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Journal articles on the topic 'Computer assisted structure elucidation'

Author: Grafiati

Published: 4 June 2021

Last updated: 2 February 2022

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1

Gray, Neil A. B., and Albert Platt. "Computer assisted structure elucidation." Analytica Chimica Acta 201 (1987): 367. http://dx.doi.org/10.1016/s0003-2670(00)85366-0.

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2

Warr, Wendy A. "COMPUTER-ASSISTED STRUCTURE ELUCIDATION." Analytical Chemistry 65, no. 24 (1993): 1087A—1095A. http://dx.doi.org/10.1021/ac00072a728.

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3

Richards, W. G. "Computer-assisted structure elucidation." Endeavour 11, no. 2 (1987): 107–8. http://dx.doi.org/10.1016/0160-9327(87)90262-6.

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4

DeTar, DeLosF. "Computer-Assisted Structure Elucidation." Computers & Chemistry 11, no. 3 (1987): 228. http://dx.doi.org/10.1016/0097-8485(87)80024-4.

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5

Elyashberg, Mikhail, Kirill Blinov, Sergey Molodtsov, and Antony Williams. "Elucidating ‘undecipherable’ chemical structures using computer-assisted structure elucidation approaches." Magnetic Resonance in Chemistry 50, no. 1 (2012): 22–27. http://dx.doi.org/10.1002/mrc.2849.

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6

CHEN, L., and M. ZHANG. "ChemInform Abstract: Computer-Assisted Structure Elucidation." ChemInform 23, no. 38 (2010): no. http://dx.doi.org/10.1002/chin.199238333.

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7

FUNATSU, Kimito. "Computer-Assisted Structure Elucidation for Organic Compound." Journal of Synthetic Organic Chemistry, Japan 51, no. 6 (1993): 516–28. http://dx.doi.org/10.5059/yukigoseikyokaishi.51.516.

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8

Elyashberg, M. E., A. J. Williams, and G. E. Martin. "Computer-assisted structure verification and elucidation tools in NMR-based structure elucidation." Progress in Nuclear Magnetic Resonance Spectroscopy 53, no. 1-2 (2008): 1–104. http://dx.doi.org/10.1016/j.pnmrs.2007.04.003.

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9

Burns, Darcy C., Eugene P. Mazzola, and William F. Reynolds. "The role of computer-assisted structure elucidation (CASE) programs in the structure elucidation of complex natural products." Natural Product Reports 36, no. 6 (2019): 919–33. http://dx.doi.org/10.1039/c9np00007k.

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10

Lipkus, Alan H., and Morton E. Munk. "Automated classification of candidate structures for computer-assisted structure elucidation." Journal of Chemical Information and Modeling 28, no. 1 (1988): 9–18. http://dx.doi.org/10.1021/ci00057a002.

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11

Elyashberg, Mikhail, Kirill Blinov, Sergey Molodtsov, and Antony J. Williams. "Structure Revision of Asperjinone Using Computer-Assisted Structure Elucidation Methods." Journal of Natural Products 76, no. 1 (2013): 113–16. http://dx.doi.org/10.1021/np300218g.

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12

Han, Yongquan, and Christoph Steinbeck. "Evolutionary-Algorithm-Based Strategy for Computer-Assisted Structure Elucidation." Journal of Chemical Information and Computer Sciences 44, no. 2 (2004): 489–98. http://dx.doi.org/10.1021/ci034132y.

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13

FUNATSU, K. "ChemInform Abstract: Computer-Assisted Structure Elucidation for Organic Compounds." ChemInform 24, no. 45 (2010): no. http://dx.doi.org/10.1002/chin.199345331.

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14

Elyashberg, Mikhail, and Dimitris Argyropoulos. "Computer‐assisted structure elucidation (CASE): Current and future perspectives." Magnetic Resonance in Chemistry 59, no. 7 (2021): 667–68. http://dx.doi.org/10.1002/mrc.5162.

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15

Elyashberg, Mikhail E., Kirill A. Blinov, Antony J. Williams, Sergey G. Molodtsov, and Gary E. Martin. "Are Deterministic Expert Systems for Computer-Assisted Structure Elucidation Obsolete?" Journal of Chemical Information and Modeling 46, no. 4 (2006): 1643–56. http://dx.doi.org/10.1021/ci050469j.

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16

Christie, Bradley D., and Morton E. Munk. "Structure generation by reduction: a new strategy for computer-assisted structure elucidation." Journal of Chemical Information and Modeling 28, no. 2 (1988): 87–93. http://dx.doi.org/10.1021/ci00058a009.

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17

Massiot, G., and J. M. Nuzillard. "Computer-assisted elucidation of structures of natural products." Phytochemical Analysis 3, no. 4 (1992): 153–59. http://dx.doi.org/10.1002/pca.2800030403.

