{"id":25043,"date":"2022-04-18T19:09:13","date_gmt":"2022-04-18T18:09:13","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=25043"},"modified":"2022-04-19T09:05:08","modified_gmt":"2022-04-19T08:05:08","slug":"geometries-of-proton-transfers-modelled-using-total-energy-or-free-energy","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25043","title":{"rendered":"Geometries of proton transfers: modelled using total energy or free energy?"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"25043\">\n<p>Proton transfers are amongst the most common of all chemical reactions. They are often thought of as &#8220;trivial&#8221; and even may not feature in many mechanistic schemes, other than perhaps the notation &#8220;PT&#8221;.\u00a0The types with the lowest energy barriers for transfer often involve heteroatoms such as N and O, and the conventional transition state might be supposed to be when the proton is located at about the half way distance between the two heteroatoms. This should be the energy high point between the two positions for the proton. But what if a crystal structure is determined with the proton in exactly this position?\u00a0Well, the first hypothesis is that using X-rays as the diffracting radiation is unreliable, because protons scatter x-rays very poorly.\u00a0Then a more arduous neutron diffraction study is sometimes undertaken, which is generally assumed to be more reliable in determining the position of the proton. Just such a study was undertaken for the structure shown below (RAKQOJ)<span id=\"cite_ITEM-25043-0\" name=\"citation\"><a href=\"#ITEM-25043-0\">[1]<\/a><\/span>, dataDOI: <a href=\"https:\/\/doi.org\/10.5517\/cc57db3\" target=\"_blank\" rel=\"noopener\">10.5517\/cc57db3<\/a> for the 80K determination. <a href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/RAKQOJ.svg\"><img decoding=\"async\" class=\"aligncenter size-medium wp-image-25064\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/RAKQOJ.svg\" alt=\"\" width=\"540\" \/><\/a> The\u00a0substituents had been selected to try to maximise the symmetry of the O&#8230;H&#8230;N motif\u00a0<em>via<\/em>\u00a0pKa tuning (for another tuning attempt, <a href=\"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=13252\" target=\"_blank\" rel=\"noopener\">see this blog<\/a>). The more general landscape this molecule fits into<span id=\"cite_ITEM-25043-1\" name=\"citation\"><a href=\"#ITEM-25043-1\">[2]<\/a><\/span> is shown below:<\/p>\n<p><a href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/plot.png\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-large wp-image-25120\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/plot-1024x734.png\" alt=\"\" width=\"450\" height=\"323\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/plot-1024x734.png 1024w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/plot-300x215.png 300w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/plot-768x551.png 768w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/plot.png 1071w\" sizes=\"auto, (max-width: 450px) 100vw, 450px\" \/><\/a><\/p>\n<p>The results obtained for the position of the proton for RAKQOJ were fascinating. They were very dependent on the temperature of the crystal! At room temperatures (using X-rays), the proton was measured as 1.09\u00c5 from the oxygen and 1.47\u00c5 from the nitrogen (neutral form above).\u00a0At 20K, the OH distance was 1.309\u00c5 and the\u00a0HN 1.206\u00c5 (~ionic form above). Indeed, the very title of this article is\u00a0<em>First O-H-N Hydrogen Bond with a Centered Proton Obtained by Thermally Induced Proton Migration.\u00a0<\/em>The authors give a number of reasons for this behaviour (their ref 17<span id=\"cite_ITEM-25043-0\" name=\"citation\"><a href=\"#ITEM-25043-0\">[1]<\/a><\/span> and also<span id=\"cite_ITEM-25043-1\" name=\"citation\"><a href=\"#ITEM-25043-1\">[2]<\/a><\/span>), but one they do not mention is thermally induced changes in the dielectric constant of the crystal with temperature, given that in one position for the proton the molecule is ionic and in the other neutral. So I decided to model the system as a function of solvent. In this model, the solvent dielectric is used to approximate the crystal dielectric. My first choice of energy function is to compute geometries using the B3LYP+GD3BJ\/Def2=TZVPP\/SCRF=solvent method to see\u00a0what might emerge and as a possible prelude to trying other functionals. FAIR data for these calculations are collected at DOI: <a href=\"https:\/\/doi.org\/10.14469\/hpc\/10368\" target=\"_blank\" rel=\"noopener\">10.14469\/hpc\/10368<\/a>.