Properties HW: Properties, you need to copy the same numbers with same sig figs.
November 12th 2009 (Class 8)
How do you use chemsketch?
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.
(Class 7)
Workshop - entire class
reviewed DOI
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.
October 22th, 2009 (Class 5):
Good time to start writing your project.
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
October 8th, 2009 (Lecture Notes): Drexel"s Library Has:
Over 500 DB
Over 20000 Articles
Interlibrary Loans: 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.
Databases Web of Science- cross discipline database - can manipulate the body of literature you are searching for
October 1st, 2009:
In class: Wiki Review
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
New Wiki Page: Publishing in Chemistry
Document Source Types:
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; ]
Copyrights: Print Rights arrangement of words is important
Project: Pick a very small area and exhaust it to virtual certainty.
Open Access Journals:
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 http://dx.doi.org/ JCB]
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
Main Page | Log Book | Class Notes | Assignment(s) Page
November 19th 2009 (Class 9)
Puzzle, Nick completed! Way to go Nick! Your results were sent to chemspider and approved.
Properties HW: Properties, you need to copy the same numbers with same sig figs.
November 12th 2009 (Class 8)
How do you use chemsketch?
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.
(Class 7)
Workshop - entire class
reviewed DOI
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.
October 22th, 2009 (Class 5):
Good time to start writing your project.
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
October 8th, 2009 (Lecture Notes):
Drexel"s Library Has:
Over 500 DB
Over 20000 Articles
Interlibrary Loans:
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.
Databases
Web of Science- cross discipline database - can manipulate the body of literature you are searching for
October 1st, 2009:
In class: Wiki Review
New Wiki Page: Publishing in Chemistry
Document Source Types:
Copyrights: Print Rights arrangement of words is important
Project: Pick a very small area and exhaust it to virtual certainty.
Open Access Journals:
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 http://dx.doi.org/ JCB]
September 24th, 2009:
Intro to class/syllabus:
Possible addition to Social networks: [Perfect - please add JCB]