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18

Yirik, Mehmet Aziz, and Christoph Steinbeck. "Chemical graph generators." PLOS Computational Biology 17, no. 1 (2021): e1008504. http://dx.doi.org/10.1371/journal.pcbi.1008504.

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Chemical graph generators are software packages to generate computer representations of chemical structures adhering to certain boundary conditions. Their development is a research topic of cheminformatics. Chemical graph generators are used in areas such as virtual library generation in drug design, in molecular design with specified properties, called inverse QSAR/QSPR, as well as in organic synthesis design, retrosynthesis or in systems for computer-assisted structure elucidation (CASE). CASE systems again have regained interest for the structure elucidation of unknowns in computational metabolomics, a current area of computational biology.

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19

Buevich, Alexei V., and Mikhail E. Elyashberg. "Enhancing computer-assisted structure elucidation with DFT analysis of J -couplings." Magnetic Resonance in Chemistry 58, no. 6 (2020): 594–606. http://dx.doi.org/10.1002/mrc.4996.

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20

Soong, Ronald, Brent G. Pautler, Arvin Moser, et al. "CASE (Computer-Assisted Structure Elucidation) Study for an Undergraduate Organic Chemistry Class." Journal of Chemical Education 97, no. 3 (2020): 855–60. http://dx.doi.org/10.1021/acs.jchemed.9b00498.

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21

Warr, Wendy A. "Computer-assisted structure elucidation. Part II: Indirect database approaches and established systems." Analytical Chemistry 65, no. 24 (1993): 1087A—1095A. http://dx.doi.org/10.1021/ac00072a002.

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22

Elyashberg, Mikhail, Antony J. Williams, and Kirill Blinov. "Structural revisions of natural products by Computer-Assisted Structure Elucidation (CASE) systems." Natural Product Reports 27, no. 9 (2010): 1296. http://dx.doi.org/10.1039/c002332a.

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23

Troche-Pesqueira, Eduardo, Clemens Anklin, Roberto R. Gil, and Armando Navarro-Vázquez. "Computer-Assisted 3D Structure Elucidation of Natural Products using Residual Dipolar Couplings." Angewandte Chemie International Edition 56, no. 13 (2017): 3660–64. http://dx.doi.org/10.1002/anie.201612454.

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24

Troche-Pesqueira, Eduardo, Clemens Anklin, Roberto R. Gil, and Armando Navarro-Vázquez. "Computer-Assisted 3D Structure Elucidation of Natural Products using Residual Dipolar Couplings." Angewandte Chemie 129, no. 13 (2017): 3714–18. http://dx.doi.org/10.1002/ange.201612454.

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25

Jaspars, Marcel. "Computer assisted structure elucidation of natural products using two-dimensional NMR spectroscopy†." Natural Product Reports 16, no. 2 (1999): 241–48. http://dx.doi.org/10.1039/a804433c.

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26

Hashimoto, Masao S., Yasuko Tanaka, and Chutetsu F. Hattori. "Qualitative analysis of carbon-13 NMR spectra by computer-assisted structure elucidation." Chemometrics and Intelligent Laboratory Systems 4, no. 3 (1988): 251–59. http://dx.doi.org/10.1016/0169-7439(88)80100-x.

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27

Blinov, Kirill, Mikhail Elyashberg, Eduard R. Martirosian, et al. "Quindolinocryptotackieine: the elucidation of a novel indoloquinoline alkaloid structure through the use of computer-assisted structure elucidation and 2D NMR." Magnetic Resonance in Chemistry 41, no. 8 (2003): 577–84. http://dx.doi.org/10.1002/mrc.1227.

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28

Januar, Hedi Indra, Neviaty Putri Zamani, Dedi Soedharma, and Ekowati Chasanah. "Logic Structure Determination (LSD) as a Computer Assisted Structure Elucidation (Case) for Molecular Structure Determination of Cytotoxic Cembranoids from Soft Coral." Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology 11, no. 1 (2016): 1. http://dx.doi.org/10.15578/squalen.v11i1.177.

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The tropical Indonesian soft corals are a valuable resources that produce pharmacological cytotoxic cembranoids. However, manual structure determination into these compounds requires adequate knowledge of organic chemistry. This study presents the application of Logic Structure Determination (LSD), as a freeware Computer Assisted Structure Elucidation (CASE) for automatic molecular structure determination of cembranoid compounds from soft corals species. 12 Nuclear Magnetic Resonance (NMR) dataset of cytotoxic cembranoids were used to evaluate the accuracy of LSD in generating the possible structures. Results of this study shows LSD generated numerous possible molecular structures, as the data input file derived only from 2D-NMR HMQC (Heteronuclear Multiple-Quantum Correlation), COSY (Homonuclear Correlation Spectroscopy), and HMBC (Heteronuclear Multiple Bond Correlation). The accuracy significantly enhanced (only 2-4 possible cembranoid structures from each NMR dataset) with addition of H2BC (Heteronuclear 2 Bond Correlation) experimental data. This may indicates that VLRC (Very Long-Range Correlations) affects significantly to LSD capability. Furthermore, LSD with direct 2 bond NMR experimental data is a reliable CASE technique for identification of cembranoid compounds. In general, this freeware-CASE is potential to be applied to other type of small molecule compounds and may serves as a potential solution for elucidation bottleneck step in Indonesian natural products studies.