<\/p>\n<table border=\"1\">\n<tbody>\n<tr>\n<th>Solvent<\/th>\n<th>\u03b5<\/th>\n<th>\u0394G<sub>298<\/sub> for O&#8230;HN<\/th>\n<th>r<sub>O&#8230;H<\/sub><\/th>\n<th>r<sub>HN<\/sub><\/th>\n<th>\u0394G<sub>298<\/sub> for OH&#8230;N<\/th>\n<th>r<sub>OH<\/sub><\/th>\n<th>r<sub>H&#8230;N<\/sub><\/th>\n<th>\u0394G<sub>298<\/sub><br \/>\nTS (PT)<\/th>\n<th>r<sub>OH<\/sub><\/th>\n<th>r<sub>HN<\/sub><\/th>\n<\/tr>\n<tr>\n<td><span style=\"font-size: 10pt;\">Water<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">78.4<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.387188<\/span><br \/>\n<span style=\"font-size: 10pt;\">-2893.334325<sup>\u2660<\/sup><\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.4913<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.0827<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.386705<\/span><br \/>\n<span style=\"font-size: 10pt;\">-2893.334333<sup>\u2660<\/sup><\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.0364<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.5696<\/span><\/td>\n<td><span style=\"color: #ff0000; font-size: 10pt;\">-2893.387668<\/span><br \/>\n<span style=\"color: #ff0000; font-size: 10pt;\">-2893.336183<sup>\u2660<\/sup><\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.1852<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.2899<\/span><\/td>\n<\/tr>\n<tr>\n<td><span style=\"font-size: 10pt;\">Dichloro<br \/>\nmethane<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">8.9<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.385173<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.4566<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.0945<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.385662<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.0309<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.5878<\/span><\/td>\n<td><span style=\"color: #ff0000; font-size: 10pt;\">-2893.386022<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.2072<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.2642<\/span><\/td>\n<\/tr>\n<tr>\n<td><span style=\"font-size: 10pt;\">Chloroform<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">4.7<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.382254<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.4227<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.1082<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.384514<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.0261<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.6049<\/span><\/td>\n<td><span style=\"font-size: 10pt; color: #ff0000;\">-2893.384773<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.2321<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.2388<\/span><\/td>\n<\/tr>\n<tr>\n<td><span style=\"font-size: 10pt;\">Dibutyl ether<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">3.1<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.380813<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.3778<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.1302<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.383511<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.0213<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.6235<\/span><\/td>\n<td><span style=\"color: #000000; font-size: 10pt;\">-2893.382918<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.2667<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.2078<\/span><\/td>\n<\/tr>\n<tr>\n<td><span style=\"font-size: 10pt;\">Toluene<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">2.4<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.379752<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.3248<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.1635<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.382915<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.0178<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.6385<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.379773<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.2851<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.1934<\/span><\/td>\n<\/tr>\n<tr>\n<td><span style=\"font-size: 10pt;\">Gas phase<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">0<\/span><\/td>\n<td colspan=\"3\"><span style=\"font-size: 10pt;\">n\/a<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">-2893.377949<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.0009<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.7387<\/span><\/td>\n<td colspan=\"3\"><span style=\"font-size: 10pt;\">n\/a<\/span><\/td>\n<\/tr>\n<tr>\n<td><span style=\"font-size: 10pt;\">Expt (RT)<\/span><br \/>\n<span id=\"cite_ITEM-25043-0\" name=\"citation\"><a href=\"#ITEM-25043-0\">[1]<\/a><\/span><\/td>\n<td><span style=\"font-size: 10pt;\">?