - 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=1174\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The Fine-tuned principle in chemistry - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The \u00a0so-called \u00a0Fine tuned model of the universe asserts that any small change in several of the\u00a0dimensionless fundamental physical constants would make the universe radically different (and hence one in which life as we know it could not exist). I suggest here that there may be molecules which epitomize the same principle in chemistry. Consider […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1174\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2009-11-29T09:20:17+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2011-04-05T10:13:54+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/11\/dmf.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 Fine-tuned principle in chemistry - 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=1174","og_locale":"en_GB","og_type":"article","og_title":"The Fine-tuned principle in chemistry - Henry Rzepa's Blog","og_description":"The \u00a0so-called \u00a0Fine tuned model of the universe asserts that any small change in several of the\u00a0dimensionless fundamental physical constants would make the universe radically different (and hence one in which life as we know it could not exist). 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Other journals (e.g.\u00a0Nature Chemistry ran the article as a research highlight (where the purpose\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\/11\/cbd.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":14043,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14043","url_meta":{"origin":1174,"position":1},"title":"Discovering chemical concepts from crystal structure statistics: The Jahn-Teller effect","author":"Henry Rzepa","date":"May 30, 2015","format":false,"excerpt":"I am on a mission to persuade my colleagues that the statistical analysis of crystal structures is a useful teaching tool. \u00a0One colleague asked for a demonstration and suggested exploring the classical Jahn-Teller effect\u00a0(thanks Milo!). This is a geometrical distortion associated with certain molecular electronic configurations, of which the best\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":"","width":0,"height":0},"classes":[]},{"id":17333,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17333","url_meta":{"origin":1174,"position":2},"title":"Ritonavir: a look at a famous example of conformational polymorphism.","author":"Henry Rzepa","date":"January 2, 2017","format":false,"excerpt":"Here is an inside peek at another one of Derek Lowe's 250 milestones in chemistry, the polymorphism of Ritonavir.\u00a0The story in a nutshell concerns one of a pharma company's worst nightmares; a drug which has been successfully brought to market unexpectedly\u00a0\"changes\" after a few years on market to a less\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":9894,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9894","url_meta":{"origin":1174,"position":3},"title":"To be cyclobutadiene, or not to be, that is the question? You decide.","author":"Henry Rzepa","date":"March 21, 2013","format":false,"excerpt":"A quartet of articles has recently appeared on the topic of cyclobutadiene.,,,. You will find a great deal discussed there, but I can boil it down to this essence. Do the following coordinates (obtained from a (disordered) previously published x-ray refinement) correspond to a van der Waals complex of 1,3-dimethyl\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":4814,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4814","url_meta":{"origin":1174,"position":4},"title":"Mindless chemistry or creative science?","author":"Henry Rzepa","date":"September 3, 2011","format":false,"excerpt":"The (hopefully tongue-in-cheek) title Mindless chemistry was given to an article reporting an automated stochastic search procedure for locating all possible minima with a given composition using high-level quantum mechanical calculations. \"Many new structures, often with nonintuitive geometries, were found\". Well, another approach is to follow unexpected hunches. One such\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\/09\/fe2.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":5763,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5763","url_meta":{"origin":1174,"position":5},"title":"So near and yet so far. The story of the electrocyclic ring opening of a cyclohexadiene.","author":"Henry Rzepa","date":"December 6, 2011","format":false,"excerpt":"My previous three posts set out my take on three principle categories of pericyclic reaction. Here I tell a prequel to the understanding of these reactions. In 1965, Woodward and Hoffmann in their theoretical analysis (submitted Nov 30, 1964) for which the Nobel prize (to Hoffmann only of the pair,\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\/12\/ht.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\/1174","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=1174"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/1174\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1174"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1174"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1174"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=1174"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}