lvpp/sigma

LVPP sigma-profile database + COSMO-SAC parametrizations

sigma's Issues

N-Acetylglucosamin (C8H15NO6) = NAG

For the reaction:
NAG + H3O+ <-> H2O + NAGH+
I need the LVPP sigma-profile database for COSMO-based models for two new components N-Acetylglucosamin and its hydrated ion NAGH+

NAGH+ = C8H16NO6+

NAG.txt
NAGH+.txt

Mint doi for release?

I would like to cite your repository in our upcoming paper, but the best way to do that is to have an archival release version with a DOI. Could you please mint a DOI for your release version so I can make direct reference to that particular release? Systems like zenodo make this process seamless.

Please add g-valerolactone

Please add the gamma-valerolactone molecule to the database.

Further information is available at: https://en.wikipedia.org/wiki/Gamma-Valerolactone

NA+1 not supported

Hello,
NA+1 present in the library is not supported by jcosmo, it displays the message 'Compound not found'. The problem is the same for a new gout file obtained with GAMESS.

Is it a normal issue?
Please find attached the gout files in .txt format.
NA+1_library.txt
NA+1_new.txt

Best,
Guillaume Simon

Identification list for species:

Chemical names are nice for humans, but less practical for computers.
It would be nice if the cavities were accompanied by a list of CAS numbers (asked for by many journals nowadays too), to uniquely identify each compound.

There is an online tool available - and I have been running the names through the tool. (This is the one I used: http://cts.fiehnlab.ucdavis.edu/ )
I did not (!) verify every match of name to CAS number, but I suspect between nothing or some errors, some errors are the lesser evil. In addition, I determined that using the cavities with the "regular sigma range" is not posible for ions. Radicals as well as some heavier atom also seem to cause issues.

Here is the 'result' of matching names to CAS numbers for the MOPAC cavities:
POA1_working_compounds.txt
POA1_ions_radicals_CAS_not_found.txt

Add new molecule sigma file for database

TCB-1

The TCB-1 ion has the surface information missing for GAMESS and is wrong (exploded) for POA1

Please add Quercetin

Please add to the database the Quercetin molecule.

Details are available here: https://en.wikipedia.org/wiki/Quercetin

Cinnamic acid derivatives (CADs)

Please add the following CADs:

• p-coumaric acid
• caffeic acid
• methyl p-coumarate
• methyl ferulate
• methyl sinapate

Sigma Profile of Melanoidins Calculation

Hello, I would like to request the Calculation and inclusion of melanoidins in LVPP's sigma-profile database for COSMO-based models. Attached are the 5 possible structures since the final structure has not yet been defined, thank you I appreciate any help.

Structures Melanoidins.zip

Calculation COSMO activity coefficient for riluzole drug and carbon dioxid

Hello Prof.Paula Bettio Staudt
I want to do the calculations for the riluzole drug and carbon dioxide.
I drew the structure through wxMacMolplt software and then converted it to (file.inp) with optimization and DFT calculation. Then, use from the OPENBABEL software, the file was converted to (file.mol) .The structure of two materials and (file.mol) is attached.
reregardingaboutcosmoactivitycoefficient (2).zip

error 127 and error 1

When I run scons with GAMESS appears error 1 and error 127. The files can not be found although they do exist.

Calculate COSMO activity coffecient for riluzole drug and carbon dioxid

I want to do the calculations for the riluzole drug and carbon dioxide.
I drew the structure through wxMacMolplt software and then converted it to (file.inp) with optimization and DFT calculation. Then, use from the OPENBABEL software, the file was converted to (file.mol) .The structure of two materials and (file.mol) is attached.

Cyclopentyl methyl ether

Olá Rafael! Você poderia incluir a molécula Cyclopentyl methyl ether (CAS 5614-37-9, SMILE COC1CCCC1) no JCOSMO? Tenho usado suas referências em meus trabalhos de extração de óleo de soja utilizando solventes verdes:

https://doi.org/10.1016/j.jiec.2022.06.020

Atenciosamente! Abraço!

