From owner-chemistry@ccl.net Tue Aug 14 01:35:00 2012 From: "Ram Shankar chemistry ramchemistry2011**gmail.com" To: CCL Subject: CCL:G: Problem in CIS optimization calculation Message-Id: <-47363-120814013316-15714-+rWKkXBrzPIeh0pjOJhYaw(~)server.ccl.net> X-Original-From: "Ram Shankar chemistry" Date: Tue, 14 Aug 2012 01:33:15 -0400 Sent to CCL by: "Ram Shankar chemistry" [ramchemistry2011(0)gmail.com] Dear All, I have been trying to perform CIS optimization calculation on a organic molecule (i.e 65 atoms having C,H,N,O) with Gaussian 09. When I do optimization using the keyword OPT CIS/6-31G(d), the program stops with the following message "Error termination in NtrErr: NtrErr Called from FileIO." I have tried increasing the maxdisk and memory. But it didn't help The program allways stops at the same point. Can you suggest me something to solve this problem?. Any help and hints are really appreciated! Thanks in advance With Regards, RAAM From owner-chemistry@ccl.net Tue Aug 14 07:59:01 2012 From: "Serdar Badoglu sbadoglu__gazi.edu.tr" To: CCL Subject: CCL:G: Tautomeric equilibrium Message-Id: <-47364-120813161625-17558-p57myq/Tri41XiyWvdlh7A%%server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Mon, 13 Aug 2012 16:16:23 -0400 Sent to CCL by: "Serdar Badoglu" [sbadoglu-$-gazi.edu.tr] Dear CCL'ers, This will be little long message, sorry. I'm studying on a heterocyclic compound which exhibits tautomerism, and every tautomer has its several conformations. The experimental data I have are from the IR, and Ra. I have computed the geometrical parameters and vibrational frequencies of every single conformer in the gas phase by using Gaussian 03. After putting the Gibbs free energy values (obtained from that calculations)into Boltzmann distribution, I have found that %67 population for Tautomer 1 (one conformer >%1) and %33 pop for Tautomer 2 (one conformer >%1). So I have decided to interpret the experimental vibrational spectra (belong to solid phase) according to these two conformers. When I found several bands remained still unassigned, I have considered dimerization in solid phase. Then calculated the possible dimers of the compound (again in gas phase), and seen that unassigned bands are computed in dimers' frequencies. So I have concluded that the sample may contain both tautomers and a dimeric structure. At this point I need to say that I couldn't be able to assign all the experimental bands to a single structure (and be informed that the peaks in the experimental IR spectrum are not sharp. You may guess the rest, I'm pretty sure that you have read many such studies published in many journals. Recently I have a message from a journal's editor, and the comments of one of the reviewers are puzzled me. And that's why I'm writing all of these. I need your opinion. First, he/she claims that the calculations for gas phase are useless since the compound is in solid phase. He/she says that instead of doing it in this way I should solve the crystal structure (I couldn't obtain crystals of this compound). He/she suggests that otherwise assignments should be done only and unequivocally to one tautomer (which seems improbable to me). Second, he/she claims that the Boltzmann distribution cannot be used in my case because my tautomers don't seem in equilibrium to him/her. Also he/she says that I cannot apply gas phase BD to crystalline phase sample (I know this. I had some 30 possible conformers and I was just trying to eliminate themi that's all.). Furthermore, he/she says that the relative amounts of the tautomers in gas phase would depend on the way the vapor is produced (in this case I think that if the composition depends on the way of vapor production, then using BD for gas phase is also useless??). Finally, he/she has found my conclusion of coexistance of two tautomers and a dimer is not plausible. So, I wonder what you think. Regards. From owner-chemistry@ccl.net Tue Aug 14 09:18:00 2012 From: "Jan Jensen jhjensen||chem.ku.dk" To: CCL Subject: CCL: Introducing the Molecule Calculator Message-Id: <-47365-120814090834-19273-n5dikaJA3MhSysYXvPD2IQ%%server.ccl.net> X-Original-From: "Jan Jensen" Date: Tue, 14 Aug 2012 09:08:33 -0400 Sent to CCL by: "Jan Jensen" [jhjensen%chem.ku.dk] MolCalc is a web interface that allows anyone to build (small) molecules and estimate molecular properties such as molecular structure, heats of formation, vibrational frequencies and vibrational modes, and molecular orbitals and orbital energies in a matter of seconds or minutes - depending on the size. MolCalc is designed for teaching as opposed to research - specifically for assignments in which students build their own molecules and estimate their own molecular properties. More information: http://molecularmodelingbasics.blogspot.dk/2012/08/the-molecule- calculator.html MolCalc: http://dgu.ki.ku.dk/molcalc/editor Best regards, Jan From owner-chemistry@ccl.net Tue Aug 14 11:06:00 2012 From: "Andrew Yeung andrew.yeung__chem.tamu.edu" To: CCL Subject: CCL:G: Problem in CIS optimization calculation Message-Id: <-47366-120814110449-20309-q/2dzDmchTYf9CTnWcad8g-x-server.ccl.net> X-Original-From: Andrew Yeung Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 14 Aug 2012 10:04:34 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung]~[chem.tamu.edu] It probably couldn't find a file it needed. Are you using "geom=allcheck", "guess=read", "opt(readfc)" or something similar that requires access to a checkpoint file? If so, check that the "%chk=" line is set correctly. Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 Fax: 979 845 0158 On 2012-08-14 12:33 AM, Ram Shankar chemistry ramchemistry2011**gmail.com wrote: > Sent to CCL by: "Ram Shankar chemistry" [ramchemistry2011(0)gmail.com] > Dear All, > I have been trying to perform CIS optimization calculation on a organic molecule (i.e 65 atoms having C,H,N,O) with Gaussian 09. When I do optimization using the keyword OPT CIS/6-31G(d), the program stops with the following message > > "Error termination in NtrErr: > NtrErr Called from FileIO." > > I have tried increasing the maxdisk and memory. But it didn't help > The program allways stops at the same point. Can you suggest me something to solve this problem?. Any help and hints are really appreciated! > > Thanks in advance > > With Regards, > RAAM> > From owner-chemistry@ccl.net Tue Aug 14 11:58:00 2012 From: "krishnamohan%x%iist.ac.in" To: CCL Subject: CCL: EELS spectrum with Gaussian 09: Possibility Message-Id: <-47367-120814102834-10308-NNcuKTMm5Hn6Q/U/s6rWsg=-=server.ccl.net> X-Original-From: Content-Type: multipart/alternative; boundary="=_2c892369b8bf7ebfaffab6514191af73" Date: Tue, 14 Aug 2012 19:55:54 +0530 MIME-Version: 1.0 Sent to CCL by: [krishnamohan|-|iist.ac.in] --=_2c892369b8bf7ebfaffab6514191af73 Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Dear CCL list, I tried G09 to simulate EELS spectra (in the low-loss region of 0-50 eV) of aromatic compounds (The difference between EELS and UV/Vis. is that, EELS consider electronic transitions from the 'inner electrons' to the unoccupied states, More details is at: http://www.eelsmodel.ua.ac.be/files/documentation/thesis.pdf) In my study I use the following keywords for the benzene (within the D6H6 geometry): #P B3LYP/6-31G(d',p') TD(50-50,NStates=900) Pop=Full gfinput And it neatly produces the well known UV-Vis spectrum for the Benzene but NOT the continuous EELS spectrum. Actually, I got many non-zero peaks (from 10 to 35 eV), but it is not worth to make a continuous/convoluted EELS spectrum. If we assume that EELS spectra obey the selection rule (for oscillator strength): < initialState | dipoleMoment | finalState > =/= 0, as well as, only the, gerade < ---- > ungerade transition is allowed, G09 MUST reproduce the EELS spectrum as well. But it is not observed. Is any error in my input? Does any one know about the capability of G09 to simulate EELS spectrum? In other words, can we only do the normal UV/Vis spectrum (TD-DFT -) calculation with G09 and nothing beyond? Thanks in advance, Krishna Mohan G P --=_2c892369b8bf7ebfaffab6514191af73 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=UTF-8

