assignments

​Assignments

  1. Write a summary of one of the articles you are reading for your project paragraph by paragraph. One or two sentences per paragraph is fine. You must do this in your own words. No significant amount of text can be copied from the abstract or any part of the paper. Either put the summary in bullet form on your research log or on AcaWiki. Due November 5, 2009 20:50 PM
  2. Answer one of the FAQ questions or create and answer an FAQ question relating to a topic relating to chemistry publishing. You must provide at least one relevant reference. You must summarize in your own words - copying text from anywhere verbatim is not allowed. If all the questions have been answered create a reasonable one on some aspect of chemistry publishing not yet asked. Due November 5, 2009 20:50 PM
  3. Find 5 independent sources of 5 properties associated with a molecule of your choice. Provide all references. (see jcblog as an example of the format) Due November 12, 2009

Optional Puzzles

  1. There are multiple entries for the following structures in ChemSpider. Identify the correct structure based on information from primary sources for one of the structures. If successful, take 500 words off the minimum for your main report.

1. Paromomycin

2. Hygromycin B

C20H37N3O13
D-Streptamine, O-6-amino-6-deoxy-L-glycero-D-galacto-heptopyranosylidene-(1→2-3)-O-β-D-talopyranosyl-(1→5)-2-deoxy-N3-methyl-
After careful examination of all ChemSpider Hygromycin B structures, none of the structures was identified as correct. The closest match to the correct structure was Chemspider ID32900.
[if that is the case then please create a new entry in ChemSpider and put in the correct structure - you will need to use ChemSketch and create an account on ChemSpider - I can help at the workshop JCB]
ChemSpider_Hygromycin_B.JPGHygromycin_B.JPG
The structure of Hygromycin B was confirmed by 13C NMR (CMR):
Hygromycin_B_1.JPG
Hygromyci_B_2.JPGHygromycin_B_3.JPG

  • ChemSpider
  • SciFinder search
  • DOI N. News, K. F. Koch, B. B. Molloy, W. Day, L. L. HuckstepX, D. E. Dorrnan, and J. D. Roberts (1970), Structure of Hygromycin B, an Antibiotic from Streptomyces hygroscopicus; The Use of CMR. Spectra in Structure Determination, I, HELVETICCAH IMICAA CTA 53, Fasc. 8 - Nr. 275
  • DOI Joyce A Sutcliffe (2005), Improving on nature: antibiotics that target the ribosome, Current Opinion in Microbiology, 8, p. 534–542
  • DOI Maria A. Borovinskaya, Shinichiro Shoji, Kurt Fredrick, and Jamie H.D. Cate (2008), Structural basis for hygromycin B inhibition of protein biosynthesis, RNA, 14, p. 1590-1599

Based on the above structures, the following structure (as pasted below) of Hygromycin B is proposed (with the aid of RSC Publishing)
Hygromycin_B_4.JPG
Smiles [H][C@@]12O[C@@]3(O[C@H]([C@@H](N)CO)[C@H](O)[C@@H](O)[C@H]3O)O[C@]1([H])[C@@H](O[C@H](CO)[C@@H]2O)O[C@@H]1[C@@H](O)[C@H](N)C[C@H](NC)[C@H]1O
[Submitted to ChemSpider JCB]
[A.Caltabiano]

3. Bekanamycin



The structure for Bekanamycin (or Kanamycin B) was confimed in an articles referennced below:
Complete proton and carbon-13 NMR assignments for kanamycin A, kanamycin B and penta-N-acetyl- kanamycin B. Eneva, G.; Spassov, S. L.; Khaimova, M. Inst. Org. Chem., Sofia, Bulg. Spectrochimica Acta, Part A: Molecular and Biomolecular Spectroscopy (1991), 47A(7), 875-80. CODEN: SAMCAS ISSN: 0584-8539. Journal written in English. CAN 115:183704 AN 1991:583704 CAPLUS

[Li Li]

4. Ribostamycin

5. Midecamycin

6. Josamycin

7. Troleandomycin

8. Nargenicin

The article shows the exact stereochemistry of nargenicin extracted from Nocardia. On chemspider, most of the structures have no stereochemistry listed. In the article they compared the NMR spectra of authenitc nargenicin and the nargenicin extracted from the Nocardia. Both spectra matched peak for peak with only a difference of 0.3 ppm or less.
Nargenicin.JPG
    • [Nick Paparoidamis]
    • Smiles: C[C@@H](O)[C@H]2OC(=O)[C@H](C[C@H]1C=CC5[C@H]4O[C@]1(C(C)=C[C@H]2C)[C@@H]5[C@H](O)[C@@H](C)[C@H]4OC(=O)c3cccn3)OC
    • nargenicin
    • Article found from Scifinder
    • The closest chemspider ID for nargenicin is 4885360. In chemspider, not all the stereocenters are specified. This article has the exact stereochemistry of nargenicin for every stereocenter in the compound.
    • The stereostructure of nodusmicin was established by X-ray crystallographic studies, while that of nargenicin A1 was confirmed by its synthesis from nodusmicin. The absolute configuration of the nargenicins, originally assigned by Cane by the nonempirical CD exciton method, was subsequently verified via Kallmerten’s enantioselective total synthesis of (+)-18-deoxynargenicin A1 (3).
[Approved by ChemSpider JCB]


9. Uvaricin

Uvaricin - a bis(tertahydrofuranoid) fatty Acid Lactone that was extracted from Uvaria accuminata
Scifinder Search revealed 21 references:

    • Yazbak, A.; Sinha, S. C.; Keinan, E. (1998). J. Org. Chem 63: 5863–5868. doi:10.1021/jo980453a
This structure was confirmed by FT-IR, 1H-NMR, 13C-NMR, COSY in this synthesis paper.
jo980453an00001.gif
jo980453an00001.gif


This is the SMILES for [+]-Uvaricin

SMILES:
O[C@@H]([C@@H]1O[C@@H]([C@@H]2O[C@]([C@@H](OC(C)=O)CCCCCCCCCC)([H])CC2)CC1)CCCCCCCCCCCCC3=C[C@H](C)OC3=O
[Approved by ChemSpider JCB]

SLN:
OHC[S=N]H(C[9:S=N]HOC[S=N]H(C[15:S=N]HOC[S=I](C[S=N]H(OC(CH3)=O)CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3)(H)CC@15)CC@10)CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2C[4]=CC[S=I]H(CH3)OC(@5)=O

Article was discovered by means of Scifinder Scholar.
Structure was drawn in ChemDraw to get SMILES, INChI, and SLN (Image shown is from primary source).

A ChemSpider search gave 3 structures, however the stereochemistry was not specified specifically in 2 of them and the 3rd did not match the structure in the article found. Attached is the ID of the structure with the patent link, as mentioned stereochemistry is not specified:
ChemSpider ID: 3679026

[JBS]

10. Digitonin

see ChemSpider post
and ChemPedia