Can we trust the experiment? Anisotropic displacement parameters in 1‐(halomethyl)‐3‐nitrobenzene (halogen = Cl or Br)
1‐(Chloromethyl)‐3‐nitrobenzene, C7H6NClO2, and 1‐(bromomethyl)‐3‐nitrobenzene, C7H6NBrO2, were chosen as test compounds for benchmarking anisotropic displacement parameters (ADPs) calculated from first principles in the harmonic approximation. Crystals of these compounds are isomorphous, and theory...
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Veröffentlicht in: | Acta crystallographica. Section C, Crystal structure communications Crystal structure communications, 2020-06, Vol.76 (6), p.591-597 |
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description | 1‐(Chloromethyl)‐3‐nitrobenzene, C7H6NClO2, and 1‐(bromomethyl)‐3‐nitrobenzene, C7H6NBrO2, were chosen as test compounds for benchmarking anisotropic displacement parameters (ADPs) calculated from first principles in the harmonic approximation. Crystals of these compounds are isomorphous, and theory predicted similar ADPs for both. In‐house diffraction experiments with Mo Kα radiation were in apparent contradiction to this theoretical result, with experimentally observed ADPs significantly larger for the bromo derivative. In contrast, the experimental and theoretical ADPs for the lighter congener matched reasonably well. As all usual quality indicators for both sets of experimental data were satisfactory, complementary diffraction experiments were performed at a synchrotron beamline with shorter wavelength. Refinements based on these intensity data gave very similar ADPs for both compounds and were thus in agreement with the earlier in‐house results for the chloro derivative and the predictions of theory. We speculate that strong absorption by the heavy halogen may be the reason for the observed discrepancy.
Anisotropic displacement parameters for the isomorphous compounds 1‐(halomethyl)‐3‐nitrobenzene (halo = chloro and bromo) were calculated from first principles and determined by X‐ray diffraction experiments. Unexpectedly, the experiment for the bromo compound proved more challenging than theory. |
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Anisotropic displacement parameters for the isomorphous compounds 1‐(halomethyl)‐3‐nitrobenzene (halo = chloro and bromo) were calculated from first principles and determined by X‐ray diffraction experiments. Unexpectedly, the experiment for the bromo compound proved more challenging than theory.</description><identifier>ISSN: 2053-2296</identifier><identifier>ISSN: 0108-2701</identifier><identifier>EISSN: 2053-2296</identifier><identifier>EISSN: 1600-5759</identifier><identifier>DOI: 10.1107/S2053229620006221</identifier><identifier>PMID: 32499457</identifier><language>eng</language><publisher>5 Abbey Square, Chester, Cheshire CH1 2HU, England: International Union of Crystallography</publisher><subject>ADP ; anisotropic displacement parameters ; crystal structure ; Crystals ; density functional theory ; DFT ; Diffraction ; First principles ; Mathematical analysis ; molecular crystal ; Nitrobenzene ; Parameters ; phonon calculations ; Radiation ; synchrotron</subject><ispartof>Acta crystallographica. Section C, Crystal structure communications, 2020-06, Vol.76 (6), p.591-597</ispartof><rights>2020 Mroz et al. published by IUCr Journals.</rights><rights>open access.