Dear CCL list,

 

I tried G09 to simulate EELS spectra (in the low-loss region of 0-50 eV)= of aromatic compounds (The difference between EELS and UV/Vis. is that, EE= LS consider electronic transitions from the ‘inner electrons’ t= o the unoccupied states, More details is at: http://www.eelsmodel.ua.ac.be/= files/documentation/thesis.pdf)

 

In my study I use the following keywords for the benzene (within the D6H= 6 geometry):

 

            #P B3LYP/6-31G(d',p') TD(50-50= ,NStates=3D900) Pop=3DFull gfinput 

 

And it neatly produces the well known UV-Vis spectrum for the Benzene bu= t NOT the continuous EELS spectrum. Actually, I got many non-zero peaks (fr= om 10 to 35 eV), but it is not worth to make a continuous/convoluted EELS s= pectrum.

 

If we assume that EELS spectra obey the selection rule (for oscillator s= trength): < initialState | dipoleMoment | finalState > =3D/=3D 0, as = well as,

only the, gerade < ---- > ungerade transition is allowed, G09 MUST= reproduce the EELS spectrum as well. But it is not observed.

 

Is any error in my input? 

Does any one know about the capability of G09 to simulate EELS spectrum?= In other words, can we only do the normal UV/Vis spectrum (TD-DFT -) calcu= lation with G09 and nothing beyond?

 

Thanks in advance,

 

Krishna Mohan G P

--=_2c892369b8bf7ebfaffab6514191af73-- From owner-chemistry@ccl.net Tue Aug 14 12:33:00 2012 From: "Alex Allardyce aallardyce-,-chemaxon.com" To: CCL Subject: CCL: ChemAxon Announces New Version of chemicalize.org for Tablet PCs Message-Id: <-47368-120814110253-20188-JAbZIIyVutLQVf99X7fk9A!=!server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="----=_Part_1132_15585667.1344956558430" Date: Tue, 14 Aug 2012 17:02:40 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aallardyce..chemaxon.com] ------=_Part_1132_15585667.1344956558430 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Excuse cross postings:=20 ChemAxon announces that its free, open access, web-based chemistry search a= nd extraction service, chemicalize.org, is now supported on touchscreen tab= let PCs including Apple iPad and Android devices. This new version provides= users with high resolution chemically-intelligent web search and extractio= n on the move.=20 Powered by ChemAxon technology and used by scientists worldwide, chemicaliz= e.org identifies chemical names (SMILES, InChI, traditional and IUPAC names= ) on websites, in text and PDF files, converting them to 2D structures. Res= earchers can also calculate and explore a range of structure-based properti= es, search by structure in the ever expanding chemicalize.org knowledge-bas= e, and search the internet to find all websites citing a particular chemica= l structure.=20 The new chemicalize.org features:=20 * higher resolution images for =E2=80=9CRetina=E2=80=9D-type displays f= ound in the iPhone 4, iPad and new Android devices, including the Samsung G= alaxy Nexus and SIII,=20 * the ability to focus on the most relevant information/properties when= accessing from a mobile device,=20 * Home Screen shortcuts for rapid access, and=20 * user interface controls and performance optimized for tablets and sma= rtphones.=20 To try for yourself visit http://www.chemicalize.org=20 Thanks/Alex=20 More information about chemicalize.org=20 * Recent Software Review by Matthew Swain in J. Chem. Inf. Model=20 * Recent UGM presentation: Synergies between ChemAxon's chemicalize and= other open resources...=20 How to video's=20 * 1 minute overview (oldish)=20 * Seeing chemistry on web pages with webpage viewer=20 * Working with Calculated and predicted properties=20 * Substructure, similarity or full structure searches on the chemicaliz= e.org structure database=20 * Searching the web with chemicalize.org=20 Alex Allardyce=20 Marketing Dir.=20 ------=_Part_1132_15585667.1344956558430 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable <= div style=3D'font-family: arial,helvetica,sans-serif; font-size: 10pt; colo= r: #000000'>Excuse cross postings:

ChemAxon=20 announces that its free, open access, web-based chemistry search and=20 extraction service, chemicalize.org, is now supported on touchscreen=20 tablet PCs including Apple iPad and Android devices. This new version=20 provides users with high resolution chemically-intelligent web search=20 and extraction on the move.

Powered by ChemAxon technology and used by scientists worldwide,=20 chemicalize.org identifies chemical names (SMILES, InChI, traditional=20 and IUPAC names) on websites, in text and PDF files, converting them to=20 2D structures. Researchers can also calculate and explore a range of=20 structure-based properties, search by structure in the ever expanding=20 chemicalize.org knowledge-base, and search the internet to find all=20 websites citing a particular chemical structure.  

The new chemicalize.org features:
  • =09=09higher resolution images for =E2=80=9CRetina=E2=80=9D-type displays f= ound in the=20 iPhone 4, iPad and new Android devices, including the Samsung Galaxy=20 Nexus and SIII,
  • =09=09the ability to focus on the most relevant information/properties when= accessing from a mobile device,
  • =09=09Home Screen shortcuts for rapid access, and
  • =09=09user interface controls and performance optimized for tablets and sma= rtphones.
To try for yourself visit http://www.chemicalize.org

Thanks/Alex

More information about chemicalize.org How to video's

Alex Allardyce
<= font style=3D"color: rgb(102, 102, 102);" size=3D"1">Marketing Dir.<= br>
------=_Part_1132_15585667.1344956558430--