<\/span><\/td>\n<td colspan=\"4\"><span style=\"font-size: 10pt;\">n\/a<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.09<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.47<\/span><\/td>\n<td colspan=\"3\"><span style=\"font-size: 10pt;\">n\/a<\/span><\/td>\n<\/tr>\n<tr>\n<td><span style=\"font-size: 10pt;\">Expt (20K)<\/span><br \/>\n<span id=\"cite_ITEM-25043-0\" name=\"citation\"><a href=\"#ITEM-25043-0\">[1]<\/a><\/span><\/td>\n<td><span style=\"font-size: 10pt;\">?<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">n\/a<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.309<\/span><\/td>\n<td><span style=\"font-size: 10pt;\">1.206<\/span><\/td>\n<td colspan=\"6\"><span style=\"font-size: 10pt;\">n\/a<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><small><sup>\u2660<\/sup> At 20K<\/small><\/p>\n<p><b>Results:<\/b><\/p>\n<ol>\n<li>The geometries for each model are obtained by minimising the <strong>total energy<\/strong> of the system as a function of the 3N-6 geometric variables (coordinates).\u00a0<\/li>\n<li>The geometries show that for all solvents, TWO minima in the total energy are obtained, one for the ionic and one for the neutral form. This is called a double-well energy potential. Even a\u00a0non-polar solvent such as toluene produces a solvation energy of ~3.1 kcal\/mol compared to the gas phase, which is sufficient to induce a double-well potential.<\/li>\n<li>Without solvent (gas phase), only the neutral geometry is obtained.\u00a0<\/li>\n<li>In the most polar solvent water, the double well potential looks like this:<br \/>\n<a href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/OHN-water_ener.svg\"><img decoding=\"async\" class=\"aligncenter size-medium wp-image-25063\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/OHN-water_ener.svg\" alt=\"\" width=\"400\" \/><\/a><br \/>\nThe ionic well is about 0.4 kcal\/mol lower in total energy (and ~0.3 kcal\/mol in free energy, see table above) than the neutral form, with a barrier connecting neutral to ionic only 1.0 kcal\/mol.\u00a0A transition state + intrinsic reaction coordinate (IRC) can be easily located on this total energy potential, confirming the double-well form.<\/li>\n<li>When free energies \u0394G are computed, which include thermal effects such as entropy and zero-point energy, the transition state emerges as <span style=\"color: #ff0000;\">0.3 kcal\/mol<\/span> less than the total energy of the ionic form (red entries, Table). In effect, the free energy potential surface is INVERTED compared to the total energy surface and the &#8220;transition state&#8221; becomes the lowest point on the energy surface. So this point is a minimum in the free energy but a maximum in the total energy, the result of adding\u00a0thermal effects to the total energy.<\/li>\n<li>In dichloromethane, the free energy of the neutral form is now lower by 0.3 kcal\/mol than the ionic form. The OH bond is starting to get shorter and the NH one longer. The transition state is now 0.22 kcal\/mol lower than the neutral form. With chloroform, the OH and HN bonds have become ~equal in length, the proton is symmetrically disposed.<\/li>\n<li>By the time dibutyl ether as solvent is reached, the transition state is no longer lower in \u0394G\u00a0than the neutral form, moving on to being 2.0 kcal\/mol higher for toluene. So as the solvent polarity decreases, we see a change in the potential from a single well in \u0394G, in which the proton is centred, to a very asymmetric well in which the proton is attached to the oxygen.<br \/>\n<a href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/Tol_ener.svg\"><img decoding=\"async\" class=\"aligncenter size-medium wp-image-25096\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/Tol_ener.svg\" alt=\"\" width=\"400\" \/><\/a><\/li>\n<li>Can we match the observed neutron diffraction results to the calculations? As the temperature decreases, the neutron diffraction shows the start of proton transfer from oxygen to nitrogen to form an ionic species. The calculations show that this can be modelled by an increase in the effective dielectric constant of the \u00a0medium. The computed &#8220;transition state&#8221; for proton transfer somewhere between dibutyl ether and toluene (as a dielectric media) emerges as approximately the best model for the structure of this species. At this dielectric, the calculated \u0394G is no longer quite the lowest free energy point in the potential. This might be due to the many approximations used in this model such as minimisation of total energy, the partition function method used to calculate entropy, the nature of the DFT functional, the continuum solvation model, the basis set, etc.