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29

Köck, Matthias, Thomas Lindel, and Jochen Junker. "Incorporation of 4J-HMBC and NOE Data into Computer-Assisted Structure Elucidation with WebCocon." Molecules 26, no. 16 (2021): 4846. http://dx.doi.org/10.3390/molecules26164846.

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Over the past decades, different software programs have been developed for the Computer-Assisted Structure Elucidation (CASE) with NMR data using with various approaches. WebCocon is one of them that has been continuously improved over the past 20 years. Here, we present the inclusion of 4JCH correlations (4J-HMBC) in the HMBC interpretation of Cocon and NOE data in WebCocon. The 4J-HMBC data is used during the structure generation process, while the NOE data is used in post-processing of the results. The marine natural product oxocyclostylidol was selected to demonstrate WebCocon’s enhanced HMBC data processing capabilities. A systematic study of the 4JCH correlations of oxocyclostylidol was performed. The application of NOEs in CASE is demonstrated using the NOE correlations of the diterpene pyrone asperginol A known from the literature. As a result, we obtained a conformation that corresponds very well to the existing X-ray structure.

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30

Christie, Bradley D., and Morton E. Munk. "The application of two-dimensional nuclear magnetic resonance spectroscopy in computer-assisted structure elucidation." Analytica Chimica Acta 200 (1987): 347–61. http://dx.doi.org/10.1016/s0003-2670(00)83782-4.

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31

Elyashberg, Mikhail, Antony J. Williams, and Kirill Blinov. "ChemInform Abstract: Structural Revisions of Natural Products by Computer-Assisted Structure Elucidation (CASE) Systems." ChemInform 41, no. 51 (2010): no. http://dx.doi.org/10.1002/chin.201051271.

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32

Elyashberg, Mikhail, Kirill Blinov, Sergey Molodtsov, Yegor Smurnyy, Antony J. Williams, and Tatiana Churanova. "ChemInform Abstract: Computer-Assisted Methods for Molecular Structure Elucidation: Realizing a Spectroscopist′s Dream." ChemInform 41, no. 28 (2010): no. http://dx.doi.org/10.1002/chin.201028271.

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33

Jaspars, Marcel. "ChemInform Abstract: Computer-Assisted Structure Elucidation of Natural Products Using Two-Dimensional NMR Spectroscopy." ChemInform 30, no. 38 (2010): no. http://dx.doi.org/10.1002/chin.199938275.

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34

Elyashberg, M. E., K. A. Blinov, S. G. Molodtsov, and E. D. Smurnyi. "New computer-assisted methods for the elucidation of molecular structure from 2-D spectra." Journal of Analytical Chemistry 63, no. 1 (2008): 13–20. http://dx.doi.org/10.1134/s1061934808010036.

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35

Robien, Wolfgang. "Computer-assisted structure elucidation of organic compounds III: Automatic fragment generation from13C-NMR spectra." Mikrochimica Acta 89, no. 1-6 (1986): 271–79. http://dx.doi.org/10.1007/bf01207321.

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36

Plainchont, Bertrand, Jean-Marc Nuzillard, Gilberto V. Rodrigues, Marcelo J. P. Ferreira, Marcus T. Scotti, and Vicente P. Emerenciano. "New Improvements in Automatic Structure Elucidation Using the LSD (Logic for Structure Determination) and the SISTEMAT Expert Systems." Natural Product Communications 5, no. 5 (2010): 1934578X1000500. http://dx.doi.org/10.1177/1934578x1000500517.

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This article describes the integration of the LSD (Logic for Structure Determination) and SISTEMAT expert systems that were both designed for the computer-assisted structure elucidation of small organic molecules. A first step has been achieved towards the linking of the SISTEMAT database with the LSD structure generator. The skeletal descriptions found by the SISTEMAT programs are now easily transferred to LSD as substructural constraints. Examples of the synergy between these expert systems are given for recently reported natural products.

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37

Williams, A. J., M. E. Elyashberg, K. A. Blinov, et al. "Applying Computer-Assisted Structure Elucidation Algorithms for the Purpose of Structure Validation: Revisiting the NMR Assignments of Hexacyclinol." Journal of Natural Products 71, no. 4 (2008): 581–88. http://dx.doi.org/10.1021/np070557t.

