{"id":242,"date":"2016-09-29T10:08:08","date_gmt":"2016-09-29T14:08:08","guid":{"rendered":"http:\/\/williamkennerly.com\/blog\/?p=242"},"modified":"2016-11-22T15:45:59","modified_gmt":"2016-11-22T20:45:59","slug":"a-look-at-various-methods-of-computationally-computing-absorbance-spectra","status":"publish","type":"post","link":"http:\/\/williamkennerly.com\/blog\/a-look-at-various-methods-of-computationally-computing-absorbance-spectra\/","title":{"rendered":"A Look at Various Methods of Computationally Computing Absorbance Spectra"},"content":{"rendered":"

Yesterday was my senior seminar presentation. \u00a0I chose a paper entitled Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents<\/em>, which examined\u00a0the absorbance spectra — and therefore also the vertical excitation energies — of a molecule called 5-methylcytidine in different solvents. \u00a0The authors (Martinez-Fernandez et. al.) use a range of solvation models and a mix of QM\/MM\/MD methods to find their spectra, and it is a fairly interesting look at different ways to computationally solve the problem.<\/p>\n

 <\/p>\n

In the paper, the absorption and emission spectra of 5-methylcytidine in water, acetonitrile, and tetrahydrofuran are studied both experimentally and computationally.\u00a0 This molecule is chosen because it is the nucleoside associated with 5-methylcytosine, a derivative of the C base linked to UV caused mutations in DNA1,2<\/sup>.\u00a0 The nucleoside is used instead of 5-methylcytosine itself because the sugar ring affects the absorbance and thus must be included for the results to be accurate to those of living systems.<\/p>\n

When studying 5-methylcytidine, the paper seeks to answer two main questions: how the molecule\u2019s spectra can be most accurately modelled computationally, and what insights into the solvent\u2019s effects on the spectra can be found.\u00a0 To answer these questions, the results of three computational methods were compared to experimental spectra.\u00a0 In the first, the molecule was modelled using a static quantum mechanical approach, with the solvent being treated using a PCM model.\u00a0 In the second, a static mixed quantum mechanical\/molecular modelling approach is used, where the solvent-molecule interaction is initially simulated and optimized to a low energy point using MM, and then the absorption\/emission energies are found using QM.\u00a0 In the third, a molecular dynamics simulation is run, from which a sample of the different conformations of molecule and solvent are chosen.\u00a0 The absorption\/emission energies are then found at each of these points using MM single point calculations.\u00a0 In each case, the absorption spectra obtained were stick spectra.\u00a0 Over each peak, a Gaussian was fit to simulate vibrational effects and provide complete spectra.\u00a0 Note for the emission spectra, only the first two methods were used as the third was computationally infeasible.<\/p>\n

The computationally obtained absorption spectra all successfully predicted the three main peaks shown in the experimental spectra at 278 nm, 242 nm, 200 nm, though in some cases the peaks were blue shifted due to the lack of vibrational effects in the calculations.\u00a0 Of the three computational methods, the third was most successful at predicting the experimental results, as it closely matched the experimental and included some absorbance between the two higher wavelength bands which the other models missed.\u00a0 This was thought to likely be due to the increased accuracy of this method at representing the solvent.\u00a0 The spectra also mirrored the solvent shifts seen in the experimental data, with acetonitrile and tetrahydrofuran having for the most part similar effects on the absorbance.\u00a0 Their spectra relative to that of water were red shifted for the band at 278 nm and of higher intensity but similar energy for the other bands.<\/p>\n

The computational emission spectra were consistent with those found experimentally for water.\u00a0 The spectra of the other two solvents were similar to each other both experimentally and computationally.\u00a0 For both solvents, the shift in the spectra from that of water were overestimated using both computational methods.\u00a0 It was concluded that the main errors in both absorption and emission spectra were due to the lack of accounting for vibrational effects.<\/p>\n

The differences in the absorption spectra for the solvents were concluded to be due to the hydrogen bonding ability of the solvent.\u00a0 The HOMO and LUMO of the molecule in acetonitrile and tetrahydrofuran were very similar in shape and energy, despite the difference in polarity3<\/sup> between the solvents.\u00a0 This accounted for their similar absorbance, and suggested that solvent polarity is not the main factor in the solvent effect.\u00a0 In water, hydrogen bonding dramatically changed the shapes of the HOMO and LUMO orbitals, thus changing their energies and the wavelengths which could be absorbed.\u00a0 Therefore, hydrogen bonding was concluded to be the main cause of the solvent effects observed.<\/p>\n

 <\/p>\n

The paper can be found at:<\/p>\n

Matrinez-Fernandez, L.; Pepino, A.; Segarra-Marti, J.; Banyasz, A.; Garavelli, M, Importa, R. Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models.\u00a0 Journal of Chemical Theory and Computation<\/em>. \u00a0http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jctc.6b00518?journalCode=jctcce<\/a><\/p>\n

 <\/p>\n

-Kristine<\/p>\n","protected":false},"excerpt":{"rendered":"

Yesterday was my senior seminar presentation. \u00a0I chose a paper entitled Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents, which examined\u00a0the absorbance spectra — and therefore also the vertical excitation energies — of a molecule called 5-methylcytidine … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":5,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[26],"tags":[17,13,15],"class_list":["post-242","post","type-post","status-publish","format-standard","hentry","category-paper-review","tag-amber","tag-gaussian","tag-molecular-dynamics"],"_links":{"self":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts\/242","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/comments?post=242"}],"version-history":[{"count":5,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts\/242\/revisions"}],"predecessor-version":[{"id":253,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts\/242\/revisions\/253"}],"wp:attachment":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/media?parent=242"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/categories?post=242"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/tags?post=242"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}