\u00a0<\/li>\n<\/ol>\n<p><strong>Conclusions:<\/strong><\/p>\n<p>These results were obtained with the approximation that minimising the total molecular energy produces a computed geometry that can be compared to the experimental neutron diffraction structures. But can one do better? Obtaining molecular geometries by minimising the computed free energies would be non-trivial. Firstly, minimisation would depend on availability of first derivatives of the energy function with respect to coordinates, in this case \u0394G. These are not available for any DFT codes. The result would itself be temperature dependent (as indeed are the experimental results shown above). Furthermore, \u0394G is computed from normal vibrational modes and these are only appropriate when the first derivatives of the function are zero, at which point the so-called six rotations and translations of the molecule in free space also have zero energy. So we need vibrations to compute derivatives, but we need derivatives to compute vibrations in this classical approach.<\/p>\n<p>It would be great for example if the approximate model of the potential for a hydrogen transfer used above as based on minimising total energies for derivatives could be checked against a model based on geometries optimised using free energies instead. Such procedures do exist,<span id=\"cite_ITEM-25043-2\" name=\"citation\"><a href=\"#ITEM-25043-2\">[3]<\/a><\/span> using molecular dynamics trajectory methods.<\/p>\n<hr \/>\n<p>This post has DOI: 10.14469\/hpc\/10382 <span id=\"cite_ITEM-25043-3\" name=\"citation\"><a href=\"#ITEM-25043-3\">[4]<\/a><\/span><\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-25043-0\">T. Steiner, I. Majerz, and C.C. Wilson, \"First O\u2212H\u2212N Hydrogen Bond with a Centered Proton Obtained by Thermally Induced Proton Migration\", <i>Angewandte Chemie International Edition<\/i>, vol. 40, pp. 2651-2654, 2001. <a href=\"https:\/\/doi.org\/10.1002\/1521-3773(20010716)40:142651::aid-anie26513.0.co;2-2\">https:\/\/doi.org\/10.1002\/1521-3773(20010716)40:14&lt;2651::aid-anie2651&gt;3.0.co;2-2<\/a>\n\n<\/li>\n<li id=\"ITEM-25043-1\">I. Majerz, and M.J. Gutmann, \"Mechanism of proton transfer in the strong OHN intermolecular hydrogen bond\", <i>RSC Advances<\/i>, vol. 1, pp. 219, 2011. <a href=\"https:\/\/doi.org\/10.1039\/c1ra00219h\">https:\/\/doi.org\/10.1039\/c1ra00219h<\/a>\n\n<\/li>\n<li id=\"ITEM-25043-2\">M. Higashi, S. Hayashi, and S. Kato, \"Geometry optimization based on linear response free energy with quantum mechanical\/molecular mechanical method: Applications to Menshutkin-type and Claisen rearrangement reactions in aqueous solution\", <i>The Journal of Chemical Physics<\/i>, vol. 126, 2007. <a href=\"https:\/\/doi.org\/10.1063\/1.2715941\">https:\/\/doi.org\/10.1063\/1.2715941<\/a>\n\n<\/li>\n<li id=\"ITEM-25043-3\">H. Rzepa, \"Geometries of proton transfers: modelled using total energy or free energy?\", 2022. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/10368\">https:\/\/doi.org\/10.14469\/hpc\/10368<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 25043 -->","protected":false},"excerpt":{"rendered":"<p>Proton transfers are amongst the most common of all chemical reactions. They are often thought of as &#8220;trivial&#8221; and even may not feature in many mechanistic schemes, other than perhaps the notation &#8220;PT&#8221;.\u00a0The types with the lowest energy barriers for transfer often involve heteroatoms such as N and O, and the conventional transition state might [&hellip;]<\/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":[1745,1086],"tags":[],"ppma_author":[2661],"class_list":["post-25043","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","category-reaction-mechanism-2"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.7 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Geometries of proton transfers: modelled using total energy or free energy? - 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=25043\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Geometries of proton transfers: modelled using total energy or free energy? - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Proton transfers are amongst the most common of all chemical reactions. They are often thought of as &#8220;trivial&#8221; and even may not feature in many mechanistic schemes, other than perhaps the notation &#8220;PT&#8221;.\u00a0The types with the lowest energy barriers for transfer often involve heteroatoms such as N and O, and the conventional transition state might [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25043\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2022-04-18T18:09:13+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2022-04-19T08:05:08+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/04\/RAKQOJ.