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38

Peng, Chen, Geoffrey Bodenhausen, Shengxiang Qiu, et al. "Computer-assisted structure elucidation: application of CISOC-SES to the resonance assignment and structure generation of betulinic acid." Magnetic Resonance in Chemistry 36, no. 4 (1998): 267–78. http://dx.doi.org/10.1002/(sici)1097-458x(199804)36:4<267::aid-omr256>3.0.co;2-6.

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39

Navarro-Vázquez, Armando, Roberto R. Gil, and Kirill Blinov. "Computer-Assisted 3D Structure Elucidation (CASE-3D) of Natural Products Combining Isotropic and Anisotropic NMR Parameters." Journal of Natural Products 81, no. 1 (2018): 203–10. http://dx.doi.org/10.1021/acs.jnatprod.7b00926.

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40

Blinov, K. A., A. V. Buevich, R. T. Williamson, and G. E. Martin. "The impact of LR-HSQMBC very long-range heteronuclear correlation data on computer-assisted structure elucidation." Org. Biomol. Chem. 12, no. 47 (2014): 9505–9. http://dx.doi.org/10.1039/c4ob01418a.

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41

Peng, Chen, Shengang Yuan, Chongzhi Zheng, and Yongzheng Hui. "Efficient Application of 2D NMR Correlation Information in Computer-Assisted Structure Elucidation of Complex Natural Products." Journal of Chemical Information and Modeling 34, no. 4 (1994): 805–13. http://dx.doi.org/10.1021/ci00020a013.

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42

Steinbeck, Christoph. "SENECA: A Platform-Independent, Distributed, and Parallel System for Computer-Assisted Structure Elucidation in Organic Chemistry." Journal of Chemical Information and Computer Sciences 41, no. 6 (2001): 1500–1507. http://dx.doi.org/10.1021/ci000407n.

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43

Hilton, Bruce D., and Gary E. Martin. "The Impact of Long-Range1H-15N Heteronuclear Shift Correlation Data on Computer-Assisted Structure Elucidation: Posaconazole." Journal of Heterocyclic Chemistry 49, no. 3 (2012): 526–32. http://dx.doi.org/10.1002/jhet.803.

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44

Codina, Anna, Robert W. Ryan, Richard Joyce, and Don S. Richards. "Identification of Multiple Impurities in a Pharmaceutical Matrix Using Preparative Gas Chromatography and Computer-Assisted Structure Elucidation." Analytical Chemistry 82, no. 21 (2010): 9127–33. http://dx.doi.org/10.1021/ac102151g.

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45

Peng, Chen, Shengang Yuan, Chongzhi Zheng, Zhengshuang Shi, and Houming Wu. "Practical Computer-Assisted Structure Elucidation for Complex Natural Products: Efficient Use of Ambiguous 2D NMR Correlation Information." Journal of Chemical Information and Modeling 35, no. 3 (1995): 539–46. http://dx.doi.org/10.1021/ci00025a023.

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46

Blinov, Kirill A., Dean Carlson, Mikhail E. Elyashberg, et al. "Computer-assisted structure elucidation of natural products with limited 2D NMR data: application of the StrucEluc system." Magnetic Resonance in Chemistry 41, no. 5 (2003): 359–72. http://dx.doi.org/10.1002/mrc.1187.

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47

Diallo, Mamadou S., Alejandro Strachan, Jean-Loup Faulon, and William A. Goddard. "Thermodynamic Properties of Asphaltenes Through Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Bulk Arabian Light Asphaltenes." Petroleum Science and Technology 22, no. 7-8 (2004): 877–99. http://dx.doi.org/10.1081/lft-120040254.

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48

Steinbeck, Christoph. "ChemInform Abstract: SENECA: A Platform-Independent, Distributed, and Parallel System for Computer-Assisted Structure Elucidation in Organic Chemistry." ChemInform 33, no. 9 (2010): no. http://dx.doi.org/10.1002/chin.200209263.

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49

Naman, C. Benjamin, Jie Li, Arvin Moser, et al. "Computer-Assisted Structure Elucidation of Black Chokeberry (Aronia melanocarpa) Fruit Juice Isolates with a New Fused Pentacyclic Flavonoid Skeleton." Organic Letters 17, no. 12 (2015): 2988–91. http://dx.doi.org/10.1021/acs.orglett.5b01284.

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50

Hashimoto, Masao S., Yasuko Tanaka, Hitoshi Sasabuchi, and Chutetsu F. Hattori. "A computer-assisted structure elucidation scheme based upon the pattern of assembly of peaks in carbon-13/ proton NMR spectra." Chemometrics and Intelligent Laboratory Systems 6, no. 2 (1989): 143–55. http://dx.doi.org/10.1016/0169-7439(87)80056-4.

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