JBS45+Class+Notes

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Puzzle, Nick completed! **Way to go Nick**! Your results were sent to chemspider and [|approved].
 * November 19th 2009 (Class 9)**

Properties HW: Properties, you need to copy the same numbers with same sig figs.

How do you use chemsketch?
 * November 12th 2009 (Class 8)**

For complex molecules an alternative to drawing it, in particular with complex 3D structures use chemspider copy the SMILES go to -tools -generate -paste the SMILEs [ctrl-v] -- can get different smiles for different compounds

can make 3D modify it and save it as another structure. You can convert from R-S -click on R-S and then click on the atom you would like to convert and then reoptimize. Then can view multiple ways. can export under tools using the SMILEs notation.

Workshop - entire class** reviewed DOI
 * (Class 7)


 * October 29th, 2009** (Class 6):
 * Week extension of HW**

Workshop: Today we will studt Physical Properties How do you find these properties and how do you interpret them.

Compounds that have multiple entries in chemspider - identify the correct one through primary literature search (ambiguous in the DB).

Should have identified a single molecule to search for at this point - now we will find properties

I will investigate one of the extra assignments during this class - in particular that of Josamycin (a macrolide antibiotic)

In Chem spider look at Supplemental information - predicted property gives you a guideline for the experimental, if they are not in close agreement further research into the property and the calculation might need to be further investigated.

Rules 1: Act Paranoid! - Is chemspider making this up? Is it a conspiracy theory to throw your research off? First look to see if a primary source is referenced. Match MP and BP - cross reference to a primary source? Always predicts the same properties. Look at density/specific gravity (for this class). Then look at another source again.

Look at (Make Clickable) MP BP Density/Specific Gravity log P log D - distribution at pH Solubility

2: Look at MSDS to find as another source.

3: Try Google - but to not trust all that you read.

4: Wikipedia - try it but again we careful of what you use, remember rule #1.

5. Looking at the range show do you determine which is incorrect. Pool the data and see where there is a cluster. If there is an oddiity look further, was the compound Pure? What date was it researched, 1700's? Is it all the same form (ie Salt form)?

6. If it is from a peer reviewed source it can be seen as more reliable.

Good time to start writing your project.
 * October 22th, 2009** (Class 5):

Two assignments, due next week.

A good exam question, what is the difference between the results vs the discussion.

Peer Review - does not double check, or repeat all data presented. It is assumed that the researcher can collect and analyze the data they are presenting. (Modern peer review started in 1967) - there are many angles of approach for this topic.

PloS is completely open access. Chemistry will be in PLoS one only does the peer review with respect to the validity of what is presented.

New Database was added to the list called Scirus - covers high quality secondary and tertiary literature. It is like searching wikipedia plus other peer revue papers.

For exam know creative commons types and


 * October 15th, 2009** (Class 4):

To fix the wiki - use text edit, or the notepad use Digital Object Identifiers in your wiki use friendfeed to get useful information

CHEMSPIDER : Searching - recognize features of SMILE and InChi: CAS SMILE InChI (cannot use Google to search for these, not capable for understanding) @ denotes chirality + - refers to chiral centers

InChI key has two parts: The Right has the stereochemistry information (this will pull the one searched for in particular) The Left has the core information (this will pull all matches)

Wikipedia entries are embeded here - very useful

Associated Data sources: Easy to purchase items, or might find useful things directed to what you are investigating.

Will need the predicted properties part of chemspider for the next HW.

Use SDBS for obtaining spectra or try sigmadirectly.

Kegg deals with metabolic pathways MeSH descriptors EPI for environmental info SimBioSys LASSO - compares against PDB and scores possible interaction with enzymes

Moving onto the next tool:[| Beilstein Crossfire] Searches through primary sources to get experimental information

Over 500 DB Over 20000 Articles
 * October 8th, 2009 (Lecture Notes):**
 * Drexel"s Library Has:**

EZ Borrow to access through University ID - Simple search performed across many universities (UPenn, PennState) - I dont believe I have tried this but I will in the future. ILLiad Interlibrary Loan - getting materials we do not have on site at Drexel (I have already used this as well) RefWorks - citation organizer, helps you to manage and organize citations (already using this, my boss uses Endnote but we can easily import and export the data files). Can cut and paste bibliographic output into the wiki.
 * Interlibrary Loans:**

Web of Science- cross discipline database - can manipulate the body of literature you are searching for
 * Databases**

In class: Wiki Review
 * October 1st, 2009:**
 * Use of the Text Editor - This will help you fix the text and make use of the format commands
 * Use of Wikitext - See help menu

Document Source Types:**
 * New Wiki Page: Publishing in Chemistry
 * 1) //Primary Source//: The Source of the information, nothing that you can cite that provides more info than that source [Journal Article; Conference Proceedings; Patents; Lab Notebook; Blog; ]
 * 2) //Secondary Source//:[Review Article; Handbooks; Wikipiedia; Databases; Blog; ]
 * 3) //Tertiary Source//: [Magazines; ]


 * Copyrights:** Print Rights arrangement of words is important


 * Project:** Pick a very small area and exhaust it to virtual certainty.

Hindawi Publishing Corp. **- [|Bioinorganic Chemistry and Applications] -** I have actually participated in an open access journal last year with another group.**[That's awesome! JCB**] The link is to that article. doi:10.1155/2008/257038 **[BTW if you want to convert a doi to a link use [] JCB]
 * Open Access Journals:**

**September 24th, 2009:
 * Intro to class/syllabus:**


 * Set up Wiki (Completed)
 * Second Life
 * ChemSpider (Downloaded iPhone App a while ago - ChemMobi )**[Didn't know about this - please add JCB]**
 * Wikipedia
 * Sigma Aldrich
 * Web of Science - Looked at Journal citation list JACS is 13th Most cited in all chemistry journals
 * Added CRC Handbook to the resource Page

Possible addition to Social networks: **[Perfect - please add JCB]**
 * SciLink
 * MyNet Research - Empowering Collaboration