Biodiesel related compounds

Please complete the database with more biodiesel related compounds like:

• methyl/ethyl hexanoate
• methyl/ethyl heptanoate
• and others listed on DOI:10.1021/ie800018x

Not necessarily use the nomenclature considered in that paper.

Also fix some of the compounds currently without the underline, like: METHYLOLEATE, METHYLLINOLEATE and possibly others.

Empty Cavities

Dear all,

looking through the list of GAMESS COSMO cavities, I stumbled across files that lack the cavity data.
I did not (!!) check all files manually that caused an issue, however the ones I did check by hand were indeed lacking the cavity data, which makes me suspect the same is true for the other files in the list.

This is the list I obtained:

1,2,3-TRIMETHYLBENZENE
1,4-DIMETHYLNAPHTHALENE
1,5-DIMETHYLNAPHTHALENE
1-BUTYNE
1-OCTYNE
2,3-PENTADIENE
2-BUTYNE-1,4-DIOL
2-HEPTYNE
2-HEXYNE
3-DECYNE
3-HEPTYNE
3-METHYL-1-HEXYNE
4-METHYL-1-HEXYNE
4-METHYL-1-PENTYNE
4-METHYL-2-HEXYNE
5-METHYL-1-HEXYNE
5-METHYL-2-HEXYNE
A-PINENE
ETHYLACETYLENE
ETHYL_CYANOACETATE
ETOSO3-1
FRUCTOSE
HEPTENE-6-NITRILES
HEXAMETHYLPHOSPHORAMIDE
IBUPROFEN
ISO-VALERONITRILE
LINALOOL
METHYLGLUTARONITRILE
MPY+1
PARACETAMOL
PENTANOIC_ACID
SACCHAROSE
TCB-1

D-Glucose molecule

The current D-Glucose molecule do not have the closed ring as described, e.g., here: https://en.wikipedia.org/wiki/Glucose

Please check if this is correct and possibly fix it.

Thank you in advance.

Chlorophyll a and Chlorophyll b

Hello, I would like to request the inclusion of chlorophyll a and chlorophyll b in LVPP's sigma-profile database for COSMO-based models.

chlorophylls.zip

Files containing molecules with minimum energy structures are attached. Please verify your agreement with these structures since I found a variety of representations to the bonds with Mg in these molecules.

Best regards,

Allan Morcelli

sigma profiles difference

Hi,

Can you please help me understand the reason for different sigma profiles put out by GAMESS and Turbomole for the same molecule such as simple H2O (water) with the same DFT basis BP-TZVP? i have attached the two files for easy reference. The Turbomole file using BP-TZVP formulation was taken from the supply of: https://dx.doi.org/10.1021/acs.iecr.0c00449 which also contains a new BP-TZVPD formulation but that one can be different. This difference due to different DFT formulation was mentioned in: https://doi.org/10.3303/CET1543314

The averaged sigma profile over charge densities -2.5 to 2.5 is different as shown in the attached pic. The averaged profiles were generated using VT-2005 procedure.
WATER-GAMESS.txt

water_c0-Turbomole.TXT

1,1,2-TRICHLOROETHANE conformers

Please check if the 1,1,2-TRICHLOROETHANE conformation should be as here: https://webbook.nist.gov/cgi/cbook.cgi?Str3View=C79005&Type=JSmol

Carotenoids

Hello, I would like to request the inclusion of some key carotenoids found in microalgae in LVPP's sigma-profile database for COSMO-based models.

all-trans-betacarotene
all-trans-lutein
all-trans-zeaxanthin
all-trans-violaxanthin

carotenoids.zip

Files containing molecules with minimum energy structures are attached.

Best regards,

Allan Morcelli

scons [tab error] inconsisten used of tab or indentation

Hello,

Im having a error message when running scons, it states that "
scons: Reading SConscript files ...
File "/home/anggawirya/sigma-master/GAMESS/SConstruct", line 102

print(len(gamess_version))

                          ^

TabError: inconsistent use of tabs and spaces in indentation

do you know what might wrong in my case ? Many thanks