</rights><rights>2020. This article is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4229-2510f4da6cd20a630012c33fcd62dfcbb779063ee2b9917e1af2783557ee80e73</citedby><cites>FETCH-LOGICAL-c4229-2510f4da6cd20a630012c33fcd62dfcbb779063ee2b9917e1af2783557ee80e73</cites><orcidid>0000-0002-2623-0061 ; 0000-0002-1925-9624</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1107%2FS2053229620006221$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1107%2FS2053229620006221$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32499457$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mroz, Damian</creatorcontrib><creatorcontrib>Wang, Ruimin</creatorcontrib><creatorcontrib>Englert, Ulli</creatorcontrib><creatorcontrib>Dronskowski, Richard</creatorcontrib><title>Can we trust the experiment? Anisotropic displacement parameters in 1‐(halomethyl)‐3‐nitrobenzene (halogen = Cl or Br)</title><title>Acta crystallographica. Section C, Crystal structure communications</title><addtitle>Acta Crystallogr C Struct Chem</addtitle><description>1‐(Chloromethyl)‐3‐nitrobenzene, C7H6NClO2, and 1‐(bromomethyl)‐3‐nitrobenzene, C7H6NBrO2, were chosen as test compounds for benchmarking anisotropic displacement parameters (ADPs) calculated from first principles in the harmonic approximation. Crystals of these compounds are isomorphous, and theory predicted similar ADPs for both. In‐house diffraction experiments with Mo Kα radiation were in apparent contradiction to this theoretical result, with experimentally observed ADPs significantly larger for the bromo derivative. In contrast, the experimental and theoretical ADPs for the lighter congener matched reasonably well. As all usual quality indicators for both sets of experimental data were satisfactory, complementary diffraction experiments were performed at a synchrotron beamline with shorter wavelength. Refinements based on these intensity data gave very similar ADPs for both compounds and were thus in agreement with the earlier in‐house results for the chloro derivative and the predictions of theory. We speculate that strong absorption by the heavy halogen may be the reason for the observed discrepancy.
Anisotropic displacement parameters for the isomorphous compounds 1‐(halomethyl)‐3‐nitrobenzene (halo = chloro and bromo) were calculated from first principles and determined by X‐ray diffraction experiments. Unexpectedly, the experiment for the bromo compound proved more challenging than theory.</description><subject>ADP</subject><subject>anisotropic displacement parameters</subject><subject>crystal structure</subject><subject>Crystals</subject><subject>density functional theory</subject><subject>DFT</subject><subject>Diffraction</subject><subject>First principles</subject><subject>Mathematical analysis</subject><subject>molecular crystal</subject><subject>Nitrobenzene</subject><subject>Parameters</subject><subject>phonon calculations</subject><subject>Radiation</subject><subject>synchrotron</subject><issn>2053-2296</issn><issn>0108-2701</issn><issn>2053-2296</issn><issn>1600-5759</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><recordid>eNqFkcFO3DAQhq0KVBDsA_RSWeoFDlvscRyvDxVaIgqIlXoADpwix5mwQVkntRPRrTj0EXhGnqReFipUDhws2_9888vjn5BPnH3lnKmDC2BSAOgUGGMpAP9AtlfSeKVtvDpvkVEItxHiHKRS_CPZEpBonUi1Te4z4-gd0t4Poaf9HCn-6tDXC3T9IZ26OrS9b7va0rIOXWMsriq0M94ssEcfaO0of_zzsDc3TRul-bLZj1cRl6tja4HuNzqkT_UbdPQbzRraenrk93fJZmWagKPnfYdcfT--zE7Hsx8nZ9l0NrZJHGAMkrMqKU1qS2AmFXESsEJUtkyhrGxRKKVZKhCh0Jor5KYCNRFSKsQJQyV2yN7at_PtzwFDny_qYLFpjMN2CDkknAmpJlJH9Mt_6G07eBdfFymmJUsmDCLF15T1bQgeq7yLX2b8MucsX6WTv0kn9nx-dh6KBZb_Ol6yiIBeA3d1g8v3HfPpdQYX50IlWvwFSv2bqw</recordid><startdate>202006</startdate><enddate>202006</enddate><creator>Mroz, Damian</creator><creator>Wang, Ruimin</creator><creator>Englert, Ulli</creator><creator>Dronskowski, Richard</creator><general>International Union of Crystallography</general><general>Wiley Subscription Services, Inc</general><scope>24P</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SR</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>L7M</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-2623-0061</orcidid><orcidid>https://orcid.org/0000-0002-1925-9624</orcidid></search><sort><creationdate>202006</creationdate><title>Can we trust the experiment? Anisotropic displacement parameters in 1‐(halomethyl)‐3‐nitrobenzene (halogen = Cl or Br)</title><author>Mroz, Damian ; Wang, Ruimin ; Englert, Ulli ; Dronskowski, Richard</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4229-2510f4da6cd20a630012c33fcd62dfcbb779063ee2b9917e1af2783557ee80e73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>ADP</topic><topic>anisotropic displacement parameters</topic><topic>crystal structure</topic><topic>Crystals</topic><topic>density functional theory</topic><topic>DFT</topic><topic>Diffraction</topic><topic>First principles</topic><topic>Mathematical analysis</topic><topic>molecular crystal</topic><topic>Nitrobenzene</topic><topic>Parameters</topic><topic>phonon calculations</topic><topic>Radiation</topic><topic>synchrotron</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mroz, Damian</creatorcontrib><creatorcontrib>Wang, Ruimin</creatorcontrib><creatorcontrib>Englert, Ulli</creatorcontrib><creatorcontrib>Dronskowski, Richard</creatorcontrib><collection>Wiley Online Library Open Access</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Engineered Materials Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><jtitle>Acta crystallographica. Section C, Crystal structure communications</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mroz, Damian</au><au>Wang, Ruimin</au><au>Englert, Ulli</au><au>Dronskowski, Richard</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Can we trust the experiment? Anisotropic displacement parameters in 1‐(halomethyl)‐3‐nitrobenzene (halogen = Cl or Br)</atitle><jtitle>Acta crystallographica. Section C, Crystal structure communications</jtitle><addtitle>Acta Crystallogr C Struct Chem</addtitle><date>2020-06</date><risdate>2020</risdate><volume>76</volume><issue>6</issue><spage>591</spage><epage>597</epage><pages>591-597</pages><issn>2053-2296</issn><issn>0108-2701</issn><eissn>2053-2296</eissn><eissn>1600-5759</eissn><abstract>1‐(Chloromethyl)‐3‐nitrobenzene, C7H6NClO2, and 1‐(bromomethyl)‐3‐nitrobenzene, C7H6NBrO2, were chosen as test compounds for benchmarking anisotropic displacement parameters (ADPs) calculated from first principles in the harmonic approximation. Crystals of these compounds are isomorphous, and theory predicted similar ADPs for both. In‐house diffraction experiments with Mo Kα radiation were in apparent contradiction to this theoretical result, with experimentally observed ADPs significantly larger for the bromo derivative. In contrast, the experimental and theoretical ADPs for the lighter congener matched reasonably well. As all usual quality indicators for both sets of experimental data were satisfactory, complementary diffraction experiments were performed at a synchrotron beamline with shorter wavelength. Refinements based on these intensity data gave very similar ADPs for both compounds and were thus in agreement with the earlier in‐house results for the chloro derivative and the predictions of theory. We speculate that strong absorption by the heavy halogen may be the reason for the observed discrepancy.
Anisotropic displacement parameters for the isomorphous compounds 1‐(halomethyl)‐3‐nitrobenzene (halo = chloro and bromo) were calculated from first principles and determined by X‐ray diffraction experiments. Unexpectedly, the experiment for the bromo compound proved more challenging than theory.</abstract><cop>5 Abbey Square, Chester, Cheshire CH1 2HU, England</cop><pub>International Union of Crystallography</pub><pmid>32499457</pmid><doi>10.1107/S2053229620006221</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0002-2623-0061</orcidid><orcidid>https://orcid.org/0000-0002-1925-9624</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | ADP anisotropic displacement parameters crystal structure Crystals density functional theory DFT Diffraction First principles Mathematical analysis molecular crystal Nitrobenzene Parameters phonon calculations Radiation synchrotron |
title | Can we trust the experiment? Anisotropic displacement parameters in 1‐(halomethyl)‐3‐nitrobenzene (halogen = Cl or Br) |
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