Groups search result 5 for "tobias Kind" |
Dear Colleagues,
an "integrated approach" for GC-MS and LC-MS analysis
(small molecules) may improve our lab work - therefore
I recommend to use the freely available (copyrighted) EPA EPI suite:
It contains some 103.000 structures + CAS numbers (SMILECAS database)
and (PHYSPROP database) with around 25,000 compounds with
some experimental data (logP, bp, henry..) and you can also calculate
a lot of physico-chemical properties.
Instead of repeating all the important things from
http://www.epa.gov/opptintr/exposure/docs/episuite.htm
I will pick out some things:
AOPWIN - estimates atmospheric oxidation rates
BCFWIN - estimates bioconcentration factor (BCF)
BIOWIN - estimates biodegradation probability
ECOSAR - estimates aquatic toxicity (LD50, LC50)
HENRYWIN - estimates Henry’s law constant
HYDROWIN - estimates aqueous hydrolysis rates (acid-, base-catalyzed)
KOWWIN - estimates octanol-water partition coefficient
MPBPWIN - estimates melting point, boiling point, and vapor pressure
PCKOCWIN - estimates soil sorption coefficient (Koc)
WSKOWWIN - estimates water solubility
DERMWIN - Dermal Permeability Program
STPWIN - (Sewage Treatment Plant Fugacity Model)
WVOLWIN - (Volatilization Rate from Water)
LEVEL3NT - (Level III Fugacity Model)
* EPIWIN allows batch file input for a large number of compounds
* MPBWIN has an experimental database of
11347 compounds (8948 melting points, 6381 boiling points,
and 2857 vapor pressures) - this may be useful for retention time
fitting (assuming same class of compounds).
* KowWIN - contains a database of 13200 experimental log P values.
and also a algorithm for calculating unknowns via smiles structure
input.
(Please take care: blind usage of calculated logP values is like walking
in a mine field:-)
further reading: http://www.lnh.unil.ch/Appl/cchem2.html
and http://esc.syrres.com/interkow/kowdemo.htm
* I also recommend to read:
Identifying Unknowns with “Spectraless” Databases from James Little
http://users.chartertn.net/slittle/files\TSCA_Poster%20Session.pdf
from http://users.chartertn.net/slittle/tsca.html
because it gives some important hints how mass spectra, mol masses,
formulas and databases can be linked together.
* Some rare EPIWIN examples for testing
Consul : (CAS 86479-06-3)
Fc1cccc(F)c1C(=O)NC(=O)Nc2cc(Cl)c(OC(F)(F)C(F)F)c(Cl)c2
Transfluthrin: (CAS 118712-89-3)
Fc1c(F)cc(F)c(F)c1COC(=O)C2C(C)(C)C2C=C(Cl)Cl
Viridicatin (CAS 129-24-8) remember ?
c(ccc1C(c(ccc2)c(c2)N3)=C(O)C3=O)cc1
With kind regards
Tobias Kind
P.S.: Thanks to U.S.EPA Office of Pollution Prevention Toxics
and Syracuse Research Corporation (SRC) and ...
P.P.S.: Try the incredible CACTVS system at
http://www2.ccc.uni-erlangen.de/ncidb2
It has enhanced features now - this is truly a state-of-the-art "open
database concept"
it has dozen of (multiple) input and output options. Try molsurf and
orbvis!
P.P.P.S.: Most molecular editors and some java applets import and export
smiles.
If you have a CAS number you can now use SMILECAS or CHEMIDplus - later
Merlin or ISIS/Base or whatyouwant for a structural
similarity/substructure search.
After data retrieval you can search with the obtained structures
for similiar mass spectra or substructures using NIST MS search V2.0
http://www.nist.gov/srd/nist1a.htm
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