Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography
Structure analysis of small crystals is important in areas ranging from synthetic organic chemistry to pharmaceutical and material sciences, as many compounds do not yield large crystals. Here we present the detailed characterization of the structure of an organic molecule, rhodamine-6G, determined...
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| Veröffentlicht in: | Nature chemistry 2023-04, Vol.15 (4), p.491-497 |
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| creator | Takaba, Kiyofumi Maki-Yonekura, Saori Inoue, Ichiro Tono, Kensuke Hamaguchi, Tasuku Kawakami, Keisuke Naitow, Hisashi Ishikawa, Tetsuya Yabashi, Makina Yonekura, Koji |
| description | Structure analysis of small crystals is important in areas ranging from synthetic organic chemistry to pharmaceutical and material sciences, as many compounds do not yield large crystals. Here we present the detailed characterization of the structure of an organic molecule, rhodamine-6G, determined at a resolution of 0.82 Å by an X-ray free-electron laser (XFEL). Direct comparison of this structure with that obtained by electron crystallography from the same sample batch of microcrystals shows that both methods can accurately distinguish the position of some of the hydrogen atoms, depending on the type of chemical bond in which they are involved. Variations in the distances measured by XFEL and electron diffraction reflect the expected differences in X-ray and electron scatterings. The reliability for atomic coordinates was found to be better with XFEL, but the electron beam showed a higher sensitivity to charges.
The structural analysis of small crystals has remained challenging. Now, the structure of a small organic molecule, rhodamine-6G, has been resolved from microcrystals using an X-ray free-electron laser and electron diffraction. The former showed better reliability for atomic coordinates, whereas the latter was more sensitive to charges; both techniques accurately determined the position of hydrogen atoms. |
| doi_str_mv | 10.1038/s41557-023-01162-9 |
| format | Article |
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The structural analysis of small crystals has remained challenging. Now, the structure of a small organic molecule, rhodamine-6G, has been resolved from microcrystals using an X-ray free-electron laser and electron diffraction. The former showed better reliability for atomic coordinates, whereas the latter was more sensitive to charges; both techniques accurately determined the position of hydrogen atoms.</description><identifier>ISSN: 1755-4330</identifier><identifier>EISSN: 1755-4349</identifier><identifier>DOI: 10.1038/s41557-023-01162-9</identifier><identifier>PMID: 36941396</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>639/638/403/936 ; 639/925/930/2735 ; Analytical Chemistry ; Biochemistry ; Chemical bonds ; Chemistry ; Chemistry and Materials Science ; Chemistry/Food Science ; Crystallography ; Crystals ; Electron beams ; Electron diffraction ; Free electron lasers ; Hydrogen atoms ; Inorganic Chemistry ; Lasers ; Microcrystals ; Molecular structure ; Organic Chemistry ; Physical Chemistry ; Reliability ; Rhodamine ; Structural analysis</subject><ispartof>Nature chemistry, 2023-04, Vol.15 (4), p.491-497</ispartof><rights>The Author(s) 2023. corrected publication 2023</rights><rights>2023. The Author(s), under exclusive licence to Springer Nature Limited.</rights><rights>The Author(s) 2023. corrected publication 2023. This work 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><rights>The Author(s) 2023, corrected publication 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c541t-6c671f02e26055887021509025a6cadd1a0b215c4901a78fef7bd7d4defe1ab3</citedby><cites>FETCH-LOGICAL-c541t-6c671f02e26055887021509025a6cadd1a0b215c4901a78fef7bd7d4defe1ab3</cites><orcidid>0000-0002-8295-8794 ; 0000-0001-5520-4391 ; 0000-0001-7567-231X ; 0000-0002-1689-1819 ; 0000-0003-0876-7700 ; 0000-0002-2472-1684 ; 0000-0003-1218-3759 ; 0000-0002-2927-0608</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/s41557-023-01162-9$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/s41557-023-01162-9$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36941396$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Takaba, Kiyofumi</creatorcontrib><creatorcontrib>Maki-Yonekura, Saori</creatorcontrib><creatorcontrib>Inoue, Ichiro</creatorcontrib><creatorcontrib>Tono, Kensuke</creatorcontrib><creatorcontrib>Hamaguchi, Tasuku</creatorcontrib><creatorcontrib>Kawakami, Keisuke</creatorcontrib><creatorcontrib>Naitow, Hisashi</creatorcontrib><creatorcontrib>Ishikawa, Tetsuya</creatorcontrib><creatorcontrib>Yabashi, Makina</creatorcontrib><creatorcontrib>Yonekura, Koji</creatorcontrib><title>Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography</title><title>Nature chemistry</title><addtitle>Nat. Chem</addtitle><addtitle>Nat Chem</addtitle><description>Structure analysis of small crystals is important in areas ranging from synthetic organic chemistry to pharmaceutical and material sciences, as many compounds do not yield large crystals. Here we present the detailed characterization of the structure of an organic molecule, rhodamine-6G, determined at a resolution of 0.82 Å by an X-ray free-electron laser (XFEL). Direct comparison of this structure with that obtained by electron crystallography from the same sample batch of microcrystals shows that both methods can accurately distinguish the position of some of the hydrogen atoms, depending on the type of chemical bond in which they are involved. Variations in the distances measured by XFEL and electron diffraction reflect the expected differences in X-ray and electron scatterings. The reliability for atomic coordinates was found to be better with XFEL, but the electron beam showed a higher sensitivity to charges.