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=\"6 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Geometries of proton transfers: modelled using total energy or free energy? - 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=25043","og_locale":"en_GB","og_type":"article","og_title":"Geometries of proton transfers: modelled using total energy or free energy? - Henry Rzepa&#039;s Blog","og_description":"Proton transfers are amongst the most common of all chemical reactions. 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Here I extend that by probing\u00a0the role of water molecules\u00a0in the mechanism of acetal hydrolysis. Water molecules can participate in three ways: One water acts as a nucleophile to\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":7822,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7822","url_meta":{"origin":25043,"position":2},"title":"Oxime formation from hydroxylamine and ketone. Part 2: Elimination.","author":"Henry Rzepa","date":"September 25, 2012","format":false,"excerpt":"This is the follow-up to the previous post exploring a typical nucleophilic addition-elimination reaction. Here is the elimination step, which as before requires proton transfers. We again adopt a cyclic mechanism to try to avoid the build up of charge separation during those proton movements. Overall, the transition state for\u2026","rel":"","context":"In \"Reaction Mechanism\"","block_context":{"text":"Reaction Mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=reaction-mechanism"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/N-2H2O-8-ring-2.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":25338,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25338","url_meta":{"origin":25043,"position":3},"title":"Unexpected Isomerization of Oxetane-Carboxylic Acids \u2013 a viable mechanism","author":"Henry Rzepa","date":"August 12, 2022","format":false,"excerpt":"In the previous post, I looked at the intramolecular rearrangement of the oxetane carboxylic acid to a lactone, finding the barrier to the Sn2 reaction with retention was unfeasibly high. Here I explore alternatives. This first attempt uses a second molecule of a carboxylic acid (modelled as formic acid for\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/Rtn.gif?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/Rtn.gif?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/Rtn.gif?resize=525%2C300&ssl=1 1.5x"},"classes":[]},{"id":10279,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10279","url_meta":{"origin":25043,"position":4},"title":"Hidden intermediates in the (acid catalysed) ring opening of propene epoxide.","author":"Henry Rzepa","date":"May 6, 2013","format":false,"excerpt":"In a previous post on the topic, I remarked how the regiospecific ethanolysis of propene epoxide could be quickly and simply rationalised by inspecting the localized NBO orbital calculated for either the neutral or the protonated epoxide. This is an application of Hammond's postulate[ in extrapolating the properties of a\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":"Click for  3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/05\/hidden-intermediate-1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":19807,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19807","url_meta":{"origin":25043,"position":5},"title":"A Theoretical Method for Distinguishing X\u2010H Bond Activation Mechanisms.","author":"Henry Rzepa","date":"July 25, 2018","format":false,"excerpt":"Consider the four reactions. The first two are taught in introductory organic chemistry as (a) a proton transfer,\u00a0often abbreviated PT,\u00a0from X to B (a base) and (b) a hydride transfer from X to A (an acid). The third example is taught as a hydrogen atom transfer or HAT from X\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\/07\/024-1024x350.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","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\/25043","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=25043"}],"version-history":[{"count":91,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25043\/revisions"}],"predecessor-version":[{"id":25141,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25043\/revisions\/25141"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25043"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25043"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25043"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=25043"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}