The structural analysis of small crystals has remained challenging. Now, the structure of a small organic molecule, rhodamine-6G, has been resolved from microcrystals using an X-ray free-electron laser and electron diffraction. The former showed better reliability for atomic coordinates, whereas the latter was more sensitive to charges; both techniques accurately determined the position of hydrogen atoms.</description><subject>639/638/403/936</subject><subject>639/925/930/2735</subject><subject>Analytical Chemistry</subject><subject>Biochemistry</subject><subject>Chemical bonds</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Chemistry/Food Science</subject><subject>Crystallography</subject><subject>Crystals</subject><subject>Electron beams</subject><subject>Electron diffraction</subject><subject>Free electron lasers</subject><subject>Hydrogen atoms</subject><subject>Inorganic Chemistry</subject><subject>Lasers</subject><subject>Microcrystals</subject><subject>Molecular structure</subject><subject>Organic Chemistry</subject><subject>Physical Chemistry</subject><subject>Reliability</subject><subject>Rhodamine</subject><subject>Structural analysis</subject><issn>1755-4330</issn><issn>1755-4349</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>BENPR</sourceid><recordid>eNp9Uctu1DAUtRCItgM_wAJZYsPGcB2_4hVCFRSkSizogp3lODfTVE482AlS_h7DlOGxYGHZuudxfXQIecbhFQfRvi6SK2UYNIIB57ph9gE550YpJoW0D09vAWfkopQ7AK0E14_JmdBWcmH1Ocmfl7yGZc0-0owlxXUZ00zTQD0tk4-Rprz38xjolCKGNSLtNlowj1XwhWW_0SEjMqzgkqsy-gpSP_f0NAp5K0u1SvvsD7fbE_Jo8LHg0_t7R27ev7u5_MCuP119vHx7zYKSfGE6aMMHaLDRoFTbGmi4AguN8jr4vuceujoJ0gL3ph1wMF1vetnjgNx3YkfeHG0PazdhH3Beakh3yOPk8-aSH93fyDzeun365jgYbjm01eHlvUNOX1csi5vGEjBGP2Nai2tMaxshTD078uIf6l1a81zjVZaVEloNsrKaIyvkVErG4fQbDu5Hpe5YqauVup-VOltFz__McZL86rASxJFQKjTvMf_e_R_b7202ruI</recordid><startdate>20230401</startdate><enddate>20230401</enddate><creator>Takaba, Kiyofumi</creator><creator>Maki-Yonekura, Saori</creator><creator>Inoue, Ichiro</creator><creator>Tono, Kensuke</creator><creator>Hamaguchi, Tasuku</creator><creator>Kawakami, Keisuke</creator><creator>Naitow, Hisashi</creator><creator>Ishikawa, Tetsuya</creator><creator>Yabashi, Makina</creator><creator>Yonekura, Koji</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QR</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PDBOC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-8295-8794</orcidid><orcidid>https://orcid.org/0000-0001-5520-4391</orcidid><orcidid>https://orcid.org/0000-0001-7567-231X</orcidid><orcidid>https://orcid.org/0000-0002-1689-1819</orcidid><orcidid>https://orcid.org/0000-0003-0876-7700</orcidid><orcidid>https://orcid.org/0000-0002-2472-1684</orcidid><orcidid>https://orcid.org/0000-0003-1218-3759</orcidid><orcidid>https://orcid.org/0000-0002-2927-0608</orcidid></search><sort><creationdate>20230401</creationdate><title>Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography</title><author>Takaba, Kiyofumi ; 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Chem</stitle><addtitle>Nat Chem</addtitle><date>2023-04-01</date><risdate>2023</risdate><volume>15</volume><issue>4</issue><spage>491</spage><epage>497</epage><pages>491-497</pages><issn>1755-4330</issn><eissn>1755-4349</eissn><abstract>Structure analysis of small crystals is important in areas ranging from synthetic organic chemistry to pharmaceutical and material sciences, as many compounds do not yield large crystals. Here we present the detailed characterization of the structure of an organic molecule, rhodamine-6G, determined at a resolution of 0.82 Å by an X-ray free-electron laser (XFEL). Direct comparison of this structure with that obtained by electron crystallography from the same sample batch of microcrystals shows that both methods can accurately distinguish the position of some of the hydrogen atoms, depending on the type of chemical bond in which they are involved. Variations in the distances measured by XFEL and electron diffraction reflect the expected differences in X-ray and electron scatterings. The reliability for atomic coordinates was found to be better with XFEL, but the electron beam showed a higher sensitivity to charges.
The structural analysis of small crystals has remained challenging. Now, the structure of a small organic molecule, rhodamine-6G, has been resolved from microcrystals using an X-ray free-electron laser and electron diffraction. The former showed better reliability for atomic coordinates, whereas the latter was more sensitive to charges; both techniques accurately determined the position of hydrogen atoms.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>36941396</pmid><doi>10.1038/s41557-023-01162-9</doi><tpages>7</tpages><orcidid>https://orcid.org/0000-0002-8295-8794</orcidid><orcidid>https://orcid.org/0000-0001-5520-4391</orcidid><orcidid>https://orcid.org/0000-0001-7567-231X</orcidid><orcidid>https://orcid.org/0000-0002-1689-1819</orcidid><orcidid>https://orcid.org/0000-0003-0876-7700</orcidid><orcidid>https://orcid.org/0000-0002-2472-1684</orcidid><orcidid>https://orcid.org/0000-0003-1218-3759</orcidid><orcidid>https://orcid.org/0000-0002-2927-0608</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | 639/638/403/936 639/925/930/2735 Analytical Chemistry Biochemistry Chemical bonds Chemistry Chemistry and Materials Science Chemistry/Food Science Crystallography Crystals Electron beams Electron diffraction Free electron lasers Hydrogen atoms Inorganic Chemistry Lasers Microcrystals Molecular structure Organic Chemistry Physical Chemistry Reliability Rhodamine Structural analysis |
| title | Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography |
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